{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T22:27:25Z","timestamp":1761863245761},"reference-count":62,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2013,9,24]],"date-time":"2013-09-24T00:00:00Z","timestamp":1379980800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Cheminform"],"published-print":{"date-parts":[[2013,12]]},"DOI":"10.1186\/1758-2946-5-42","type":"journal-article","created":{"date-parts":[[2013,9,24]],"date-time":"2013-09-24T07:45:02Z","timestamp":1380008702000},"source":"Crossref","is-referenced-by-count":66,"title":["Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets"],"prefix":"10.1186","volume":"5","author":[{"given":"Gerard JP","family":"van Westen","sequence":"first","affiliation":[]},{"given":"Remco F","family":"Swier","sequence":"additional","affiliation":[]},{"given":"Isidro","family":"Cortes-Ciriano","sequence":"additional","affiliation":[]},{"given":"J\u00f6rg K","family":"Wegner","sequence":"additional","affiliation":[]},{"given":"John P","family":"Overington","sequence":"additional","affiliation":[]},{"given":"Adriaan P","family":"IJzerman","sequence":"additional","affiliation":[]},{"given":"Herman WT","family":"van Vlijmen","sequence":"additional","affiliation":[]},{"given":"Andreas","family":"Bender","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,9,24]]},"reference":[{"key":"481_CR1","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1016\/S0304-4165(00)00187-2","volume":"1525","author":"M Lapinsh","year":"2001","unstructured":"Lapinsh M, Prusis P, Gutcaits A, Lundstedt T, Wikberg JE: Development of proteo-chemometrics: a novel technology for the analysis of drug-receptor interactions. Biochim Biophys Acta. 2001, 1525: 180-190. 10.1016\/S0304-4165(00)00187-2.","journal-title":"Biochim Biophys Acta"},{"key":"481_CR2","first-page":"21","volume-title":"Annals of the New York Academy of Sciences Volume 994","author":"JES Wikberg","year":"2003","unstructured":"Wikberg JES, Mutulis F, Mutule I, Veiksina S, Lapinsh M, Petrovska R, Prusis P: Melanocortin receptors: ligands and proteochemometrics modeling. Annals of the New York Academy of Sciences Volume 994. Edited by: Braaten D. 2003, New York: Blackwell Publishing Ltd, 21-26."},{"key":"481_CR3","doi-asserted-by":"publisher","first-page":"e48","DOI":"10.1371\/journal.pcbi.0030048","volume":"3","author":"A Kontijevskis","year":"2007","unstructured":"Kontijevskis A, Prusis P, Petrovska R, Yahorava S, Mutulis F, Mutule I, Komorowski J, Wikberg JE: A look inside HIV resistance through retroviral protease interaction maps. PLoS Comput Biol. 2007, 3: e48-10.1371\/journal.pcbi.0030048.","journal-title":"PLoS Comput Biol"},{"key":"481_CR4","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1039\/C0MD00165A","volume":"2","author":"GJP Van Westen","year":"2011","unstructured":"Van Westen GJP, Wegner JK, Ijzerman AP, Van Vlijmen HWT, Bender A: Proteochemometric modeling as a tool for designing selective compounds and extrapolating to novel targets. Med Chem Commun. 2011, 2: 16-30. 10.1039\/c0md00165a.","journal-title":"Med Chem Commun"},{"issue":"16","key":"481_CR5","doi-asserted-by":"publisher","first-page":"7010","DOI":"10.1021\/jm3003069","volume":"55","author":"GJP Van Westen","year":"2012","unstructured":"Van Westen GJP, Van den Hoven OO, Van der Pijl R, Mulder-Krieger T, de Vries H, Wegner JK, Ijzerman AP, Van Vlijmen HWT, Bender A: Identifying novel adenosine receptor ligands by simultaneous proteochemometric modeling of Rat and human bioactivity data. J Med Chem. 2012, 55 (16): 7010-7020. 10.1021\/jm3003069.","journal-title":"J Med Chem"},{"issue":"6","key":"481_CR6","doi-asserted-by":"publisher","first-page":"1257","DOI":"10.1124\/mol.112.084152","volume":"83","author":"T De Bruyn","year":"2013","unstructured":"De Bruyn T, Van Westen GJP, IJzerman AP, Stieger B, de Witte P, Augustijns PF, Annaert PP: Structure-based Identification of OATP1B1\/3 Inhibitors. Mol Pharmacol. 2013, 83 (6): 1257-1267. 10.1124\/mol.112.084152.","journal-title":"Mol Pharmacol"},{"issue":"2","key":"481_CR7","doi-asserted-by":"publisher","first-page":"e1002899","DOI":"10.1371\/journal.pcbi.1002899","volume":"9","author":"GJP Van Westen","year":"2013","unstructured":"Van Westen GJP, Hendriks A, Wegner JK, IJzerman AP, Van Vlijmen HWT, Bender A: Significantly improved HIV inhibitor efficacy prediction employing proteochemometric models generated from antivirogram data. PLoS Comput Biol. 2013, 9 (2): e1002899-10.1371\/journal.pcbi.1002899.","journal-title":"PLoS Comput Biol"},{"key":"481_CR8","doi-asserted-by":"publisher","first-page":"1465","DOI":"10.1124\/mol.61.6.1465","volume":"61","author":"M Lapinsh","year":"2002","unstructured":"Lapinsh M, Prusis P, Lundstedt T, Wikberg JES: Proteochemometrics modeling of the interaction of amine G-protein coupled receptors with a diverse set of ligands. Mol Pharmacol. 2002, 61: 1465-1475. 10.1124\/mol.61.6.1465.","journal-title":"Mol Pharmacol"},{"issue":"5","key":"481_CR9","doi-asserted-by":"publisher","first-page":"1402","DOI":"10.1021\/ci050006d","volume":"45","author":"JR Bock","year":"2005","unstructured":"Bock JR, Gough DA: Virtual screen for ligands of orphan G protein-coupled receptors. J Chem Inf Model. 2005, 45 (5): 1402-1414. 10.1021\/ci050006d.","journal-title":"J Chem Inf Model"},{"key":"481_CR10","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1186\/1471-2105-7-167","volume":"7","author":"P Prusis","year":"2006","unstructured":"Prusis P, Uhl\u00e9n S, Petrovska R, Lapinsh M, Wikberg JES: Prediction of indirect interactions in proteins. BMC Bioinforma. 2006, 7: 167-10.1186\/1471-2105-7-167.","journal-title":"BMC Bioinforma"},{"key":"481_CR11","doi-asserted-by":"publisher","first-page":"1126","DOI":"10.1021\/jm00390a003","volume":"30","author":"S Hellberg","year":"1987","unstructured":"Hellberg S, Sj\u00f6str\u00f6m M, Skagerberg B, Wold S: Peptide quantitative structure-activity relationships, a multivariate approach. J Med Chem. 1987, 30: 1126-1135. 10.1021\/jm00390a003.","journal-title":"J Med Chem"},{"key":"481_CR12","doi-asserted-by":"publisher","first-page":"733","DOI":"10.1093\/nar\/21.3.733","volume":"21","author":"J Jonsson","year":"1993","unstructured":"Jonsson J, Norberg T, Carlsson L, Gustafsson C, Wold S: Quantitative sequence-activity models (QSAM)\u2013tools for sequence design. Nucleic Acids Res. 1993, 21: 733-739. 10.1093\/nar\/21.3.733.","journal-title":"Nucleic Acids Res"},{"issue":"14","key":"481_CR13","doi-asserted-by":"publisher","first-page":"2705","DOI":"10.1021\/jm00014a022","volume":"38","author":"ER Collantes","year":"1995","unstructured":"Collantes ER, Dunn WJ: Amino acid side chain descriptors for quantitative structure-activity relationship studies of peptide analogs. J Med Chem. 1995, 38 (14): 2705-2713. 10.1021\/jm00014a022.","journal-title":"J Med Chem"},{"key":"481_CR14","doi-asserted-by":"publisher","first-page":"2481","DOI":"10.1021\/jm9700575","volume":"41","author":"M Sandberg","year":"1998","unstructured":"Sandberg M, Eriksson L, Jonsson J, Sj\u00f6str\u00f6m M, Wold S: New chemical descriptors relevant for the design of biologically active peptides. A multivariate characterization of 87 amino acids. J Med Chem. 1998, 41: 2481-2491. 10.1021\/jm9700575.","journal-title":"J Med Chem"},{"issue":"1","key":"481_CR15","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1007\/s00726-008-0228-1","volume":"38","author":"P Zhou","year":"2010","unstructured":"Zhou P, Chen X, Wu Y, Shang Z: Gaussian process: an alternative approach for QSAM modeling of peptides. Amino Acids. 2010, 38 (1): 199-212. 10.1007\/s00726-008-0228-1.","journal-title":"Amino Acids"},{"key":"481_CR16","doi-asserted-by":"publisher","first-page":"568","DOI":"10.1002\/prot.21163","volume":"65","author":"H Strombergsson","year":"2006","unstructured":"Strombergsson H, Kryshtafovych A, Prusis P, Fidelis K, Wikberg JES, Komorowski J, Hvidsten TR: Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures. Proteins: Struct, Funct, Bioinf. 2006, 65: 568-579. 10.1002\/prot.21163.","journal-title":"Proteins: Struct, Funct, Bioinf"},{"key":"481_CR17","doi-asserted-by":"publisher","first-page":"2278","DOI":"10.1021\/ci800200e","volume":"48","author":"H Str\u00f6mbergsson","year":"2008","unstructured":"Str\u00f6mbergsson H, Daniluk P, Kryshtafovych A, Fidelis K, Wikberg JES, Kleywegt GJ, Hvidsten TR: Interaction model based on local protein substructures generalizes to the entire structural enzyme-ligand space. J Chem Inf Model. 2008, 48: 2278-2288. 10.1021\/ci800200e.","journal-title":"J Chem Inf Model"},{"issue":"4","key":"481_CR18","doi-asserted-by":"publisher","first-page":"1049","DOI":"10.1021\/ci800447g","volume":"49","author":"N Weill","year":"2009","unstructured":"Weill N, Rognan D: Development and validation of a novel protein\u2009\u2212\u2009ligand fingerprint to mine chemogenomic space: application to G protein-coupled receptors and their ligands. J Chem Inf Model. 2009, 49 (4): 1049-1062. 10.1021\/ci800447g.","journal-title":"J Chem Inf Model"},{"key":"481_CR19","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1186\/1471-2105-11-339","volume":"11","author":"M Lapins","year":"2010","unstructured":"Lapins M, Wikberg J: Kinome-wide interaction modelling using alignment-based and alignment-independent approaches for kinase description and linear and non-linear data analysis techniques. BMC Bioinforma. 2010, 11: 339-10.1186\/1471-2105-11-339.","journal-title":"BMC Bioinforma"},{"issue":"4","key":"481_CR20","doi-asserted-by":"publisher","first-page":"943","DOI":"10.1021\/ci300083r","volume":"52","author":"J Meslamani","year":"2012","unstructured":"Meslamani J, Li J, Sutter J, Stevens A, Bertrand H-O, Rognan D: Protein\u2013ligand-based pharmacophores: generation and utility assessment in computational ligand profiling. J Chem Inf Model. 2012, 52 (4): 943-955. 10.1021\/ci300083r.","journal-title":"J Chem Inf Model"},{"key":"481_CR21","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1186\/1758-2946-5-41","volume":"5","author":"GJP Van Westen","year":"2013","unstructured":"Van Westen GJP, Swier RF, Wegner JK, IJzerman AP, Van Vlijmen HWT, Bender A: Benchmarking of protein descriptors in proteochemometric modeling (Part 1): comparative study of 13 amino acid descriptors. J Cheminform. 2013, 5: 41-10.1186\/1758-2946-5-41.","journal-title":"J Cheminform"},{"key":"481_CR22","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1002\/bip.20296","volume":"80","author":"H Mei","year":"2005","unstructured":"Mei H, Liao ZH, Zhou Y, Li SZ: A new set of amino acid descriptors and its application in peptide QSARs. Biopolymers. 2005, 80: 775-786. 10.1002\/bip.20296.","journal-title":"Biopolymers"},{"key":"481_CR23","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1016\/j.molstruc.2006.07.004","volume":"830","author":"F Tian","year":"2007","unstructured":"Tian F, Zhou P, Li Z: T-scale as a novel vector of topological descriptors for amino acids and its application in QSARs of peptides. J Mol Struct. 2007, 830: 106-115. 10.1016\/j.molstruc.2006.07.004.","journal-title":"J Mol Struct"},{"key":"481_CR24","doi-asserted-by":"publisher","first-page":"805","DOI":"10.1007\/s00726-009-0287-y","volume":"38","author":"L Yang","year":"2010","unstructured":"Yang L, Shu M, Ma K, Mei H, Jiang Y, Li Z: ST-scale as a novel amino acid descriptor and its application in QSAM of peptides and analogues. Amino Acids. 2010, 38: 805-816. 10.1007\/s00726-009-0287-y.","journal-title":"Amino Acids"},{"key":"481_CR25","doi-asserted-by":"publisher","first-page":"754","DOI":"10.1002\/qsar.200630145","volume":"26","author":"G Liang","year":"2007","unstructured":"Liang G, Li Z: Factor analysis scale of generalized amino acid information as the source of a New Set of descriptors for elucidating the structure and activity relationships of cationic antimicrobial peptides. QSAR Comb Sci. 2007, 26: 754-763. 10.1002\/qsar.200630145.","journal-title":"QSAR Comb Sci"},{"key":"481_CR26","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1021\/ci980211b","volume":"39","author":"A Zaliani","year":"1999","unstructured":"Zaliani A, Gancia E: MS-WHIM scores for amino acids: a New 3D-description for peptide QSAR and QSPR studies. J Chem Inf Comput Sci. 1999, 39: 525-533. 10.1021\/ci980211b.","journal-title":"J Chem Inf Comput Sci"},{"key":"481_CR27","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1089\/cmb.2008.0173","volume":"16","author":"AG Georgiev","year":"2009","unstructured":"Georgiev AG: Interpretable numerical descriptors of amino acid space. J Comput Biol. 2009, 16: 703-723. 10.1089\/cmb.2008.0173.","journal-title":"J Comput Biol"},{"key":"481_CR28","doi-asserted-by":"publisher","first-page":"e27518","DOI":"10.1371\/journal.pone.0027518","volume":"6","author":"GJP Van Westen","year":"2011","unstructured":"Van Westen GJP, Wegner JK, Geluykens P, Kwanten L, Vereycken I, Peeters A, IJzerman AP, Van Vlijmen HWT, Bender A: Which compound to select in lead optimization? prospectively validated proteochemometric models guide preclinical development. PLoS ONE. 2011, 6: e27518-10.1371\/journal.pone.0027518.","journal-title":"PLoS ONE"},{"issue":"5","key":"481_CR29","doi-asserted-by":"publisher","first-page":"414","DOI":"10.1111\/j.1399-3011.1991.tb00756.x","volume":"37","author":"S Hellberg","year":"1991","unstructured":"Hellberg S, Eriksson L, Jonsson J, Lindgren F, Sjostrom M, Skagerberg B, Wold S, Andrews P: Minimum analogue peptide sets (MAPS) for quantitative structure activity relationships. Int J Pept Protein Res. 1991, 37 (5): 414-424.","journal-title":"Int J Pept Protein Res"},{"issue":"D1","key":"481_CR30","doi-asserted-by":"publisher","first-page":"D1100","DOI":"10.1093\/nar\/gkr777","volume":"40","author":"A Gaulton","year":"2012","unstructured":"Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, Al-Lazikani B, et al: ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res. 2012, 40 (D1): D1100-D1107. 10.1093\/nar\/gkr777.","journal-title":"Nucleic Acids Res"},{"key":"481_CR31","doi-asserted-by":"publisher","first-page":"3049","DOI":"10.1021\/jm960290n","volume":"39","author":"DE Patterson","year":"1996","unstructured":"Patterson DE, Cramer RD, Ferguson AM, Clark RD, Weinberger LE: Neighborhood behavior: a useful concept for validation of \"molecular diversity\" descriptors. J Med Chem. 1996, 39: 3049-3059. 10.1021\/jm960290n.","journal-title":"J Med Chem"},{"key":"481_CR32","doi-asserted-by":"publisher","first-page":"442","DOI":"10.1016\/0005-2795(75)90109-9","volume":"405","author":"BW Matthews","year":"1975","unstructured":"Matthews BW: Comparison of the predicted and observed secondary structure of t4 phage lysozyme. Biochim Biophys Acta. 1975, 405: 442-451. 10.1016\/0005-2795(75)90109-9.","journal-title":"Biochim Biophys Acta"},{"issue":"7\u20138","key":"481_CR33","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1016\/j.drudis.2012.12.003","volume":"18","author":"C de Graaf","year":"2013","unstructured":"de Graaf C, Vischer HF, de Kloe GE, Kooistra AJ, Nijmeijer S, Kuijer M, Verheij MHP, England PJ, van Muijlwijk-Koezen JE, Leurs R, et al: Small and colorful stones make beautiful mosaics: fragment-based chemogenomics. Drug Discov Today. 2013, 18 (7\u20138): 323-330.","journal-title":"Drug Discov Today"},{"issue":"1","key":"481_CR34","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1111\/bph.12248","volume":"170","author":"AJ Kooistra","year":"2013","unstructured":"Kooistra AJ, Kuhne S, de Esch IJP, Leurs R, de Graaf C: A structural chemogenomics analysis of aminergic GPCRs: lessons for histamine receptor ligand design. Br J Pharmacol. 2013, 170 (1): 101-126. 10.1111\/bph.12248.","journal-title":"Br J Pharmacol"},{"key":"481_CR35","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1002\/prot.20768","volume":"62","author":"J-S Surgand","year":"2006","unstructured":"Surgand J-S, Rodrigo J, Kellenberger E, Rognan D: A chemogenomic analysis of the transmembrane binding cavity of human G-protein-coupled receptors. Proteins. 2006, 62: 509-538.","journal-title":"Proteins"},{"issue":"1","key":"481_CR36","first-page":"6","volume":"21","author":"VA Johnson","year":"2013","unstructured":"Johnson VA, Calvez V, Gunthard HF, Paredes R, Pillay D, Shafer RW, Wensing AM, Richman DD: Update of the drug resistance mutations in HIV-1: March 2013. Top Antivir Med. 2013, 21 (1): 6-14.","journal-title":"Top Antivir Med"},{"issue":"6","key":"481_CR37","doi-asserted-by":"publisher","first-page":"80","DOI":"10.2307\/3001968","volume":"1","author":"F Wilcoxon","year":"1945","unstructured":"Wilcoxon F: Individual comparisons by ranking methods. Biometrics Bull. 1945, 1 (6): 80-83. 10.2307\/3001968.","journal-title":"Biometrics Bull"},{"issue":"1","key":"481_CR38","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1186\/1471-2105-9-363","volume":"9","author":"L Jacob","year":"2008","unstructured":"Jacob L, Hoffmann B, Stoven V, Vert J-P: Virtual screening of GPCRs: an in silico chemogenomics approach. BMC Bioinforma. 2008, 9 (1): 363-10.1186\/1471-2105-9-363.","journal-title":"BMC Bioinforma"},{"key":"481_CR39","doi-asserted-by":"publisher","first-page":"3707","DOI":"10.1016\/j.bmcl.2005.05.102","volume":"15","author":"TM Frimurer","year":"2005","unstructured":"Frimurer TM, Ulven T, Elling CE, Gerlach L-O, Kostenis E, H\u00f6gberg T: A physicogenetic method to assign ligand-binding relationships between 7TM receptors. Bioorg Med Chem Lett. 2005, 15: 3707-3712. 10.1016\/j.bmcl.2005.05.102.","journal-title":"Bioorg Med Chem Lett"},{"key":"481_CR40","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1016\/S1367-5931(02)00341-1","volume":"6","author":"C Ha","year":"2002","unstructured":"Ha C: Protein flexibility and drug design: how to hit a moving target. Curr Opin Chem Biol. 2002, 6: 447-452. 10.1016\/S1367-5931(02)00341-1.","journal-title":"Curr Opin Chem Biol"},{"key":"481_CR41","doi-asserted-by":"publisher","first-page":"742","DOI":"10.1002\/pro.350","volume":"19","author":"GJP Van Westen","year":"2010","unstructured":"Van Westen GJP, Wegner JK, Bender A, IJzerman AP, Van Vlijmen HWT: Mining protein dynamics from sets of crystal structures using \u201cconsensus structures\u201d. Protein Sci. 2010, 19: 742-752. 10.1002\/pro.350.","journal-title":"Protein Sci"},{"issue":"suppl 2","key":"481_CR42","doi-asserted-by":"publisher","first-page":"W32","DOI":"10.1093\/nar\/gkl305","volume":"34","author":"ZR Li","year":"2006","unstructured":"Li ZR, Lin HH, Han LY, Jiang L, Chen X, Chen YZ: PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence. Nucleic Acids Res. 2006, 34 (suppl 2): W32-W37.","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"481_CR43","doi-asserted-by":"publisher","first-page":"e57680","DOI":"10.1371\/journal.pone.0057680","volume":"8","author":"D-S Cao","year":"2013","unstructured":"Cao D-S, Liang Y-Z, Deng Z, Hu Q-N, He M, Xu Q-S, Zhou G-H, Zhang L-X, Deng Z-x, Liu S: Genome-scale screening of drug-target associations relevant to Ki using a chemogenomics approach. PLoS ONE. 2013, 8 (4): e57680-10.1371\/journal.pone.0057680.","journal-title":"PLoS ONE"},{"issue":"7","key":"481_CR44","doi-asserted-by":"publisher","first-page":"960","DOI":"10.1093\/bioinformatics\/btt072","volume":"29","author":"D-S Cao","year":"2013","unstructured":"Cao D-S, Xu Q-S, Liang Y-Z: propy: a tool to generate various modes of Chou\u2019s PseAAC. Bioinformatics. 2013, 29 (7): 960-962. 10.1093\/bioinformatics\/btt072.","journal-title":"Bioinformatics"},{"issue":"2","key":"481_CR45","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1038\/nbt1284","volume":"25","author":"MJ Keiser","year":"2007","unstructured":"Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK: Relating protein pharmacology by ligand chemistry. Nat Biotechnol. 2007, 25 (2): 197-206. 10.1038\/nbt1284.","journal-title":"Nat Biotechnol"},{"issue":"2","key":"481_CR46","doi-asserted-by":"publisher","first-page":"116","DOI":"10.1038\/nmeth.2339","volume":"10","author":"GJP Van Westen","year":"2013","unstructured":"Van Westen GJP, Overington JP: A ligand\u2019s-eye view of protein similarity. Nat Methods. 2013, 10 (2): 116-117. 10.1038\/nmeth.2339.","journal-title":"Nat Methods"},{"issue":"7","key":"481_CR47","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1093\/bioinformatics\/14.7.617","volume":"14","author":"K Mizuguchi","year":"1998","unstructured":"Mizuguchi K, Deane CM, Blundell TL, Johnson MS, Overington JP: JOY: protein sequence-structure representation and analysis. Bioinformatics. 1998, 14 (7): 617-623. 10.1093\/bioinformatics\/14.7.617.","journal-title":"Bioinformatics"},{"issue":"suppl 1","key":"481_CR48","doi-asserted-by":"publisher","first-page":"D309","DOI":"10.1093\/nar\/gkq1009","volume":"39","author":"B Vroling","year":"2011","unstructured":"Vroling B, Sanders M, Baakman C, Borrmann A, Verhoeven S, Klomp J, Oliveira L, de Vlieg J, Vriend G: GPCRDB: information system for G protein-coupled receptors. Nucleic Acids Res. 2011, 39 (suppl 1): D309-D319.","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"481_CR49","doi-asserted-by":"publisher","first-page":"1595","DOI":"10.1021\/ci4002712","volume":"53","author":"K Heikamp","year":"2013","unstructured":"Heikamp K, Bajorath J: Comparison of confirmed inactive and randomly selected compounds as negative training examples in support vector machine-based virtual screening. J Chem Inf Model. 2013, 53 (7): 1595-1601. 10.1021\/ci4002712.","journal-title":"J Chem Inf Model"},{"key":"481_CR50","unstructured":"Accelrys Software Inc: Pipeline pilot. Version 8.5."},{"key":"481_CR51","first-page":"102","volume":"3","author":"B Korber","year":"1998","unstructured":"Korber B, Foley BT, Kuiken C, Pillai SK, Sodroski JG: Numbering positions in HIV relative to HXB2CG. AIDS Res Hum Retroviruses. 1998, 3: 102-111.","journal-title":"AIDS Res Hum Retroviruses"},{"key":"481_CR52","doi-asserted-by":"publisher","first-page":"1202","DOI":"10.1021\/ci800453k","volume":"49","author":"M Lapins","year":"2009","unstructured":"Lapins M, Wikberg JES: Proteochemometric modeling of drug resistance over the mutational space for multiple HIV protease variants and multiple protease inhibitors. J Chem Inf Model. 2009, 49: 1202-1210. 10.1021\/ci800453k.","journal-title":"J Chem Inf Model"},{"key":"481_CR53","doi-asserted-by":"publisher","first-page":"5229","DOI":"10.1016\/j.bmc.2009.05.045","volume":"17","author":"A Kontijevskis","year":"2009","unstructured":"Kontijevskis A, Petrovska R, Yahorava S, Komorowski J, Wikberg JES: Proteochemometrics mapping of the interaction space for retroviral proteases and their substrates. Bioorg Med Chem. 2009, 17: 5229-5237. 10.1016\/j.bmc.2009.05.045.","journal-title":"Bioorg Med Chem"},{"key":"481_CR54","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1186\/1471-2105-9-181","volume":"9","author":"M Lapins","year":"2008","unstructured":"Lapins M, Eklund M, Spjuth O, Prusis P, Wikberg JES: Proteochemometric modeling of HIV protease susceptibility. BMC Bioinformatics. 2008, 9: 181-10.1186\/1471-2105-9-181.","journal-title":"BMC Bioinformatics"},{"key":"481_CR55","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1186\/1471-2105-11-316","volume":"11","author":"E van der Horst","year":"2010","unstructured":"van der Horst E, Peironcely J, IJzerman AP, Beukers M, Lane J, van Vlijmen HWT, Emmerich M, Okuno Y, Bender A: A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. BMC Bioinformatics. 2010, 11: 316-10.1186\/1471-2105-11-316.","journal-title":"BMC Bioinformatics"},{"issue":"15","key":"481_CR56","doi-asserted-by":"publisher","first-page":"1964","DOI":"10.2174\/156802611796391230","volume":"11","author":"E van der Horst","year":"2011","unstructured":"van der Horst E, Peironcely EJ, van Westen JP G, van den Hoven O, Galloway RJD W, Spring RD, Wegner KJ, van Vlijmen WT H, IJzerman PA, Overington PJ: Chemogenomics approaches for receptor deorphanization and extensions of the chemogenomics concept to phenotypic space. Curr Top Med Chem. 2011, 11 (15): 1964-1977. 10.2174\/156802611796391230.","journal-title":"Curr Top Med Chem"},{"key":"481_CR57","doi-asserted-by":"publisher","first-page":"742","DOI":"10.1021\/ci100050t","volume":"50","author":"D Rogers","year":"2010","unstructured":"Rogers D, Hahn M: Extended-connectivity fingerprints. J Chem Inf Model. 2010, 50: 742-754. 10.1021\/ci100050t.","journal-title":"J Chem Inf Model"},{"key":"481_CR58","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1021\/ci800249s","volume":"49","author":"A Bender","year":"2009","unstructured":"Bender A, Jenkins JL, Scheiber J, Sukuru SCK, Glick M, Davies JW: How similar are similarity searching methods? a principal component analysis of molecular descriptor space. J Chem Inf Model. 2009, 49: 108-119. 10.1021\/ci800249s.","journal-title":"J Chem Inf Model"},{"key":"481_CR59","volume-title":"A Language and Environment for Statistical Computing","author":"R Development Core Team: R","year":"2009","unstructured":"R Development Core Team: R: A Language and Environment for Statistical Computing. 2009, Vienna: R Foundation for Statistical Computing"},{"issue":"3","key":"481_CR60","first-page":"18","volume":"2","author":"A Liaw","year":"2002","unstructured":"Liaw A, Wiener M: Classification and regression by randomForest. R News. 2002, 2 (3): 18-22.","journal-title":"R News"},{"key":"481_CR61","first-page":"213","volume-title":"Handbook of Chemoinformatics Algorithms","author":"A Tropsha","year":"2010","unstructured":"Tropsha A, Golbraikh A: Predictive Quantitative Structure-Activity Relationships Modeling. Handbook of Chemoinformatics Algorithms. Edited by: Faulon JL, Faulon JL, Bender A. 2010, London: Chapman & Hall \/ CRC, 213-233."},{"issue":"5","key":"481_CR62","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1093\/bioinformatics\/16.5.412","volume":"16","author":"P Baldi","year":"2000","unstructured":"Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H: Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics. 2000, 16 (5): 412-424. 10.1093\/bioinformatics\/16.5.412.","journal-title":"Bioinformatics"}],"container-title":["Journal of Cheminformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1758-2946-5-42.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1758-2946-5-42\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1758-2946-5-42.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,6,24]],"date-time":"2019-06-24T14:34:38Z","timestamp":1561386878000},"score":1,"resource":{"primary":{"URL":"https:\/\/jcheminf.biomedcentral.com\/articles\/10.1186\/1758-2946-5-42"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,9,24]]},"references-count":62,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2013,12]]}},"alternative-id":["481"],"URL":"https:\/\/doi.org\/10.1186\/1758-2946-5-42","relation":{},"ISSN":["1758-2946"],"issn-type":[{"value":"1758-2946","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,9,24]]},"article-number":"42"}}