{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T11:43:33Z","timestamp":1780055013615,"version":"3.54.0"},"reference-count":225,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2012,1]]},"DOI":"10.1007\/s10822-011-9519-9","type":"journal-article","created":{"date-parts":[[2012,1,17]],"date-time":"2012-01-17T10:49:04Z","timestamp":1326797344000},"page":"137-150","source":"Crossref","is-referenced-by-count":42,"title":["Drug design for ever, from hype to hope"],"prefix":"10.1007","volume":"26","author":[{"given":"G.","family":"Seddon","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"V.","family":"Lounnas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R.","family":"McGuire","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"T.","family":"van den Bergh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R. P.","family":"Bywater","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"L.","family":"Oliveira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"G.","family":"Vriend","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2012,1,18]]},"reference":[{"key":"9519_CR1","unstructured":"Life expectancy (2011) http:\/\/en.wikipedia.org\/wiki\/Life_expectancy . Accessed 6 Dec 2011"},{"key":"9519_CR2","unstructured":"World War I casualties (2011) http:\/\/en.wikipedia.org\/wiki\/World_War_I_casualties . Accessed 6 Dec 2011"},{"key":"9519_CR3","unstructured":"Medecine and World War II (2011) http:\/\/www.historylearningsite.co.uk\/medicine_and_world_war_two.htm . Accessed 16 Feb 2011"},{"key":"9519_CR4","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1136\/bmj.290.6470.773","volume":"290","author":"ES Snell","year":"1985","unstructured":"Snell ES, Griffin JP (1985) How many medicines are there? Br Med J 290:773\u2013774","journal-title":"Br Med J"},{"key":"9519_CR5","volume-title":"Medicinal plants and plant extracts: a review of the importation into Europe. Traffic network report","author":"A Lewington","year":"1993","unstructured":"Lewington A (1993) Medicinal plants and plant extracts: a review of the importation into Europe. Traffic network report. Traffic International, Cambridge, UK"},{"key":"9519_CR6","doi-asserted-by":"crossref","unstructured":"Overington JP, Al-Lazikani B, Hopkins AL (2006) How many drug targets are there? Nat Rev Drug Discov. doi: 10.1038\/nrd2199","DOI":"10.1038\/nrd2199"},{"key":"9519_CR7","doi-asserted-by":"crossref","unstructured":"Munos B (2009) Lessons from 60 years of pharmaceutical innovation. Nat Rev Drug Discov. doi: 10.1038\/nrd2961","DOI":"10.1038\/nrd2961"},{"key":"9519_CR8","unstructured":"Troubled Asset Relief Program (2011) http:\/\/en.wikipedia.org\/wiki\/Troubled_Asset_Relief_Program . Accessed 6 Dec 2011"},{"key":"9519_CR9","doi-asserted-by":"crossref","unstructured":"Firestone RA (2011) Lessons from 54 years of pharmaceutical research Nat Rev Drug Discov. doi: 10.1038\/nrd2961-c1","DOI":"10.1038\/nrd2961-c1"},{"key":"9519_CR10","unstructured":"Robert B, Matthew T, Sean H, Bernard B (2000) Drug design by machine learning: support vector machine for pharmaceutical data analysis. Proceedings of the AISB\u201900 symposium on artificial intelligence in bioinformatics. pp 1\u20134"},{"key":"9519_CR11","doi-asserted-by":"crossref","first-page":"1882","DOI":"10.1021\/ci0341161","volume":"43","author":"E Byvatov","year":"2003","unstructured":"Byvatov E, Fechner U, Sadowski J, Schneider G (2003) Comparison of support vector machine and artificial neural network systems for drug\/nondrug classification. J Chem Inf Comput Sci 43:1882\u20131889","journal-title":"J Chem Inf Comput Sci"},{"key":"9519_CR12","doi-asserted-by":"crossref","unstructured":"Gagnon MA, Lexchin J (2008) The cost of pushing pills: a new estimate of pharmaceutical promotion expenditures in the United States. PLoS Med. doi: 10.1371\/journal.pmed.0050001","DOI":"10.1371\/journal.pmed.0050001"},{"key":"9519_CR13","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1002\/anie.198607673","volume":"25","author":"WGJ Hol","year":"1986","unstructured":"Hol WGJ (1986) Protein crystallography and computer-graphics toward rational drug design. Angew Chem Int Ed Engl 25:767\u2013778","journal-title":"Angew Chem Int Ed Engl"},{"key":"9519_CR14","doi-asserted-by":"crossref","first-page":"13663","DOI":"10.1016\/S0021-9258(18)33497-5","volume":"257","author":"JT Bolin","year":"1982","unstructured":"Bolin JT, Filman DJ, Matthews DA, Hamlin RC, Kraut J (1982) Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate. J Biol Chem 257:13663\u201313672","journal-title":"J Biol Chem"},{"key":"9519_CR15","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1007\/BF00123382","volume":"6","author":"PE Thompson","year":"1992","unstructured":"Thompson PE, Manallack DT, Blaney FE, Gallagher T (1992) Conformational studies on (+)-anatoxin-a and derivatives. J Comput Aided Mol Des 6:287\u2013298","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR16","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1007\/BF00126444","volume":"7","author":"J Ruiz","year":"1993","unstructured":"Ruiz J, L\u00f3pez M, Mil\u00e0 J, Lozoya E, Lozano JJ, Pouplana R (1993) QSAR and conformational analysis of the antiinflammatory agent amfenac and analogues. J Comput Aided Mol Des 7:183\u2013198","journal-title":"J Comput Aided Mol Des"},{"issue":"2","key":"9519_CR17","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1007\/BF00126447","volume":"7","author":"C Aleman","year":"1993","unstructured":"Aleman C, Perez JJ (1993) SCF-MO study of the polyglycine II structure. J Comput Aided Mol Des 7(2):241\u2013250","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR18","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1007\/BF00124407","volume":"9","author":"H Oyasu","year":"1995","unstructured":"Oyasu H, Nakanishi I, Tanaka A, Murano K, Matsuo M (1995) Conformational studies on the four stereoisomers of the novel anticholinergic 4-(dimethylamino)-2-phenyl-2-(2-pyridyl)pentanamide. J Comput Aided Mol Des 9:171\u2013180","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR19","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1023\/A:1008193805436","volume":"14","author":"G Schaftenaar","year":"2000","unstructured":"Schaftenaar G, Noordik JH (2000) Molden: a pre- and post-processing program for molecular and electronic structures. J Comput Aided Mol Des 14:123\u2013134","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR20","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1023\/B:JCAM.0000005765.13637.38","volume":"17","author":"S Manzetti","year":"2003","unstructured":"Manzetti S, McCulloch DR, Herington AC, van der Spoel D (2003) Modeling of enzyme-substrate complexes for the metalloproteases MMP-3, ADAM-9 and ADAM-10. J Comput Aided Mol Des 17:551\u2013565","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR21","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1023\/B:jcam.0000030037.67742.cb","volume":"18","author":"D Duran","year":"2004","unstructured":"Duran D, Aviyente V, Baysa C (2004) Solvent effect on the synthesis of clarithromycin: a molecular dynamics study. J Comput Aided Mol Des 18:145\u2013154","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR22","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1007\/s10822-004-7881-6","volume":"18","author":"A Curioni","year":"2004","unstructured":"Curioni A, Mordasini T, Andreoni W (2004) Enhancing the accuracy of virtual screening: molecular dynamics with quantum-refined force fields. J Comput Aided Mol Des 18:773\u2013784","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR23","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s10822-005-0096-7","volume":"19","author":"PS Hammond","year":"2005","unstructured":"Hammond PS, Wu Y, Harris R, Minehardt TJ, Car R, Schmitt JD (2005) Protonation-induced stereoisomerism in nicotine: conformational studies using classical (AMBER) and ab initio (Car-Parrinello) molecular dynamics. J Comput Aided Mol Des 19:1\u201315","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR24","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1007\/s10822-005-7003-0","volume":"19","author":"D Roccatano","year":"2005","unstructured":"Roccatano D, Sbardella G, Aschi M, Amicosante G, Bossa C, Nola AD, Mazza F (2005) Dynamical aspects of TEM-1 beta-lactamase probed by molecular dynamics. J Comput Aided Mol Des 19:329\u2013340","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR25","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1007\/s10822-005-9021-3","volume":"19","author":"C Chipot","year":"2005","unstructured":"Chipot C, Rozanska X, Dixit SB (2005) Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein. J Comput Aided Mol Des 19:765\u2013770","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR26","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1007\/s10822-006-9064-0","volume":"20","author":"F Fanelli","year":"2006","unstructured":"Fanelli F, De Benedetti PG (2006) Inactive and active states and supramolecular organization of GPCRs: insights from computational modeling. J Comput Aided Mol Des 20:449\u2013461","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR27","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1007\/s10822-008-9229-0","volume":"22","author":"K Bharatham","year":"2008","unstructured":"Bharatham K, Bharatham N, Kwon YJ, Lee KW (2008) Molecular dynamics simulation study of PTP1B with allosteric inhibitor and its application in receptor based pharmacophore modeling. J Comput Aided Mol Des 22:925\u2013933","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR28","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1007\/s10822-008-9239-y","volume":"23","author":"S Eyrisch","year":"2009","unstructured":"Eyrisch S, Helms V (2009) What induces pocket openings on protein surface patches involved in protein-protein interactions? J Comput Aided Mol Des 23:73\u201386","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR29","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1007\/BF01676960","volume":"1","author":"WF Gunsteren van","year":"1987","unstructured":"van Gunsteren WF, Berendsen HJ (1987) Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry. J Comput Aided Mol Des 1:171\u2013176","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR30","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1023\/A:1007930623000","volume":"12","author":"T Hansson","year":"1998","unstructured":"Hansson T, Marelius J, Aqvist J (1998) Ligand binding affinity prediction by linear interaction energy methods. J Comput Aided Mol Des 12:27\u201335","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR31","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1007\/BF01677276","volume":"1","author":"GL Wilcox","year":"1988","unstructured":"Wilcox GL, Quiocho FA, Levinthal C, Harvey SC, Maggiora GM, McCammon JA (1988) Symposium overview. Minnesota conference on supercomputing in biology: proteins, nucleic acids, and water. J Comput Aided Mol Des 1:271\u2013281","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR32","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1007\/BF01677277","volume":"1","author":"E Wimmer","year":"1988","unstructured":"Wimmer E (1988) Future in biomolecular computation. J Comput Aided Mol Des 1:283\u2013290","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR33","doi-asserted-by":"crossref","first-page":"8127","DOI":"10.1021\/ja00467a001","volume":"99","author":"NL Allinger","year":"1977","unstructured":"Allinger NL (1977) Conformational-analysis. 130. Mm2\u2014hydrocarbon force-field utilizing V1 and V2 torsional terms. J Am Chem Soc 99:8127\u20138134","journal-title":"J Am Chem Soc"},{"key":"9519_CR34","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/BF00128336","volume":"4","author":"JJP Stewart","year":"1990","unstructured":"Stewart JJP (1990) Special issue\u2014Mopac\u2014a semiempirical molecular-orbital program. J Comput Aided Mol Des 4:1\u201345","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR35","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1007\/BF00355046","volume":"10","author":"FH Allen","year":"1996","unstructured":"Allen FH, Harris SE, Taylor R (1996) Comparison of conformer distributions in the crystalline state with conformational energies calculated by ab initio techniques. J Comput Aided Mol Des 10:247\u2013254","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR36","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1007\/BF00123667","volume":"8","author":"G Klebe","year":"1994","unstructured":"Klebe G, Mietzner T (1994) A fast and efficient method to generate biologically relevant conformations. J Comput Aided Mol Des 8:583\u2013606","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR37","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1023\/A:1008007507641","volume":"12","author":"J Bostrom","year":"1998","unstructured":"Bostrom J, Norrby PO, Liljefors T (1998) Conformational energy penalties of protein-bound ligands. J Comput Aided Mol Des 12:383\u2013396","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR38","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/BF01680553","volume":"1","author":"D Mayer","year":"1987","unstructured":"Mayer D, Naylor CB, Motoc I, Marshall GR (1987) A unique geometry of the active site of angiotensin-converting enzyme consistent with structure-activity studies. J Comput Aided Mol Des 1:3\u201316","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR39","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1007\/BF01680557","volume":"1","author":"J Martin","year":"1987","unstructured":"Martin J, Andrews P (1987) Conformation-activity relationships of opiate analgesics. J Comput Aided Mol Des 1:53\u201372","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR40","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1007\/BF00141577","volume":"7","author":"YC Martin","year":"1993","unstructured":"Martin YC, Bures MG, Danaher EA, DeLazzer J, Lico I, Pavlik PA (1993) A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists. J Comput Aided Mol Des 7:83\u2013102","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR41","doi-asserted-by":"crossref","unstructured":"Lakdawala A, Wang M, Nevins N, Liotta D, Rusinska-Roszak D, Lozynski M, Snyder JP (2001) Calculated conformer energies for organic molecules with multiple polar functionalities are method dependent: taxol (case study). BMC Chem Biol. doi: 10.1186\/1472-6769-1-2","DOI":"10.1186\/1472-6769-1-2"},{"key":"9519_CR42","doi-asserted-by":"crossref","unstructured":"Vieth M, Hirst JD, Brooks CL (1998) Do active site conformations of small ligands correspond to low free-energy solution structures? J Comput Aided Mol Des 12:563\u2013572","DOI":"10.1023\/A:1008055202136"},{"key":"9519_CR43","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1007\/BF02174468","volume":"3","author":"G Klebe","year":"1995","unstructured":"Klebe G (1995) Toward a more efficient handling of conformational flexibility in computer-assisted modelling of drug molecules. Perspect Drug Discov Des 3:85\u2013105","journal-title":"Perspect Drug Discov Des"},{"key":"9519_CR44","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1006\/jmbi.2001.5147","volume":"314","author":"N Ota","year":"2001","unstructured":"Ota N, Agard DA (2001) Binding mode prediction for a flexible ligand in a flexible pocket using multi-conformation simulated annealing pseudo crystallographic refinement. J Mol Biol 314:607\u2013617","journal-title":"J Mol Biol"},{"key":"9519_CR45","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1023\/A:1016320106741","volume":"16","author":"DJ Diller","year":"2002","unstructured":"Diller DJ, Merz KM Jr (2002) Can we separate active from inactive conformations? J Comput Aided Mol Des 16:105\u2013112","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR46","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1016\/S0092-8674(02)00741-9","volume":"109","author":"M Huse","year":"2003","unstructured":"Huse M, Kuriyan J (2003) The conformational plasticity of protein kinases. Cell 109:275\u2013282","journal-title":"Cell"},{"key":"9519_CR47","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1038\/nrd1129","volume":"2","author":"SJ Teague","year":"2003","unstructured":"Teague SJ (2003) Implications of protein flexibility for drug discovery. Nat Rev Drug Discov 2:527\u2013541","journal-title":"Nat Rev Drug Discov"},{"key":"9519_CR48","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1038\/471151a","volume":"471","author":"T Chouard","year":"2005","unstructured":"Chouard T (2005) Structural biology: breaking the protein rules. Nature 471:151\u2013153","journal-title":"Nature"},{"key":"9519_CR49","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1038\/nrm1589","volume":"6","author":"HJ Dyson","year":"2005","unstructured":"Dyson HJ, Wright PE (2005) Intrinsically unstructured proteins and their functions. Natl Rev Mol Cell Biol 6:197\u2013208","journal-title":"Natl Rev Mol Cell Biol"},{"key":"9519_CR50","doi-asserted-by":"crossref","first-page":"1231","DOI":"10.1016\/j.bbapap.2010.01.017","volume":"1804","author":"VN Uversky","year":"2010","unstructured":"Uversky VN, Dunker AK (2010) Understanding protein non-folding. Biochim Biophys Acta 1804:1231\u20131264","journal-title":"Biochim Biophys Acta"},{"key":"9519_CR51","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/0022-2836(82)90153-X","volume":"161","author":"ID Kuntz","year":"1982","unstructured":"Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE (1982) A geometric approach to macromolecule-ligand interactions. J Mol Biol 161:269\u2013288","journal-title":"J Mol Biol"},{"key":"9519_CR52","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1007\/BF00126743","volume":"8","author":"HJ Bohm","year":"1994","unstructured":"Bohm HJ (1994) The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J Comput Aided Mol Des 8:243\u2013256","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR53","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1007\/BF00126747","volume":"8","author":"EC Meng","year":"1994","unstructured":"Meng EC, Kuntz ID, Abraham DJ, Kellogg GE (1994) Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities. J Comput Aided Mol Des 8:299\u2013306","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR54","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1007\/BF00124474","volume":"10","author":"AN Jain","year":"1996","unstructured":"Jain AN (1996) Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities. J Comput Aided Mol Des 10:427\u2013440","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR55","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1023\/A:1016357811882","volume":"16","author":"R Wang","year":"2002","unstructured":"Wang R, Lai L, Wang S (2002) Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J Comput Aided Mol Des 16:11\u201326","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR56","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1023\/A:1027346709963","volume":"17","author":"MD Kelly","year":"2003","unstructured":"Kelly MD, Mancera RL (2003) A new method for estimating the importance of hydrogen-bonding groups in the binding site of a protein. J Comput Aided Mol Des 17:401\u2013414","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR57","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1023\/B:JCAM.0000005766.95985.7e","volume":"17","author":"AE Muryshev","year":"2003","unstructured":"Muryshev AE, Tarasov DN, Butygin AV, Butygina OY, Aleksandrov AB, Nikitin SM (2003) A novel scoring function for molecular docking. J Comput Aided Mol Des 17:597\u2013605","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR58","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1023\/B:JCAM.0000035199.48747.1e","volume":"18","author":"SD Morley","year":"2004","unstructured":"Morley SD, Afshar M (2004) Validation of an empirical RNA-ligand scoring function for fast flexible docking using Ribodock. J Comput Aided Mol Des 18:189\u2013208","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR59","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1007\/s10822-005-8483-7","volume":"19","author":"JR Tame","year":"2005","unstructured":"Tame JR (2005) Scoring functions\u2014the first 100 years. J Comput Aided Mol Des 19:445\u2013451","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR60","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1007\/s10822-007-9114-2","volume":"21","author":"AN Jain","year":"2009","unstructured":"Jain AN (2009) Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. J Comput Aided Mol Des 21:281\u2013306","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR61","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1007\/s10822-008-9246-z","volume":"23","author":"G Cincilla","year":"2009","unstructured":"Cincilla G, Vidal D, Pons M (2009) An improved scoring function for suboptimal polar ligand complexes. J Comput Aided Mol Des 23:143\u2013152","journal-title":"J Comput Aided Mol Des"},{"issue":"3","key":"9519_CR62","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1007\/s10822-011-9413-5","volume":"25","author":"P Dobe\u0161","year":"2011","unstructured":"Dobe\u0161 P, Fanfrl\u00edk J, Rez\u00e1\u010d J, Otyepka M, Hobza P (2011) Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors. J Comput Aided Mol Des 25(3):223\u2013235","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR63","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1007\/s10822-006-9041-7","volume":"20","author":"K Tondel","year":"2006","unstructured":"Tondel K, Anderssen E, Drablos F (2006) Protein alpha shape (PAS) dock: a new gaussian-based score function suitable for docking in homology modelled protein structures. J Comput Aided Mol Des 20:131\u2013144","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR64","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1007\/BF00119865","volume":"8","author":"MD Miller","year":"1994","unstructured":"Miller MD, Kearsley SK, Underwood DJ, Sheridan RP (1994) FLOG: a system to select \u2018quasi-flexible\u2019 ligands complementary to a receptor of known three-dimensional structure. J Comput Aided Mol Des 8:153\u2013174","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR65","doi-asserted-by":"crossref","unstructured":"Kearsley SK, Underwood DJ, Sheridan RP, Miller MD Flexibases: a way to enhance the use of molecular docking methods. J Comput Aided Mol Des 8:565\u2013582","DOI":"10.1007\/BF00123666"},{"key":"9519_CR66","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1007\/BF00124402","volume":"9","author":"CM Oshiro","year":"1995","unstructured":"Oshiro CM, Kuntz ID, Dixon JS (1995) Flexible ligand docking using a genetic algorithm. J Comput Aided Mol Des 9:113\u2013130","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR67","doi-asserted-by":"crossref","unstructured":"Knegtel RM, Bayada DM, Engh RA, von der Saal W, van Geerestein VJ, Grootenhuis PD Comparison of two implementations of the incremental construction algorithm in flexible docking of thrombin inhibitors. J Comput Aided Mol Des 13:167\u2013183","DOI":"10.1023\/A:1008014604433"},{"key":"9519_CR68","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1023\/A:1008066310669","volume":"13","author":"S Makino","year":"1999","unstructured":"Makino S, Ewing TJ, Kuntz ID (1999) DREAM++: flexible docking program for virtual combinatorial libraries. J Comput Aided Mol Des 13:513\u2013532","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR69","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1023\/A:1011115820450","volume":"15","author":"TJ Ewing","year":"2001","unstructured":"Ewing TJ, Makino S, Skillman AG, Kuntz ID (2001) DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aided Mol Des 15:411\u2013428","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR70","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1023\/A:1016399411208","volume":"16","author":"SA Hindle","year":"2002","unstructured":"Hindle SA, Rarey M, Buning C, Lengaue T (2002) Flexible docking under pharmacophore type constraints. J Comput Aided Mol Des 16:129\u2013149","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR71","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1023\/A:1023868309253","volume":"16","author":"M Grasselli","year":"2002","unstructured":"Grasselli M, Cascone O, Birger Anspach F, Delfino JM (2002) On the molecular interaction between lactoferrin and the dye Red HE-3b. A novel approach for docking a charged and highly flexible molecule to protein surfaces. J Comput Aided Mol Des 16:917\u2013934","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR72","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1023\/B:JCAM.0000017496.76572.6f","volume":"17","author":"BD Bursulaya","year":"2003","unstructured":"Bursulaya BD, Totrov M, Abagyan R, Brooks CL 3rd (2003) Comparative study of several algorithms for flexible ligand docking. J Comput Aided Mol Des 17:755\u2013763","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR73","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1007\/s10822-008-9188-5","volume":"22","author":"G Bottegoni","year":"2008","unstructured":"Bottegoni G, Kufareva I, Totrov M, Abagyan R (2008) A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). J Comput Aided Mol Des 22:311\u2013325","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR74","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1007\/s10822-007-9148-5","volume":"22","author":"Y Zhao","year":"2008","unstructured":"Zhao Y, Sanner MF (2008) Protein-ligand docking with multiple flexible side chains. J Comput Aided Mol Des 22:673\u2013679","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR75","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s10822-008-9232-5","volume":"23","author":"L Kang","year":"2009","unstructured":"Kang L, Li H, Jiang H, Wang X (2009) An improved adaptive genetic algorithm for protein-ligand docking. J Comput Aided Mol Des 23:1\u201312","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR76","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1007\/s10822-009-9266-3","volume":"23","author":"AN Jain","year":"2009","unstructured":"Jain AN (2009) Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation. J Comput Aided Mol Des 23:355\u2013374","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR77","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1007\/s10822-009-9317-9","volume":"24","author":"DP Garden","year":"2010","unstructured":"Garden DP, Zhorov BS (2010) Docking flexible ligands in proteins with a solvent exposure- and distance-dependent dielectric function. J Comput Aided Mol Des 24:91\u2013105","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR78","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1016\/j.sbi.2008.01.004","volume":"18","author":"M Totrov","year":"2008","unstructured":"Totrov M, Abagyan R (2008) Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr Opin Struct Biol 18:178\u2013184","journal-title":"Curr Opin Struct Biol"},{"key":"9519_CR79","first-page":"2589","volume":"35","author":"HJ Bohm","year":"1996","unstructured":"Bohm HJ, Klebe G (1996) What can we learn from molecular recognition in protein-ligand complexes for the design of new drugs? Angew Chem Int Ed Engl 35:2589\u20132614","journal-title":"Angew Chem Int Ed Engl"},{"key":"9519_CR80","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1002\/(SICI)1097-0134(19990101)34:1<4::AID-PROT2>3.0.CO;2-6","volume":"34","author":"BK Shoichet","year":"1999","unstructured":"Shoichet BK, Leach AR, Kuntz ID (1999) Ligand solvation in molecular docking. Protein Sruct Funct Genet 34:4\u201316","journal-title":"Protein Sruct Funct Genet"},{"key":"9519_CR81","doi-asserted-by":"crossref","first-page":"2644","DOI":"10.1002\/1521-3773(20020802)41:15<2644::AID-ANIE2644>3.0.CO;2-O","volume":"41","author":"H Gohlke","year":"2002","unstructured":"Gohlke H, Klebe G (2002) Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. Angew Chem Int Ed 41:2644\u20132676","journal-title":"Angew Chem Int Ed"},{"key":"9519_CR82","doi-asserted-by":"crossref","first-page":"17373","DOI":"10.1021\/jp960111d","volume":"100","author":"E Demchuk","year":"1996","unstructured":"Demchuk E, Wade RC (1996) Improving the continuum dielectric approach to calculating pK(a)s of ionizable groups in proteins. J Phys Chem 100:17373\u201317387","journal-title":"J Phys Chem"},{"key":"9519_CR83","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1002\/prot.1053","volume":"43","author":"JE Nielsen","year":"2001","unstructured":"Nielsen JE, Vriend G (2001) Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations. Protein Stuct Funct Genet 43:403\u2013412","journal-title":"Protein Stuct Funct Genet"},{"key":"9519_CR84","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1006\/jmbi.1996.0477","volume":"261","author":"M Rarey","year":"1996","unstructured":"Rarey M, Kramer B, Lengauer T, Klebe G (1996) A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261:470\u2013489","journal-title":"J Mol Biol"},{"key":"9519_CR85","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/(SICI)1099-1352(199601)9:1<1::AID-JMR241>3.0.CO;2-6","volume":"9","author":"DS Goodsell","year":"1996","unstructured":"Goodsell DS, Morris GM, Olson AJ (1996) Automated docking of flexible ligands: applications of AutoDock. J Mol Recognit 9:1\u20135","journal-title":"J Mol Recognit"},{"key":"9519_CR86","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1021\/jm0306430","volume":"47","author":"RA Friesner","year":"2004","unstructured":"Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS (2004) A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47:1739\u20131749","journal-title":"J Med Chem"},{"key":"9519_CR87","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1006\/jmbi.1996.0897","volume":"267","author":"G Jones","year":"1997","unstructured":"Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267:727\u2013748","journal-title":"J Mol Biol"},{"key":"9519_CR88","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1002\/prot.22189","volume":"74","author":"C Hartmann","year":"2009","unstructured":"Hartmann C, Antes I, Lengauer T (2009) Docking and scoring with alternative side-chain conformations. Proteins 74:712\u2013726","journal-title":"Proteins"},{"key":"9519_CR89","doi-asserted-by":"crossref","first-page":"1637","DOI":"10.1002\/jcc.10295","volume":"24","author":"RD Taylor","year":"2003","unstructured":"Taylor RD, Jewsbury PJ, Essex JW (2003) FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function. J Comput Chem 24:1637\u20131656","journal-title":"J Comput Chem"},{"key":"9519_CR90","doi-asserted-by":"crossref","first-page":"5895","DOI":"10.1021\/jm050038s","volume":"49","author":"I Muegge","year":"2006","unstructured":"Muegge I (2006) PMF scoring revisited. J Med Chem 49:5895\u20135902","journal-title":"J Med Chem"},{"key":"9519_CR91","doi-asserted-by":"crossref","first-page":"1568","DOI":"10.1021\/ci8004308","volume":"49","author":"P Englebienne","year":"2009","unstructured":"Englebienne P, Moitessier N (2009) Docking ligands into flexible and solvated macromolecules. 4. Are popular scoring functions accurate for this class of proteins? J Chem Inf Model 49:1568\u20131580","journal-title":"J Chem Inf Model"},{"key":"9519_CR92","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1021\/ci050283k","volume":"46","author":"A Oda","year":"2006","unstructured":"Oda A, Tsuchida K, Takakura T, Yamaotsu N, Hirono S (2006) Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes. J Chem Inf Model 46:380\u2013391","journal-title":"J Chem Inf Model"},{"key":"9519_CR93","doi-asserted-by":"crossref","first-page":"3583","DOI":"10.2174\/092986706779026165","volume":"13","author":"N Foloppe","year":"2006","unstructured":"Foloppe N, Hubbard R (2006) Towards predictive ligand design with free-energy based computational methods? Curr Med Chem 13:3583\u20133608","journal-title":"Curr Med Chem"},{"key":"9519_CR94","doi-asserted-by":"crossref","first-page":"407","DOI":"10.2174\/138920306778559395","volume":"7","author":"AN Jain","year":"2006","unstructured":"Jain AN (2006) Scoring functions for protein-ligand docking. Curr Protein Pept Sci 7:407\u2013420","journal-title":"Curr Protein Pept Sci"},{"key":"9519_CR95","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1002\/prot.21162","volume":"66","author":"TA Robertson","year":"2007","unstructured":"Robertson TA, Varani G (2007) An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure. Proteins 66:359\u2013374","journal-title":"Proteins"},{"key":"9519_CR96","first-page":"308","volume":"10","author":"R Rajamani","year":"2007","unstructured":"Rajamani R, Good AC (2007) Ranking poses in structure-based lead discovery and optimization: current trends in scoring function development. Curr Opin Drug Discov Devel 10:308\u2013315","journal-title":"Curr Opin Drug Discov Devel"},{"key":"9519_CR97","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/0097-8485(84)85020-2","volume":"8","author":"BL Tembre","year":"1984","unstructured":"Tembre BL, McCammon JA (1984) Ligand-receptor interactions. Comput Chem 8:281\u2013283","journal-title":"Comput Chem"},{"key":"9519_CR98","doi-asserted-by":"crossref","first-page":"2654","DOI":"10.1021\/jm00112a048","volume":"34","author":"DM Ferguson","year":"1991","unstructured":"Ferguson DM, Radmer RJ, Kollman PA (1991) Determination of the relative binding free-energies of peptide inhibitors to the Hiv-1 protease. J Med Chem 34:2654\u20132659","journal-title":"J Med Chem"},{"key":"9519_CR99","doi-asserted-by":"crossref","first-page":"5959","DOI":"10.1021\/ja00226a005","volume":"110","author":"RD Cramer","year":"1988","unstructured":"Cramer RD, Patterson DE, Bunce JD (1988) Comparative molecular-field analysis (Comfa).1. Effect of shape on binding of steroids to carrier proteins. J Am Chem Soc 110:5959\u20135967","journal-title":"J Am Chem Soc"},{"key":"9519_CR100","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1007\/BF00117403","volume":"4","author":"U Norinder","year":"1990","unstructured":"Norinder U (1990) Experimental design based 3-D QSAR analysis of steroid-protein interactions: application to human CBG complexes. J Comput Aided Mol Des 4:381\u2013389","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR101","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1023\/A:1008010016362","volume":"13","author":"R Bursi","year":"1999","unstructured":"Bursi R, Grootenhuis PD (1999) Comparative molecular field analysis and energy interaction studies of thrombin-inhibitor complexes. J Comput Aided Mol Des 13:221\u2013232","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR102","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1007\/s10822-006-9090-y","volume":"21","author":"Z Zhang","year":"2007","unstructured":"Zhang Z, An L, Hu W, Xiang Y (2007) 3D-QSAR study of hallucinogenic phenylalkylamines by using CoMFA approach. J Comput Aided Mol Des 21:145\u2013153","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR103","unstructured":"Cramer RD, Milne M (1979) Lattice model\u2013general paradigm for shape-related structure-activity correlation. Abstracts of papers of the American chemical society, 19th ACS Meeting COMP 44"},{"key":"9519_CR104","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1007\/BF00130399","volume":"6","author":"MC Nicklaus","year":"1992","unstructured":"Nicklaus MC, Milne GW, Burke TR Jr (1992) QSAR of conformationally flexible molecules: comparative molecular field analysis of protein-tyrosine kinase inhibitors. J Comput Aided Mol Des 6:487\u2013504","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR105","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1007\/BF00126214","volume":"6","author":"S Rault","year":"1992","unstructured":"Rault S, Bureau R, Pilo JC, Robba M (1992) Comparative molecular field analysis of CCK-A antagonists using field-fit as an alignment technique. A convenient guide to design new CCK-A ligands. J Comput Aided Mol Des 6:553\u2013568","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR106","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1007\/BF00141574","volume":"7","author":"JA Calder","year":"1993","unstructured":"Calder JA, Wyatt JA, Frenkel DA, Casida JE (1993) CoMFA validation of the superposition of six classes of compounds which block GABA receptors non-competitively. J Comput Aided Mol Des 7:45\u201360","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR107","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1007\/BF00123997","volume":"9","author":"RT Kroemer","year":"1995","unstructured":"Kroemer RT, Hecht P (1995) A new procedure for improving the predictiveness of CoMFA models and its application to a set of dihydrofolate reductase inhibitors. J Comput Aided Mol Des 9:396\u2013406","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR108","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1023\/A:1008193217627","volume":"14","author":"K Gohda","year":"2000","unstructured":"Gohda K, Mori I, Ohta D, Kikuchi T (2000) A CoMFA analysis with conformational propensity: an attempt to analyze the SAR of a set of molecules with different conformational flexibility using a 3D-QSAR method. J Comput Aided Mol Des 14:265\u2013275","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR109","doi-asserted-by":"crossref","first-page":"1449","DOI":"10.1021\/ci9000508","volume":"49","author":"J Manchester","year":"2009","unstructured":"Manchester J, Czermi\u0144ski R (2009) CAUTION: popular \u201cBenchmark\u201d data sets do not distinguish the merits of 3D QSAR methods. J Chem Inf Model 49:1449\u20131454","journal-title":"J Chem Inf Model"},{"key":"9519_CR110","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s10822-007-9146-7","volume":"22","author":"PS Kharkar","year":"2008","unstructured":"Kharkar PS, Reith ME, Dutta AK (2008) Three-dimensional quantitative structure-activity relationship (3D QSAR) and pharmacophore elucidation of tetrahydropyran derivatives as serotonin and norepinephrine transporter inhibitors. J Comput Aided Mol Des 22:1\u201317","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR111","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1007\/s10822-004-2283-3","volume":"18","author":"H Park","year":"2004","unstructured":"Park H, Lee S (2004) Homology modeling, force field design, and free energy simulation studies to optimize the activities of histone deacetylase inhibitors. J Comput Aided Mol Des 18:375\u2013388","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR112","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1007\/s10822-005-1486-6","volume":"19","author":"CH Tomich","year":"2005","unstructured":"Tomich CH, da Silva P, Carvalho I, Taft CA (2005) Homology modeling and molecular interaction field studies of alpha-glucosidases as a guide to structure-based design of novel proposed anti-HIV inhibitors. J Comput Aided Mol Des 19:83\u201392","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR113","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1007\/s10822-005-1778-x","volume":"19","author":"KA Rossi","year":"2005","unstructured":"Rossi KA, Markwalder JA, Seitz SP, Chang CH, Cox S, Boisclair MD, Brizuela L, Brenner SL, Stouten PF (2005) Understanding and modulating cyclin-dependent kinase inhibitor specificity: molecular modeling and biochemical evaluation of pyrazolopyrimidinones as CDK2\/cyclin A and CDK4\/cyclin D1 inhibitors. J Comput Aided Mol Des 19:111\u2013122","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR114","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1007\/s10822-007-9127-x","volume":"21","author":"B Schlegel","year":"2007","unstructured":"Schlegel B, Laggner C, Meier R, Langer T, Schnell D, Seifert R, Stark H, H\u00f6ltje HD, Sippl W (2007) Generation of a homology model of the human histamine H(3) receptor for ligand docking and pharmacophore-based screening. J Comput Aided Mol Des 21:437\u2013453","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR115","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1007\/s10822-007-9138-7","volume":"21","author":"V Katritch","year":"2007","unstructured":"Katritch V, Byrd CM, Tseitin V, Dai D, Raush E, Totrov M, Abagyan R, Jordan R, Hruby DE (2007) Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches. J Comput Aided Mol Des 21:549\u2013558","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR116","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1007\/s10822-010-9393-x","volume":"24","author":"MA Neves","year":"2010","unstructured":"Neves MA, Simoes S, Sa e Melo ML (2010) Ligand-guided optimization of CXCR4 homology models for virtual screening using a multiple chemotype approach. J Comput Aided Mol Des 24:1023\u20131033","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR117","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1007\/s10822-011-9418-0","volume":"25","author":"T Knehans","year":"2011","unstructured":"Knehans T, Sch\u00fcller A, Doan DN, Nacro K, Hill J, G\u00fcntert P, Madhusudhan MS, Weil T, Vasudevan SG (2011) Structure-guided fragment-based in silico drug design of dengue protease inhibitors. J Comput Aided Mol Des 25:263\u2013274","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR118","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1007\/s10822-011-9455-8","volume":"25","author":"I Eberini","year":"2011","unstructured":"Eberini I, Daniele S, Parravicini C, Sensi C, Trincavelli ML, Martini C, Abbracchio MP (2011) In silico identification of new ligands for GPR17: a promising therapeutic target for neurodegenerative diseases. J Comput Aided Mol Des 25:743\u2013752","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR119","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1006\/jmbi.1993.1626","volume":"234","author":"A Sali","year":"1993","unstructured":"Sali A, Blundell TL (1993) Comparative protein modelling by statisfaction of spatial restraints. J Mol Biol 234:779\u2013815","journal-title":"J Mol Biol"},{"key":"9519_CR120","doi-asserted-by":"crossref","unstructured":"Vriend G (1990) WHAT IF: a molecular modeling and drug design program. J Mol Graph\u00a08:52\u201356","DOI":"10.1016\/0263-7855(90)80070-V"},{"key":"9519_CR121","doi-asserted-by":"crossref","unstructured":"Reichelt J, Dieterich G, Kvesic M, Schomburg D, Heinz DW (2005) BRAGI: linking and visualization of database information in a 3D viewer and modeling tool. Bioinformatics 21:1291\u20131293","DOI":"10.1093\/bioinformatics\/bti138"},{"key":"9519_CR122","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1002\/prot.22570","volume":"9","author":"E Krieger","year":"2009","unstructured":"Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K (2009) Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: four approaches that performed well in CASP8. Proteins 9:114\u2013122","journal-title":"Proteins"},{"key":"9519_CR123","doi-asserted-by":"crossref","first-page":"2380","DOI":"10.1002\/prot.23046","volume":"79","author":"J Thompson","year":"2011","unstructured":"Thompson J, Baker D (2011) Incorporation of evolutionary information into Rosetta comparative modeling. Protein Struct Func Bioinfo 79:2380\u20132388","journal-title":"Protein Struct Func Bioinfo"},{"key":"9519_CR124","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1002\/prot.340230304","volume":"23","author":"CASP1 proceedings","year":"1995","unstructured":"CASP1 proceedings (1995) Protein Struct Funct Genet 23:295\u2013460","journal-title":"Protein Struct Funct Genet"},{"key":"9519_CR125","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1002\/jmr.300060303","volume":"6","author":"MR Harris","year":"1993","unstructured":"Harris MR, Kihlen M, Bywater RP (1993) PLIM: a protein-ligand interaction modeller. J Mol Recognit 6:111\u2013115","journal-title":"J Mol Recognit"},{"key":"9519_CR126","doi-asserted-by":"crossref","unstructured":"Michino M, Abola E; GPCR Dock 2008 participants, Brooks CL 3rd, Dixon JS, Moult J, Stevens RC (2009) Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008 Nat Rev Drug Discov 8:455\u2013463","DOI":"10.1038\/nrd2877"},{"key":"9519_CR127","doi-asserted-by":"crossref","unstructured":"Kufareva I, Rueda M, Vsevolod K, Stevens RC, Abagyan R, GPCR Dock 2010 participants Status of GPCR modeling and docking as reflected by community wide GPCR Dock 2010 assessment. Structure\u00a019:1108\u20131126","DOI":"10.1016\/j.str.2011.05.012"},{"key":"9519_CR128","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1023\/B:JCAM.0000017491.97244.69","volume":"17","author":"BM Broer","year":"2003","unstructured":"Broer BM, Gurrath M, Holtje HD (2003) Molecular modelling studies on the ORL1-receptor and ORL1-agonists. J Comput Aided Mol Des 17:739\u2013754","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR129","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1007\/s10822-006-9037-3","volume":"20","author":"L Miguet","year":"2006","unstructured":"Miguet L, Zhang Z, Barbier M, Grigorov MG (2006) Comparison of a homology model and the crystallographic structure of human 11beta-hydroxysteroid dehydrogenase type 1 (11betaHSD1) in a structure-based identification of inhibitors. J Comput Aided Mol Des 20:67\u201381","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR130","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.3390\/ph4091196","volume":"4","author":"L Roumen","year":"2011","unstructured":"Roumen L, Sanders MP, Vroling B, De Esch IJ, De Vlieg J, Leurs R, Klomp JP, Nabuurs SB, De Graaf C (2011) The pitfalls and challenges of predicting GPCR-ligand interactions. Pharmaceuticals 4:1196\u20131215","journal-title":"Pharmaceuticals"},{"key":"9519_CR131","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1023\/A:1011128521816","volume":"15","author":"ES Henriques","year":"2001","unstructured":"Henriques ES, Floriano WB, Reuter N, Melo A, Brown D, Gomes JA, Maigret B, Nascimento MA, Ramos MJ (2001) The search for a new model structure of beta-factor XIIa. J Comput Aided Mol Des 15:309\u2013322","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR132","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1007\/s10822-004-6986-2","volume":"18","author":"N Brown","year":"2004","unstructured":"Brown N, McKay B, Gasteiger J (2004) The de novo design of median molecules within a property range of interest. J Comput Aided Mol Des 18:761\u2013771","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR133","doi-asserted-by":"crossref","unstructured":"Belda I, Madurga S, Llor\u00e0 X, Martinell M, Tarrag\u00f3 T, Piqueras MG, Nicol\u00e1s E, Giralt E (2005) ENPDA: an evolutionary structure-based de novo peptide design algorithm. J Comput Aided Mol Des 19:585\u2013601","DOI":"10.1007\/s10822-005-9015-1"},{"key":"9519_CR134","doi-asserted-by":"crossref","unstructured":"Zaliani A et al (2009) Second-generation de novo design: a view from a medicinal chemist perspective. J Comput Aided Mol Des","DOI":"10.1007\/s10822-009-9291-2"},{"key":"9519_CR135","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1021\/jm00145a002","volume":"28","author":"PJ Goodford","year":"1985","unstructured":"Goodford PJ (1985) A computational-procedure for determining energetically favorable binding-sites on biologically important macromolecules. J Med Chem 28:849\u2013857","journal-title":"J Med Chem"},{"key":"9519_CR136","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1021\/jm00053a018","volume":"36","author":"RC Wade","year":"1993","unstructured":"Wade RC, Clark KJ, Goodford PJ (1993) Further development of hydrogen-bond functions for use in determining energetically favorable binding-sites on molecules of known structure.1. Ligand probe groups with the ability to form 2 hydrogen-bonds. J Med Chem 36:140\u2013147","journal-title":"J Med Chem"},{"key":"9519_CR137","doi-asserted-by":"crossref","first-page":"1700","DOI":"10.1021\/jm00064a003","volume":"36","author":"SH Rotstein","year":"1993","unstructured":"Rotstein SH, Murcko MA (1993) GroupBuild: a fragment-based method for de novo drug design. J Med Chem 36:1700\u20131710","journal-title":"J Med Chem"},{"key":"9519_CR138","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1016\/S0167-7799(00)89015-0","volume":"13","author":"P Willett","year":"1995","unstructured":"Willett P (1995) Genetic algorithms in molecular recognition and design. Trends Biotechnol 13:516\u2013521","journal-title":"Trends Biotechnol"},{"key":"9519_CR139","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1007\/BF00124387","volume":"6","author":"HJ Bohm","year":"1992","unstructured":"Bohm HJ (1992) The computer program LUDI: a new method for the de novo design of enzyme inhibitors. J Comput Aided Mol Des 6:61\u201378","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR140","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1007\/BF00126217","volume":"6","author":"HJ Bohm","year":"1992","unstructured":"Bohm HJ (1992) LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads. J Comput Aided Mol Des 6:593\u2013606","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR141","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1007\/BF00117275","volume":"9","author":"DE Clark","year":"1995","unstructured":"Clark DE, Frenkel D, Levy SA, Li J, Murray CW, Robson B, Waszkowycz B, Westhead DR (1995) PRO-LIGAND: an approach to de novo molecular design. 1. Application to the design of organic molecules. J Comput Aided Mol Des 9:13\u201332","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR142","doi-asserted-by":"crossref","unstructured":"Westhead DR, Clark DE, Frenkel D, Li J, Murray CW, Robson B, Waszkowycz B (1995) PRO-LIGAND: an approach to de novo molecular design. 3. A genetic algorithm for structure refinement. J Comput Aided Mol Des 9:139\u2013148","DOI":"10.1007\/BF00124404"},{"key":"9519_CR143","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1007\/BF00124464","volume":"10","author":"M Rarey","year":"1996","unstructured":"Rarey M, Wefing S, Lengauer T (1996) Placement of medium-sized molecular fragments into active sites of proteins. J Comput Aided Mol Des 10:41\u201354","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR144","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1007\/BF00125175","volume":"9","author":"MT Barakat","year":"1995","unstructured":"Barakat MT, Dean PM (1995) The atom assignment problem in automated de novo drug design. 1. Transferability of molecular fragment properties. J Comput Aided Mol Des 9:341\u2013350","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR145","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1007\/BF00141573","volume":"7","author":"SH Rotstein","year":"1993","unstructured":"Rotstein SH, Murcko MA (1993) GenStar: a method for de novo drug design. J Comput Aided Mol Des 7:23\u201343","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR146","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1007\/BF00124457","volume":"9","author":"DC Roe","year":"1995","unstructured":"Roe DC, Kuntz ID (1995) BUILDER v.2: improving the chemistry of a de novo design strategy. J Comput Aided Mol Des 9:269\u2013282","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR147","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1007\/BF00126746","volume":"8","author":"AR Leach","year":"1994","unstructured":"Leach AR, Kilvington SR (1994) Automated molecular design: a new fragment-joining algorithm. J Comput Aided Mol Des 8:283\u2013298","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR148","volume-title":"Genetic algorithms in search, optimization and machine learning","author":"DE Golberg","year":"1989","unstructured":"Golberg DE (1989) Genetic algorithms in search, optimization and machine learning. Addison-Wesley, New York"},{"key":"9519_CR149","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1023\/A:1008042711516","volume":"11","author":"NP Todorov","year":"1997","unstructured":"Todorov NP, Dean PM (1997) Evaluation of a method for controlling molecular scaffold diversity in de novo ligand design. J Comput Aided Mol Des 11:175\u2013192","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR150","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1023\/A:1008184403558","volume":"14","author":"G Schneider","year":"2000","unstructured":"Schneider G, Lee ML, Stahl M, Schneider P (2000) De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks. J Comput Aided Mol Des 14:487\u2013494","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR151","doi-asserted-by":"crossref","first-page":"8732","DOI":"10.1021\/ja902302h","volume":"131","author":"LC Blum","year":"2009","unstructured":"Blum LC, Reymond JL (2009) 970 million druglike small molecules for virtual screening in the chemical universe database GDB-13. J Am Chem Soc 131:8732\u20138733","journal-title":"J Am Chem Soc"},{"key":"9519_CR152","first-page":"168","volume":"4","author":"H Kubinyi","year":"1992","unstructured":"Kubinyi H (1992) HTS technologies\u2014IBC informa conference. IDrugs 4:168\u2013173","journal-title":"IDrugs"},{"key":"9519_CR153","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1007\/BF00123378","volume":"6","author":"S Sudarsanam","year":"1992","unstructured":"Sudarsanam S, Virca GD, March CJ, Srinivasan S (1992) An approach to computer-aided inhibitor design: application to cathepsin L. J Comput Aided Mol Des 6:223\u2013233","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR154","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1023\/A:1008040531766","volume":"13","author":"HJ Bohm","year":"1999","unstructured":"Bohm HJ, Banner DW, Weber L (1999) Combinatorial docking and combinatorial chemistry: design of potent non-peptide thrombin inhibitors. J Comput Aided Mol Des 13:51\u201356","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR155","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1023\/A:1008121029716","volume":"14","author":"AV Filikov","year":"2000","unstructured":"Filikov AV, Mohan V, Vickers TA, Griffey RH, Cook PD, Abagyan RA, James TL (2000) Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR. J Comput Aided Mol Des 14:593\u2013610","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR156","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1023\/A:1011128510728","volume":"15","author":"P Furet","year":"2001","unstructured":"Furet P, Meyer T, Mittl P, Fretz H (2001) Identification of cylin-dependent kinase 1 inhibitors of a new chemical type by structure-based design and database searching. J Comput Aided Mol Des 15:489\u2013495","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR157","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1007\/s10822-006-9038-2","volume":"20","author":"A Afantitis","year":"2006","unstructured":"Afantitis A, Melagraki G, Sarimveis H, Koutentis PA, Markopoulos J, Igglessi-Markopoulou O (2006) Investigation of substituent effect of 1-(3, 3-diphenylpropyl)-piperidinyl phenylacetamides on CCR5 binding affinity using QSAR and virtual screening techniques. J Comput Aided Mol Des 20:83\u201395","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR158","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1007\/s10822-006-9077-8","volume":"20","author":"S Kortagere","year":"2006","unstructured":"Kortagere S, Welsh WJ (2006) Development and application of hybrid structure based method for efficient screening of ligands binding to G-protein coupled receptors. J Comput Aided Mol Des 20:789\u2013802","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR159","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1007\/s10822-007-9136-9","volume":"21","author":"A Talevi","year":"2007","unstructured":"Talevi A, Bellera CL, Castro EA, Bruno-Blanch LE (2007) A successful virtual screening application: prediction of anticonvulsant activity in MES test of widely used pharmaceutical and food preservatives methylparaben and propylparaben. J Comput Aided Mol Des 21:527\u2013538","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR160","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1007\/s10822-008-9189-4","volume":"22","author":"JJ Irwin","year":"2008","unstructured":"Irwin JJ (2008) Community benchmarks for virtual screening. J Comput Aided Mol Des 22:193\u2013199","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR161","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1007\/s10822-009-9304-1","volume":"23","author":"BA Krueger","year":"2009","unstructured":"Krueger BA, Weil T, Schneider G (2009) Comparative virtual screening and novelty detection for NMDA-GlycineB antagonists. J Comput Aided Mol Des 23:869\u2013881","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR162","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1007\/s10822-010-9381-1","volume":"24","author":"R Didziapetris","year":"2010","unstructured":"Didziapetris R, Dapkunas J, Sazonovas A, Japertas P (2010) Trainable structure-activity relationship model for virtual screening of CYP3A4 inhibition. J Comput Aided Mol Des 24:891\u2013906","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR163","unstructured":"Joseph-McCarthy D (2002) An overview of in silico design and screening: toward efficient drug discovery. Curr Drug Discov 20\u201323"},{"key":"9519_CR164","first-page":"24","volume":"2","author":"J Bajorath","year":"2002","unstructured":"Bajorath J (2002) Virtual screening: methods, expectations, and reality. Curr Opin Drug Discov Dev 2:24\u201328","journal-title":"Curr Opin Drug Discov Dev"},{"key":"9519_CR165","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1023\/A:1011144622059","volume":"15","author":"M Rarey","year":"2001","unstructured":"Rarey M, Stahl M (2001) Similarity searching in large combinatorial chemistry spaces. J Comput Aided Mol Des 15:497\u2013520","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR166","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1016\/S1359-6446(04)03069-7","volume":"9","author":"AL Hopkins","year":"2004","unstructured":"Hopkins AL, Groom CR, Alex A (2004) Ligand efficiency: a useful metric for lead selection. Drug Discov Today 9:430\u2013431","journal-title":"Drug Discov Today"},{"key":"9519_CR167","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1016\/S1359-6446(05)03386-6","volume":"10","author":"C Abad-Zapatero","year":"2005","unstructured":"Abad-Zapatero C, Metz JT (2005) Ligand efficiency indices as guideposts for drug discovery. Drug Discov Today 10:464\u2013469","journal-title":"Drug Discov Today"},{"key":"9519_CR168","doi-asserted-by":"crossref","first-page":"2315","DOI":"10.1021\/jm00041a010","volume":"37","author":"AN Jain","year":"1994","unstructured":"Jain AN, Koile K, Chapman D (1994) Compass: predicting biological activities from molecular surface properties. Performance comparisons on a steroid benchmark. J Med Chem 37:2315\u20132327","journal-title":"J Med Chem"},{"key":"9519_CR169","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1023\/A:1008188322239","volume":"14","author":"S Handschuh","year":"2000","unstructured":"Handschuh S, Goldfuss B, Chen J, Gasteiger J, Houk KN (2000) Steroid binding by antibodies and artificial receptors: exploration of theoretical methods to determine the origins of binding affinities and specificities. J Comput Aided Mol Des 14:611\u2013629","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR170","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1007\/BF00124012","volume":"8","author":"AN Jain","year":"1994","unstructured":"Jain AN, Dietterich TG, Lathrop RH, Chapman D, Critchlow RE Jr, Bauer BE, Webster TA, Lozano-Perez T (1994) A shape-based machine learning tool for drug design. J Comput Aided Mol Des 8:635\u2013652","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR171","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1016\/S0169-409X(02)00003-0","volume":"54","author":"WP Walters","year":"2002","unstructured":"Walters WP, Murcko MA (2002) Prediction of \u2018drug-likeness\u2019. Adv Drug Deliv Rev 54:255\u2013271","journal-title":"Adv Drug Deliv Rev"},{"key":"9519_CR172","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1007\/s10822-011-9424-2","volume":"25","author":"E Jung","year":"2011","unstructured":"Jung E, Choi SH, Lee NK, Kang SK, Choi YJ, Shin JM, Choi K, Jung DH (2011) Machine learning study for the prediction of transdermal peptide. J Comput Aided Mol Des 25:339\u2013347","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR173","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1007\/s10822-007-9161-8","volume":"22","author":"NS Sapre","year":"2008","unstructured":"Sapre NS, Gupta S, Pancholi N, Sapre N (2008) Molecular docking studies on tetrahydroimidazo-[4, 5, 1-jk][1, 4]-benzodiazepinone (TIBO) derivatives as HIV-1 NNRT inhibitors. J Comput Aided Mol Des 22:69\u201380","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR174","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1007\/BF00125376","volume":"8","author":"JD Hirst","year":"1994","unstructured":"Hirst JD, King RD, Sternberg MJ (1994) Quantitative structure-activity relationships by neural networks and inductive logic programming. II. The inhibition of dihydrofolate reductase by triazines. J Comput Aided Mol Des 8:421\u2013432","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR175","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1023\/A:1008074223811","volume":"11","author":"DJ Livingstone","year":"1997","unstructured":"Livingstone DJ, Manallack DT, Tetko IV (1997) Data modelling with neural networks: advantages and limitations. J Comput Aided Mol Des 11:135\u2013142","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR176","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1007\/s10822-007-9162-7","volume":"22","author":"AM Doweyko","year":"2008","unstructured":"Doweyko AM (2008) QSAR: dead or alive? J Comput Aided Mol Des 22:81\u201389","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR177","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1007\/s10822-006-9040-8","volume":"20","author":"Y Che","year":"2006","unstructured":"Che Y, Brooks BR, Marshall GR (2006) Development of small molecules designed to modulate protein-protein interactions. J Comput Aided Mol Des 20:109\u2013130","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR178","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1007\/BF00123380","volume":"6","author":"T Lotta","year":"1992","unstructured":"Lotta T, Taskinen J, B\u00e4ckstr\u00f6m R, Nissinen E (1992) PLS modelling of structure-activity relationships of catechol O-methyltransferase inhibitors. J Comput Aided Mol Des 6:253\u2013272","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR179","doi-asserted-by":"crossref","unstructured":"Zhou H, Lai WP, Zhang Z, Li WK, Cheung HY (2009) Computational study on the molecular inclusion of andrographolide by cyclodextrin. J Comput Aided Mol Des 23:153\u2013162","DOI":"10.1007\/s10822-008-9247-y"},{"key":"9519_CR180","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1007\/s10822-009-9265-4","volume":"23","author":"P Sarmah","year":"2009","unstructured":"Sarmah P, Deka RC (2009) DFT-based QSAR and QSPR models of several cis-platinum complexes: solvent effect. J Comput Aided Mol Des 23:343\u2013354","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR181","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1007\/s10822-006-9067-x","volume":"20","author":"N Singh","year":"2006","unstructured":"Singh N, Chev\u00e9 G, Ferguson DM, McCurdy CR (2006) A combined ligand-based and target-based drug design approach for G-protein coupled receptors: application to salvinorin A, a selective kappa opioid receptor agonist. J Comput Aided Mol Des 20:471\u2013493","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR182","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1007\/s10822-006-9080-0","volume":"20","author":"M Zheng","year":"2006","unstructured":"Zheng M, Yu K, Liu H, Luo X, Chen K, Zhu W, Jiang H (2006) QSAR analyses on avian influenza virus neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR. J Comput Aided Mol Des 20:549\u2013566","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR183","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1007\/s10822-008-9177-8","volume":"22","author":"RD Clark","year":"2008","unstructured":"Clark RD (2008) A ligand\u2019s-eye view of protein binding. J Comput Aided Mol Des 22:507\u2013521","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR184","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1007\/s10822-011-9425-1","volume":"25","author":"J Caballero","year":"2011","unstructured":"Caballero J, Quiliano M, Alzate-Morales JH, Zimic M, Deharo E (2011) Docking and quantitative structure-activity relationship studies for 3-fluoro-4-(pyrrolo[2, 1-f][1, 2, 4]triazin-4-yloxy)aniline, 3-fluoro-4-(1H-pyrrolo[2, 3-b]pyridin-4-yloxy)aniline, and 4-(4-amino-2-fluorophenoxy)-2-pyridinylamine derivatives as c-Met kinase inhibitors. J Comput Aided Mol Des 25:349\u2013369","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR185","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1007\/s10822-011-9441-1","volume":"25","author":"J Yoo","year":"2011","unstructured":"Yoo J, Medina-Franco JL (2011) Homology modeling, docking and structure-based pharmacophore of inhibitors of DNA methyltransferase. J Comput Aided Mol Des 25:555\u2013567","journal-title":"J Comput Aided Mol Des"},{"key":"9519_CR186","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1038\/nrg3033","volume":"12","author":"B Papp","year":"2011","unstructured":"Papp B, Notebaart RA, P\u00e1l C (2011) Systems-biology approaches for predicting genomic evolution. Nat Rev Genet 12:591\u2013602","journal-title":"Nat Rev Genet"},{"key":"9519_CR187","doi-asserted-by":"crossref","first-page":"2720","DOI":"10.1007\/s11095-008-9717-x","volume":"25","author":"DD Breimer","year":"2008","unstructured":"Breimer DD (2008) PK\/PD modelling and beyond: impact on drug development. Pharm Res 25:2720\u20132722","journal-title":"Pharm Res"},{"key":"9519_CR188","unstructured":"Swati Chaturvedi Outsourcing in Pharmaceutical Industry (2011) http:\/\/www.bionity.com\/en\/whitepapers\/49803\/outsourcing-in-pharmaceutical-industry.html . Accessed 6 Dec 2011"},{"key":"9519_CR189","unstructured":"Protein Data Bank (2011) http:\/\/www.pdb.org . Accessed 6 Dec 2011"},{"key":"9519_CR190","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235\u2013242","journal-title":"Nucleic Acids Res"},{"key":"9519_CR191","doi-asserted-by":"crossref","first-page":"1395","DOI":"10.1016\/j.str.2011.08.006","volume":"19","author":"RJ Read","year":"2011","unstructured":"Read RJ, Adams PD, Arendall WB 3rd, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, L\u00fctteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH (2011) A new generation of crystallographic validation tools for the protein data bank. Structure\u00a019:1395\u20131412","journal-title":"Structure"},{"key":"9519_CR192","unstructured":"PDB redo (2011) http:\/\/www.cmbi.ru.nl\/pdb_redo\/ . Accessed 29 Nov 2011"},{"key":"9519_CR193","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1126\/science.317.5835.195","volume":"317","author":"RP Joosten","year":"2007","unstructured":"Joosten RP, Vriend G (2007) PDB improvement starts with data deposition. Science 317:195\u2013196","journal-title":"Science"},{"key":"9519_CR194","doi-asserted-by":"crossref","unstructured":"Joosten RP, Joosten K, Cohen SX, Vriend G, Perrakis A (2011) Automatic rebuilding and optimization of crystallographic structures in the PDB. Bioinformatics Epub ahead of print","DOI":"10.1093\/bioinformatics\/btr590"},{"key":"9519_CR195","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1107\/S0021889809008784","volume":"42","author":"RP Joosten","year":"2009","unstructured":"Joosten RP, Salzemann J, Bloch V, Stockinger H, Berglund A, Blanchet C, Bongcam-Rudloff E, Combet C, Da Costa AL, Deleage G, Diarena M, Fabbretti R, Fettahi G, Flegel V, Gisel A, Kasam V, Kervinen T, Korpelainen E, Mattila K, Pagni M, Reichstadt M, Breton V, Tickle IJ, Vriend G (2009) PDB_REDO: automated re-refinement of X-ray structure models in the PDB. J Appl Cryst 42:376\u2013384","journal-title":"J Appl Cryst"},{"key":"9519_CR196","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1107\/S0907444908037591","volume":"65","author":"RP Joosten","year":"2009","unstructured":"Joosten RP, Womack T, Vriend G, Bricogne G (2009) Re-refinement from deposited X-ray data can deliver improved models for most PDB entries. Acta Crystallogr D Biol Crystallogr 65:176\u2013185","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"9519_CR197","first-page":"244","volume":"8","author":"TA Ban","year":"2006","unstructured":"Ban TA (2006) The role of serendipity in drug discovery. Dialogues Clin Neurosci 8:244\u2013335","journal-title":"Dialogues Clin Neurosci"},{"key":"9519_CR198","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1001\/jama.289.1.56","volume":"289","author":"HG Nurnberg","year":"2003","unstructured":"Nurnberg HG, Hensley PL, Gelenberg AJ, Fava M, Lauriello J, Paine S (2003) Treatment of antidepressant-associated sexual dysfunction with sildenafil: a randomized controlled trial. JAMA 289:56\u201364","journal-title":"JAMA"},{"key":"9519_CR199","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1124\/mol.51.5.889","volume":"51","author":"W Kuipers","year":"1997","unstructured":"Kuipers W, Link R, Standaar PJ, Stoit AR, Van Wijngaarden I, Leurs R, Ijzerman AP (1997) Study of the interaction between aryloxypropanolamines and Asn386 in helix VII of the human 5-hydroxytryptamine1A receptor. Mol Pharmacol 51:889\u2013896","journal-title":"Mol Pharmacol"},{"key":"9519_CR200","unstructured":"Kuipers W, Oliveira L, Paiva ACM, Rippman F, Sander C, IJzerman AP (1996) In: Findlay J (ed) Membrane protein models. Bios Scientific Publishers, Oxford"},{"key":"9519_CR201","unstructured":"GPCRDB information system for G protein-coupled receptors (2011) http:\/\/www.gpcr.org\/7tm\/ . Accessed 6 Dec 2011"},{"key":"9519_CR202","doi-asserted-by":"crossref","first-page":"1258","DOI":"10.1126\/science.1150577","volume":"318","author":"V Cherezov","year":"2007","unstructured":"Cherezov V, Rosenbaum DM, Hanson MA, Rasmussen SG, Thian FS, Kobilka TS, Choi HJ, Kuhn P, Weis WI, Kobilka BK, Stevens RC (2007) High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor. Science 318:1258\u20131265","journal-title":"Science"},{"key":"9519_CR203","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1007\/BF00125323","volume":"7","author":"L Oliveira","year":"1993","unstructured":"Oliveira L, Paiva ACM, Vriend G (1993) A common motif in G-protein-coupled seven transmembrane helix receptors. J Comp aided Mol Des 7:649\u2013658","journal-title":"J Comp aided Mol Des"},{"key":"9519_CR204","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1016\/0165-6147(94)90137-6","volume":"15","author":"L Oliveira","year":"1994","unstructured":"Oliveira L, Paiva ACM, Sander C, Vriend G (1994) A common step for signal transduction in G protein-coupled receptors. Trends Pharmacol Sci 15:170\u2013172","journal-title":"Trends Pharmacol Sci"},{"key":"9519_CR205","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.1093\/protein\/12.12.1087","volume":"12","author":"L Oliveira","year":"1999","unstructured":"Oliveira L, Paiva ACM, Vriend G (1999) A low resolution model for the interaction of G proteins with G protein-coupled receptors. Protein Eng 12:1087\u20131095","journal-title":"Protein Eng"},{"key":"9519_CR206","doi-asserted-by":"crossref","first-page":"11443","DOI":"10.1021\/ja105108q","volume":"132","author":"D Wacker","year":"2010","unstructured":"Wacker D, Brown MA, Fenalti G, Katritch V, Abagyan R, Cherezov V, Stevens RC (2010) Conserved binding mode of human beta(2) adrenergic receptor inverse agonists and antagonist revealed by X-ray crystallography. J Am Chem Soc 132:11443\u201311445","journal-title":"J Am Chem Soc"},{"key":"9519_CR207","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1016\/j.jmb.2007.03.007","volume":"372","author":"J Standfuss","year":"2007","unstructured":"Standfuss J, Xie G, Edwards PC, Burghammer M, Oprian DD, Schertler GFX (2007) Crystal structure of a thermally stable rhodopsin mutant. J Mol Biol 372:1179\u20131188","journal-title":"J Mol Biol"},{"key":"9519_CR208","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1073\/pnas.0711253105","volume":"105","author":"MJ Serrano-Vega","year":"2008","unstructured":"Serrano-Vega MJ, Magnani F, Shibata Y, Tate CG (2008) Conformational thermostabilization of the b1-adrenergic receptor in a detergent-resistant form of the b1-adrenergic receptor in a detergent-resistant form. Proc Natl Acad Sci USA 105:877\u2013882","journal-title":"Proc Natl Acad Sci USA"},{"key":"9519_CR209","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1038\/nature06325","volume":"450","author":"SG Rasmussen","year":"2007","unstructured":"Rasmussen SG, Choi HJ, Rosenbaum DM, Kobilka TS, Thian FS, Edwards PC, Burghammer M, Ratnala VR, Sanishvili R, Fischetti RF, Schertler GF, Weis WI, Kobilka BK (2007) Crystal structure of the human beta2 adrenergic G-protein-coupled receptor. Nature 450:383\u2013877","journal-title":"Nature"},{"key":"9519_CR210","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1038\/nature09665","volume":"469","author":"DM Rosenbaum","year":"2011","unstructured":"Rosenbaum DM, Zhang C, Lyons JA, Holl R, Aragao D, Arlow DH, Rasmussen SGF, Choi HJ, DeVree BT, Sunahara RK, Chae PS, Gellman SH, Dror RO, Shaw DE, Weis WI, Caffrey M, Gmeiner P, Kobilka BK (2011) Structure and function of an irreversible agonist-beta(2) adrenoceptor complex. Nature 469:236\u2013240","journal-title":"Nature"},{"key":"9519_CR211","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1093\/nar\/gkg103","volume":"31","author":"F Horn","year":"2003","unstructured":"Horn F, Bettler E, Oliveira L, Campagne F, Cohen FE, Vriend G (2003) GPCRDB information system for G protein-coupled receptors. Nucleic Acids Res 31:294\u2013297","journal-title":"Nucleic Acids Res"},{"key":"9519_CR212","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1093\/nar\/26.1.275","volume":"26","author":"F Horn","year":"1998","unstructured":"Horn F, Weare J, Beukers MW, H\u00f6rsch S, Bairoch A, Chen W, Edvardsen O, Campagne F, Vriend G (1998) GPCRDB: an information system for G protein-coupled receptors. Nucleic Acids Res 26:275\u2013279","journal-title":"Nucleic Acids Res"},{"key":"9519_CR213","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1186\/1471-2105-12-362","volume":"12","author":"B Vroling","year":"2011","unstructured":"Vroling B, Thorne D, McDermott P, Attwood TK, Vriend G, Pettifer S (2011) Integrating GPCR-specific information with full text articles. BMC Bioinfo 12:362","journal-title":"BMC Bioinfo"},{"key":"9519_CR214","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1002\/prot.21622","volume":"70","author":"HJ Joosten","year":"2008","unstructured":"Joosten HJ, Han Y, Niu W, Vervoort J, Dunaway-Mariano D, Schaap PJ (2008) Identification of fungal oxaloacetate hydrolyase within the isocitrate lyase\/PEP mutase enzyme superfamily using a sequence marker-based method. Proteins 70:157\u2013166","journal-title":"Proteins"},{"key":"9519_CR215","first-page":"2013","volume":"78","author":"RK Kuipers","year":"2010","unstructured":"Kuipers RK, Joosten HJ, van Berkel WJ, Leferink NG, Rooijen E, Ittmann E, van Zimmeren F, Jochens H, Bornscheuer U, Vriend G, dos Santos VA, Schaap PJ (2010) 3DM: systematic analysis of heterogeneous superfamily data to discover protein functionalities. Proteins 78:2013\u20132101","journal-title":"Proteins"},{"key":"9519_CR216","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.1002\/cbic.201000213","volume":"11","author":"R Kourist","year":"2010","unstructured":"Kourist R, Jochens H, Bartsch S, Kuipers R, Padhi SK, Gall M, B\u00f6ttcher D, Joosten HJ, Bornscheuer UT (2010) The alpha\/beta-hydrolase fold 3DM database (ABHDB) as a tool for protein engineering. Chembiochem 11:1635\u20131643","journal-title":"Chembiochem"},{"key":"9519_CR217","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1002\/humu.21317","volume":"31","author":"R Kuipers","year":"2010","unstructured":"Kuipers R, van den Bergh T, Joosten HJ, Lekanne dit Deprez RH, Mannens MM, Schaap PJ (2010) Novel tools for extraction and validation of disease-related mutations applied to Fabry disease. Hum Mutat 31:1026\u20131032","journal-title":"Hum Mutat"},{"key":"9519_CR218","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1093\/protein\/gzr042","volume":"24","author":"A Cerdobbel","year":"2011","unstructured":"Cerdobbel A, De Winter K, Aerts D, Kuipers R, Joosten HJ, Soetaert W, Desmet T (2011) Increasing the thermostability of sucrose phosphorylase by a combination of sequence- and structure-based mutagenesis. Protein Eng Des Sel 24:829\u2013834","journal-title":"Protein Eng Des Sel"},{"key":"9519_CR219","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1042\/BJ20091474","volume":"424","author":"TK Attwood","year":"2009","unstructured":"Attwood TK, Kell DB, McDermott P, Marsh J, Pettifer SR, Thorne D (2009) Calling international rescue: knowledge lost in literature and data landslide! Biochem J 424:317\u2013333","journal-title":"Biochem J"},{"key":"9519_CR220","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1126\/science.289.5480.739","volume":"289","author":"K Palczewski","year":"2000","unstructured":"Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Letrong I, Teller T, Okada T, Stenkamp RE, Yamamoto M, Miyano M (2000) Crystal structure of rhodopsin: a G protein-coupled receptor. Science 289:739\u2013745","journal-title":"Science"},{"key":"9519_CR221","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/S0014-5793(04)00320-5","volume":"564","author":"L Oliveira","year":"2004","unstructured":"Oliveira L, Hulsen T, Lutje Hulsik D, Paiva AC, Vriend G (2004) Heavier-than-air flying machines are impossible. FEBS Lett 564:269\u2013273","journal-title":"FEBS Lett"},{"key":"9519_CR222","doi-asserted-by":"crossref","first-page":"29994","DOI":"10.1074\/jbc.274.42.29994","volume":"274","author":"K Wieland","year":"1999","unstructured":"Wieland K, ter Laak AM, Smit MJ, K\u00fchne R, Timmerman H, Leurs R (1999) Mutational analysis of the antagonist-binding site of the histamine H(1) receptor. J Biol Chem 274:29994\u201330000","journal-title":"J Biol Chem"},{"key":"9519_CR223","unstructured":"Nuclear Receptors 3DM (2011) https:\/\/fungen.wur.nl\/?sfamid=NR&mode=alignment . Accessed 9 Dec 2011"},{"key":"9519_CR224","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1479-7364-5-1-1","volume":"5","author":"PD Stenson","year":"2010","unstructured":"Stenson PD, Cooper DN (2010) Prospects for the automated extraction of mutation data from the scientific literature. Hum Genomics 5:1\u20134","journal-title":"Hum Genomics"},{"key":"9519_CR225","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1186\/1471-2105-11-548","volume":"11","author":"H Venselaar","year":"2010","unstructured":"Venselaar H, Te Beek TA, Kuipers RK, Hekkelman ML, Vriend G (2010) Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. BMC Bioinfo 11:548","journal-title":"BMC Bioinfo"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-011-9519-9","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,12,26]],"date-time":"2021-12-26T07:04:13Z","timestamp":1640502253000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10822-011-9519-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,1]]},"references-count":225,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2012,1]]}},"alternative-id":["9519"],"URL":"https:\/\/doi.org\/10.1007\/s10822-011-9519-9","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"value":"0920-654X","type":"print"},{"value":"1573-4951","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,1]]}}}