{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T16:30:41Z","timestamp":1778085041283,"version":"3.51.4"},"reference-count":81,"publisher":"Springer Science and Business Media LLC","issue":"6","license":[{"start":{"date-parts":[[2016,6,1]],"date-time":"2016-06-01T00:00:00Z","timestamp":1464739200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2016,6]]},"DOI":"10.1007\/s10822-016-9923-2","type":"journal-article","created":{"date-parts":[[2016,7,5]],"date-time":"2016-07-05T07:38:35Z","timestamp":1467704315000},"page":"457-469","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["A pose prediction approach based on ligand 3D shape similarity"],"prefix":"10.1007","volume":"30","author":[{"given":"Ashutosh","family":"Kumar","sequence":"first","affiliation":[]},{"given":"Kam Y. J.","family":"Zhang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,7,5]]},"reference":[{"key":"9923_CR1","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1016\/j.drudis.2013.01.007","volume":"18","author":"Y Tanrikulu","year":"2013","unstructured":"Tanrikulu Y, Kr\u00fcger B, Proschak E (2013) The holistic integration of virtual screening in drug discovery. Drug Discov Today 18:358\u2013364","journal-title":"Drug Discov Today"},{"key":"9923_CR2","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1016\/S1359-6446(97)01163-X","volume":"3","author":"WP Walters","year":"1998","unstructured":"Walters WP, Stahl MT, Murcko MA (1998) Virtual screening\u2014an overview. Drug Discov Today 3:160\u2013178","journal-title":"Drug Discov Today"},{"key":"9923_CR3","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.ymeth.2014.07.007","volume":"71","author":"A Kumar","year":"2015","unstructured":"Kumar A, Zhang KYJ (2015) Hierarchical virtual screening approaches in small molecule drug discovery. Methods 71:26\u201337","journal-title":"Methods"},{"key":"9923_CR4","doi-asserted-by":"crossref","first-page":"2839","DOI":"10.2174\/09298673113209990001","volume":"20","author":"A Lavecchia","year":"2013","unstructured":"Lavecchia A, Di Giovanni C (2013) Virtual screening strategies in drug discovery: a critical review. Curr Med Chem 20:2839\u20132860","journal-title":"Curr Med Chem"},{"key":"9923_CR5","doi-asserted-by":"crossref","first-page":"927","DOI":"10.2174\/138955708785132792","volume":"8","author":"I Muegge","year":"2008","unstructured":"Muegge I (2008) Synergies of virtual screening approaches. Mini Rev Med Chem 8:927\u2013933","journal-title":"Mini Rev Med Chem"},{"key":"9923_CR6","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1016\/j.ddtec.2006.12.002","volume":"3","author":"I Muegge","year":"2006","unstructured":"Muegge I, Oloff S (2006) Advances in virtual screening. Drug Discov Today Technol 3:405\u2013411","journal-title":"Drug Discov Today Technol"},{"key":"9923_CR7","doi-asserted-by":"crossref","first-page":"e395","DOI":"10.1016\/j.ddtec.2013.02.002","volume":"10","author":"MN Drwal","year":"2013","unstructured":"Drwal MN, Griffith R (2013) Combination of ligand- and structure-based methods in virtual screening. Drug Discov Today Technol 10:e395\u2013e401","journal-title":"Drug Discov Today Technol"},{"key":"9923_CR8","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1124\/pr.112.007336","volume":"66","author":"G Sliwoski","year":"2014","unstructured":"Sliwoski G, Kothiwale S, Meiler J, Lowe EW (2014) Computational methods in drug discovery. Pharmacol Rev 66:334\u2013395","journal-title":"Pharmacol Rev"},{"key":"9923_CR9","doi-asserted-by":"crossref","first-page":"872","DOI":"10.2174\/138620711797537120","volume":"14","author":"N Sukumar","year":"2011","unstructured":"Sukumar N, Das S (2011) Current trends in virtual high throughput screening using ligand-based and structure-based methods. Comb Chem High Throughput Screen 14:872\u2013888","journal-title":"Comb Chem High Throughput Screen"},{"key":"9923_CR10","doi-asserted-by":"crossref","first-page":"397","DOI":"10.2174\/138620709788167890","volume":"12","author":"Y Fukunishi","year":"2009","unstructured":"Fukunishi Y (2009) Structure-based drug screening and ligand-based drug screening with machine learning. Comb Chem High Throughput Screen 12:397\u2013408","journal-title":"Comb Chem High Throughput Screen"},{"key":"9923_CR11","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1002\/jmr.1077","volume":"24","author":"E Yuriev","year":"2011","unstructured":"Yuriev E, Agostino M, Ramsland PA (2011) Challenges and advances in computational docking: 2009 in review. J Mol Recognit 24:149\u2013164","journal-title":"J Mol Recognit"},{"key":"9923_CR12","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1002\/jmr.2471","volume":"28","author":"E Yuriev","year":"2015","unstructured":"Yuriev E, Holien J, Ramsland PA (2015) Improvements, trends, and new ideas in molecular docking: 2012\u20132013 in review. J Mol Recognit 28:581\u2013604","journal-title":"J Mol Recognit"},{"key":"9923_CR13","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1002\/jmr.2266","volume":"26","author":"E Yuriev","year":"2013","unstructured":"Yuriev E, Ramsland PA (2013) Latest developments in molecular docking: 2010\u20132011 in review. J Mol Recognit 26:215\u2013239","journal-title":"J Mol Recognit"},{"key":"9923_CR14","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1517\/17460441.2010.497534","volume":"5","author":"PS Kutchukian","year":"2010","unstructured":"Kutchukian PS, Shakhnovich EI (2010) De novo design: balancing novelty and confined chemical space. Expert Opin Drug Discov 5:789\u2013812","journal-title":"Expert Opin Drug Discov"},{"key":"9923_CR15","doi-asserted-by":"crossref","first-page":"14","DOI":"10.2174\/156802610790232305","volume":"10","author":"K Loving","year":"2010","unstructured":"Loving K, Alberts I, Sherman W (2010) Computational approaches for fragment-based and de novo design. Curr Top Med Chem 10:14\u201332","journal-title":"Curr Top Med Chem"},{"key":"9923_CR16","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1038\/nature12595","volume":"503","author":"RO Dror","year":"2013","unstructured":"Dror RO, Green HF, Valant C, Borhani DW, Valcourt JR, Pan AC, Arlow DH, Canals M, Lane JR, Rahmani R, Baell JB, Sexton PM, Christopoulos A, Shaw DE (2013) Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs. Nature 503:295\u2013299","journal-title":"Nature"},{"key":"9923_CR17","doi-asserted-by":"crossref","first-page":"13118","DOI":"10.1073\/pnas.1104614108","volume":"108","author":"RO Dror","year":"2011","unstructured":"Dror RO, Pan AC, Arlow DH, Borhani DW, Maragakis P, Shan Y, Xu H, Shaw DE (2011) Pathway and mechanism of drug binding to G-protein-coupled receptors. Proc Natl Acad Sci USA 108:13118\u201313123","journal-title":"Proc Natl Acad Sci USA"},{"key":"9923_CR18","doi-asserted-by":"crossref","first-page":"10184","DOI":"10.1073\/pnas.1103547108","volume":"108","author":"I Buch","year":"2011","unstructured":"Buch I, Giorgino T, De Fabritiis G (2011) Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proc Natl Acad Sci USA 108:10184\u201310189","journal-title":"Proc Natl Acad Sci USA"},{"key":"9923_CR19","doi-asserted-by":"crossref","first-page":"12899","DOI":"10.1039\/c0cp00151a","volume":"12","author":"S-Y Huang","year":"2010","unstructured":"Huang S-Y, Grinter SZ, Zou X (2010) Scoring functions and their evaluation methods for protein\u2013ligand docking: recent advances and future directions. Phys Chem Chem Phys 12:12899\u201312908","journal-title":"Phys Chem Chem Phys"},{"key":"9923_CR20","doi-asserted-by":"crossref","first-page":"2174","DOI":"10.2174\/1381612811319120005","volume":"19","author":"JC Wang","year":"2013","unstructured":"Wang JC, Lin JH (2013) Scoring functions for prediction of protein\u2013ligand interactions. Curr Pharm Des 19:2174\u20132182","journal-title":"Curr Pharm Des"},{"key":"9923_CR21","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1007\/s10822-014-9735-1","volume":"28","author":"HS Muddana","year":"2014","unstructured":"Muddana HS, Fenley AT, Mobley DL, Gilson MK (2014) The SAMPL4 host-guest blind prediction challenge: an overview. J Comput Aided Mol Des 28:305\u2013317","journal-title":"J Comput Aided Mol Des"},{"key":"9923_CR22","doi-asserted-by":"crossref","first-page":"1853","DOI":"10.1021\/ci400025f","volume":"53","author":"KL Damm-Ganamet","year":"2013","unstructured":"Damm-Ganamet KL, Smith RD, Dunbar JB Jr, Stuckey JA, Carlson HA (2013) CSAR benchmark exercise 2011\u20132012: evaluation of results from docking and relative ranking of blinded congeneric series. J Chem Inf Model 53:1853\u20131870","journal-title":"J Chem Inf Model"},{"key":"9923_CR23","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1021\/ci400143r","volume":"53","author":"B Hu","year":"2013","unstructured":"Hu B, Lill MA (2013) Exploring the potential of protein-based pharmacophore models in ligand pose prediction and ranking. J Chem Inf Model 53:1179\u20131190","journal-title":"J Chem Inf Model"},{"key":"9923_CR24","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/1758-2946-6-14","volume":"6","author":"B Hu","year":"2014","unstructured":"Hu B, Lill MA (2014) PharmDock: a pharmacophore-based docking program. J Cheminform 6:14","journal-title":"J Cheminform"},{"key":"9923_CR25","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1021\/jm030331x","volume":"47","author":"Z Deng","year":"2004","unstructured":"Deng Z, Chuaqui C, Singh J (2004) Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein\u2013ligand binding interactions. J Med Chem 47:337\u2013344","journal-title":"J Med Chem"},{"key":"9923_CR26","doi-asserted-by":"crossref","first-page":"1942","DOI":"10.1021\/ci049870g","volume":"44","author":"MD Kelly","year":"2004","unstructured":"Kelly MD, Mancera RL (2004) Expanded interaction fingerprint method for analyzing ligand binding modes in docking and structure-based drug design. J Chem Inf Comput Sci 44:1942\u20131951","journal-title":"J Chem Inf Comput Sci"},{"key":"9923_CR27","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1021\/ci600342e","volume":"47","author":"G Marcou","year":"2007","unstructured":"Marcou G, Rognan D (2007) Optimizing fragment and scaffold docking by use of molecular interaction fingerprints. J Chem Inf Model 47:195\u2013207","journal-title":"J Chem Inf Model"},{"key":"9923_CR28","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1021\/ci050420d","volume":"46","author":"CP Mpamhanga","year":"2006","unstructured":"Mpamhanga CP, Chen B, McLay IM, Willett P (2006) Knowledge-based interaction fingerprint scoring: a simple method for improving the effectiveness of fast scoring functions. J Chem Inf Model 46:686\u2013698","journal-title":"J Chem Inf Model"},{"key":"9923_CR29","doi-asserted-by":"crossref","first-page":"1245","DOI":"10.1021\/ci900043r","volume":"49","author":"VI Perez-Nueno","year":"2009","unstructured":"Perez-Nueno VI, Rabal O, Borrell JI, Teixido J (2009) APIF: a new interaction fingerprint based on atom pairs and its application to virtual screening. J Chem Inf Model 49:1245\u20131260","journal-title":"J Chem Inf Model"},{"key":"9923_CR30","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1111\/j.1747-0285.2010.01007.x","volume":"76","author":"L Tan","year":"2010","unstructured":"Tan L, Batista J, Bajorath J (2010) Computational methodologies for compound database searching that utilize experimental protein\u2013ligand interaction information. Chem Biol Drug Des 76:191\u2013200","journal-title":"Chem Biol Drug Des"},{"key":"9923_CR31","doi-asserted-by":"crossref","first-page":"15122","DOI":"10.3390\/ijms150915122","volume":"15","author":"B Hu","year":"2014","unstructured":"Hu B, Zhu X, Monroe L, Bures MG, Kihara D (2014) PL-PatchSurfer: a novel molecular local surface-based method for exploring protein\u2013ligand interactions. Int J Mol Sci 15:15122\u201315145","journal-title":"Int J Mol Sci"},{"key":"9923_CR32","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1021\/acs.jcim.5b00625","volume":"56","author":"X Zhu","year":"2016","unstructured":"Zhu X, Shin WH, Kim H, Kihara D (2016 ) Combined approach of patch-surfer and PL-PatchSurfer for protein\u2013ligand binding prediction in CSAR 2013 and 2014. J Chem Inf Model\u00a056:1088\u20131099","journal-title":"J Chem Inf Model"},{"key":"9923_CR33","doi-asserted-by":"crossref","first-page":"4731","DOI":"10.1021\/jm0499054","volume":"47","author":"BJ Hare","year":"2004","unstructured":"Hare BJ, Walters WP, Caron PR, Bemis GW (2004) CORES: an automated method for generating three-dimensional models of protein\/ligand complexes. J Med Chem 47:4731\u20134740","journal-title":"J Med Chem"},{"key":"9923_CR34","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1016\/j.drudis.2011.02.011","volume":"16","author":"P Ripphausen","year":"2011","unstructured":"Ripphausen P, Nisius B, Bajorath J (2011) State-of-the-art in ligand-based virtual screening. Drug Discov Today 16:372\u2013376","journal-title":"Drug Discov Today"},{"key":"9923_CR35","doi-asserted-by":"crossref","first-page":"3186","DOI":"10.1021\/jm401411z","volume":"57","author":"G Maggiora","year":"2014","unstructured":"Maggiora G, Vogt M, Stumpfe D, Bajorath J (2014) Molecular similarity in medicinal chemistry. J Med Chem 57:3186\u20133204","journal-title":"J Med Chem"},{"key":"9923_CR36","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1007\/s10822-015-9846-3","volume":"29","author":"AE Cleves","year":"2015","unstructured":"Cleves AE, Jain AN (2015) Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock. J Comput Aided Mol Des 29:485\u2013509","journal-title":"J Comput Aided Mol Des"},{"key":"9923_CR37","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1002\/1097-0134(20000901)40:4<623::AID-PROT70>3.0.CO;2-I","volume":"40","author":"X Fradera","year":"2000","unstructured":"Fradera X, Knegtel RM, Mestres J (2000) Similarity-driven flexible ligand docking. Proteins 40:623\u2013636","journal-title":"Proteins"},{"key":"9923_CR38","doi-asserted-by":"crossref","first-page":"1460","DOI":"10.1021\/acs.jcim.5b00186","volume":"55","author":"C Gao","year":"2015","unstructured":"Gao C, Thorsteinson N, Watson I, Wang J, Vieth M (2015) Knowledge-based strategy to improve ligand pose prediction accuracy for lead optimization. J Chem Inf Model 55:1460\u20131468","journal-title":"J Chem Inf Model"},{"key":"9923_CR39","doi-asserted-by":"crossref","first-page":"870","DOI":"10.1021\/ci4007134","volume":"54","author":"A Kumar","year":"2014","unstructured":"Kumar A, Ito A, Takemoto M, Yoshida M, Zhang KYJ (2014) Identification of 1,2,5-oxadiazoles as a new class of SENP2 inhibitors using structure based virtual screening. J Chem Inf Model 54:870\u2013880","journal-title":"J Chem Inf Model"},{"key":"9923_CR40","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1021\/jm201168g","volume":"55","author":"KE Hevener","year":"2012","unstructured":"Hevener KE, Mehboob S, Su P-C, Truong K, Boci T, Deng J, Ghassemi M, Cook JL, Johnson ME (2012) Discovery of a novel and potent class of F. tularensis Enoyl-Reductase (FabI) inhibitors by molecular shape and electrostatic matching. J Med Chem 55:268\u2013279","journal-title":"J Med Chem"},{"key":"9923_CR41","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1038\/nchembio.150","volume":"5","author":"E Naylor","year":"2009","unstructured":"Naylor E, Arredouani A, Vasudevan SR, Lewis AM, Parkesh R, Mizote A, Rosen D, Thomas JM, Izumi M, Ganesan A, Galione A, Churchill GC (2009) Identification of a chemical probe for NAADP by virtual screening. Nat Chem Biol 5:220\u2013226","journal-title":"Nat Chem Biol"},{"key":"9923_CR42","doi-asserted-by":"crossref","first-page":"2774","DOI":"10.1002\/cbic.201402440","volume":"15","author":"SR Vasudevan","year":"2014","unstructured":"Vasudevan SR, Singh N, Churchill GC (2014) Scaffold hopping with virtual screening from IP3 to a drug-like partial agonist of the inositol trisphosphate receptor. ChemBioChem 15:2774\u20132782","journal-title":"ChemBioChem"},{"key":"9923_CR43","doi-asserted-by":"crossref","first-page":"1489","DOI":"10.1021\/jm040163o","volume":"48","author":"TS Rush 3rd","year":"2005","unstructured":"Rush TS 3rd, Grant JA, Mosyak L, Nicholls A (2005) A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction. J Med Chem 48:1489\u20131495","journal-title":"J Med Chem"},{"key":"9923_CR44","doi-asserted-by":"crossref","first-page":"3142","DOI":"10.1021\/jm040015y","volume":"47","author":"G Wu","year":"2004","unstructured":"Wu G, Vieth M (2004) SDOCKER: a method utilizing existing X-ray structures to improve docking accuracy. J Med Chem 47:3142\u20133148","journal-title":"J Med Chem"},{"key":"9923_CR45","doi-asserted-by":"crossref","first-page":"1030","DOI":"10.1016\/j.jmgm.2007.07.001","volume":"26","author":"Y Fukunishi","year":"2008","unstructured":"Fukunishi Y, Nakamura H (2008) Prediction of protein\u2013ligand complex structure by docking software guided by other complex structures. J Mol Graph Model 26:1030\u20131033","journal-title":"J Mol Graph Model"},{"key":"9923_CR46","doi-asserted-by":"crossref","first-page":"1332","DOI":"10.3390\/ph5121332","volume":"5","author":"Y Fukunishi","year":"2012","unstructured":"Fukunishi Y, Nakamura H (2012) Integration of ligand-based drug screening with structure-based drug screening by combining maximum volume overlapping score with ligand docking. Pharmaceuticals (Basel) 5:1332\u20131345","journal-title":"Pharmaceuticals (Basel)"},{"key":"9923_CR47","doi-asserted-by":"crossref","first-page":"1078","DOI":"10.1021\/acs.jcim.5b00275","volume":"56","author":"SY Huang","year":"2016","unstructured":"Huang SY, Li M, Wang J, Pan Y (2016) HybridDock: a hybrid protein\u2013ligand docking protocol integrating protein- and ligand-based approaches. J Chem Inf Model\u00a056:1078\u20131087","journal-title":"J Chem Inf Model"},{"key":"9923_CR48","doi-asserted-by":"crossref","first-page":"2372","DOI":"10.1021\/ci200060s","volume":"51","author":"X Liu","year":"2011","unstructured":"Liu X, Jiang H, Li H (2011) SHAFTS: a hybrid approach for 3D molecular similarity calculation. 1. Method and assessment of virtual screening. J Chem Inf Model 51:2372\u20132385","journal-title":"J Chem Inf Model"},{"key":"9923_CR49","doi-asserted-by":"crossref","first-page":"3564","DOI":"10.1021\/jm200139j","volume":"54","author":"W Lu","year":"2011","unstructured":"Lu W, Liu X, Cao X, Xue M, Liu K, Zhao Z, Shen X, Jiang H, Xu Y, Huang J, Li H (2011) SHAFTS: a hybrid approach for 3D molecular similarity calculation. 2. Prospective case study in the discovery of diverse p90 ribosomal S6 protein kinase 2 inhibitors to suppress cell migration. J Med Chem 54:3564\u20133574","journal-title":"J Med Chem"},{"key":"9923_CR50","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1007\/s10822-012-9584-8","volume":"26","author":"M McGann","year":"2012","unstructured":"McGann M (2012) FRED and HYBRID docking performance on standardized datasets. J Comput Aided Mol Des 26:897\u2013906","journal-title":"J Comput Aided Mol Des"},{"key":"9923_CR51","doi-asserted-by":"crossref","first-page":"1771","DOI":"10.1021\/acs.jcim.5b00142","volume":"55","author":"BP Kelley","year":"2015","unstructured":"Kelley BP, Brown SP, Warren GL, Muchmore SW (2015) POSIT: Flexible Shape-Guided Docking For Pose Prediction. J Chem Inf Model 55:1771\u20131780","journal-title":"J Chem Inf Model"},{"key":"9923_CR52","doi-asserted-by":"crossref","first-page":"1757","DOI":"10.1021\/acs.jcim.5b00232","volume":"55","author":"A Roy","year":"2015","unstructured":"Roy A, Srinivasan B, Skolnick J (2015) PoLi: a virtual screening pipeline based on template pocket and ligand similarity. J Chem Inf Model 55:1757\u20131770","journal-title":"J Chem Inf Model"},{"key":"9923_CR53","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1021\/acs.jcim.5b00279","volume":"56","author":"A Kumar","year":"2016","unstructured":"Kumar A, Zhang KYJ (2016) Application of shape similarity in pose selection and virtual screening in CSARdock2014 exercise. J Chem Inf Model\u00a056:965\u2013973","journal-title":"J Chem Inf Model"},{"key":"9923_CR54","doi-asserted-by":"crossref","first-page":"1268","DOI":"10.1006\/jmbi.1997.0926","volume":"267","author":"MJ Bower","year":"1997","unstructured":"Bower MJ, Cohen FE, Dunbrack RL Jr (1997) Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol 267:1268\u20131282","journal-title":"J Mol Biol"},{"key":"9923_CR55","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1006\/jmbi.1993.1170","volume":"230","author":"RL Dunbrack Jr","year":"1993","unstructured":"Dunbrack RL Jr, Karplus M (1993) Backbone-dependent rotamer library for proteins. Application to side-chain prediction. J Mol Biol 230:543\u2013574","journal-title":"J Mol Biol"},{"key":"9923_CR56","doi-asserted-by":"crossref","first-page":"6611","DOI":"10.1073\/pnas.84.19.6611","volume":"84","author":"Z Li","year":"1987","unstructured":"Li Z, Scheraga HA (1987) Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc Natl Acad Sci USA 84:6611\u20136615","journal-title":"Proc Natl Acad Sci USA"},{"key":"9923_CR57","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":"9923_CR58","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1107\/S0907444910045749","volume":"67","author":"MD Winn","year":"2011","unstructured":"Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67:235\u2013242","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"9923_CR59","doi-asserted-by":"crossref","first-page":"2256","DOI":"10.1107\/S0907444904026460","volume":"60","author":"E Krissinel","year":"2004","unstructured":"Krissinel E, Henrick K (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 60:2256\u20132268","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"9923_CR60","doi-asserted-by":"crossref","first-page":"2919","DOI":"10.1021\/ci300314k","volume":"52","author":"PC Hawkins","year":"2012","unstructured":"Hawkins PC, Nicholls A (2012) Conformer generation with OMEGA: learning from the data set and the analysis of failures. J Chem Inf Model 52:2919\u20132936","journal-title":"J Chem Inf Model"},{"key":"9923_CR61","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1021\/ci100031x","volume":"50","author":"PC Hawkins","year":"2010","unstructured":"Hawkins PC, Skillman AG, Warren GL, Ellingson BA, Stahl MT (2010) Conformer generation with OMEGA: algorithm and validation using high quality structures from the protein databank and Cambridge structural database. J Chem Inf Model 50:572\u2013584","journal-title":"J Chem Inf Model"},{"key":"9923_CR62","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1021\/jm0603365","volume":"50","author":"PC Hawkins","year":"2007","unstructured":"Hawkins PC, Skillman AG, Nicholls A (2007) Comparison of shape-matching and docking as virtual screening tools. J Med Chem 50:74\u201382","journal-title":"J Med Chem"},{"key":"9923_CR63","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1126\/science.132.3434.1115","volume":"132","author":"DJ Rogers","year":"1960","unstructured":"Rogers DJ, Tanimoto TT (1960) A computer program for classifying plants. Science 132:1115\u20131118","journal-title":"Science"},{"key":"9923_CR64","doi-asserted-by":"crossref","first-page":"e20161","DOI":"10.1371\/journal.pone.0020161","volume":"6","author":"SJ Fleishman","year":"2011","unstructured":"Fleishman SJ, Leaver-Fay A, Corn JE, Strauch EM, Khare SD, Koga N, Ashworth J, Murphy P, Richter F, Lemmon G, Meiler J, Baker D (2011) RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite. PLoS ONE 6:e20161","journal-title":"PLoS ONE"},{"key":"9923_CR65","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1016\/j.jmb.2008.11.010","volume":"385","author":"IW Davis","year":"2009","unstructured":"Davis IW, Baker D (2009) RosettaLigand docking with full ligand and receptor flexibility. J Mol Biol 385:381\u2013392","journal-title":"J Mol Biol"},{"key":"9923_CR66","doi-asserted-by":"crossref","first-page":"1998","DOI":"10.1002\/pro.192","volume":"18","author":"IW Davis","year":"2009","unstructured":"Davis IW, Raha K, Head MS, Baker D (2009) Blind docking of pharmaceutically relevant compounds using RosettaLigand. Protein Sci 18:1998\u20132002","journal-title":"Protein Sci"},{"key":"9923_CR67","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1002\/prot.21086","volume":"65","author":"J Meiler","year":"2006","unstructured":"Meiler J, Baker D (2006) ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins 65:538\u2013548","journal-title":"Proteins"},{"key":"9923_CR68","doi-asserted-by":"crossref","first-page":"e0132508","DOI":"10.1371\/journal.pone.0132508","volume":"10","author":"S DeLuca","year":"2015","unstructured":"DeLuca S, Khar K, Meiler J (2015) Fully flexible docking of medium sized ligand libraries with RosettaLigand. PLoS ONE 10:e0132508","journal-title":"PLoS ONE"},{"key":"9923_CR69","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) Glide: 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":"9923_CR70","doi-asserted-by":"crossref","first-page":"6177","DOI":"10.1021\/jm051256o","volume":"49","author":"RA Friesner","year":"2006","unstructured":"Friesner RA, Murphy RB, Repasky MP, Frye LL, Greenwood JR, Halgren TA, Sanschagrin PC, Mainz DT (2006) Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein\u2013ligand complexes. J Med Chem 49:6177\u20136196","journal-title":"J Med Chem"},{"key":"9923_CR71","doi-asserted-by":"crossref","first-page":"1750","DOI":"10.1021\/jm030644s","volume":"47","author":"TA Halgren","year":"2004","unstructured":"Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT, Banks JL (2004) Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 47:1750\u20131759","journal-title":"J Med Chem"},{"key":"9923_CR72","unstructured":"FRED 3.0.1: OpenEye Scientific Software, Santa Fe, NM. http:\/\/www.eyesopen.com"},{"key":"9923_CR73","doi-asserted-by":"crossref","first-page":"1623","DOI":"10.1002\/jcc.10128","volume":"23","author":"A Jakalian","year":"2002","unstructured":"Jakalian A, Jack DB, Bayly CI (2002) Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J Comput Chem 23:1623\u20131641","journal-title":"J Comput Chem"},{"key":"9923_CR74","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1002\/bip.10207","volume":"68","author":"MR McGann","year":"2003","unstructured":"McGann MR, Almond HR, Nicholls A, Grant JA, Brown FK (2003) Gaussian docking functions. Biopolymers 68:76\u201390","journal-title":"Biopolymers"},{"key":"9923_CR75","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1007\/s10822-007-9166-3","volume":"22","author":"PC Hawkins","year":"2008","unstructured":"Hawkins PC, Warren GL, Skillman AG, Nicholls A (2008) How to do an evaluation: pitfalls and traps. J Comput Aided Mol Des 22:179\u2013190","journal-title":"J Comput Aided Mol Des"},{"key":"9923_CR76","doi-asserted-by":"crossref","first-page":"1339","DOI":"10.1021\/ci5001086","volume":"54","author":"PC Hawkins","year":"2014","unstructured":"Hawkins PC, Kelley BP, Warren GL (2014) The application of statistical methods to cognate docking: a path forward? J Chem Inf Model 54:1339\u20131355","journal-title":"J Chem Inf Model"},{"key":"9923_CR77","doi-asserted-by":"crossref","first-page":"1708","DOI":"10.1021\/ci0498719","volume":"44","author":"A Bender","year":"2004","unstructured":"Bender A, Mussa HY, Glen RC, Reiling S (2004) Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): evaluation of performance. J Chem Inf Comput Sci 44:1708\u20131718","journal-title":"J Chem Inf Comput Sci"},{"key":"9923_CR78","doi-asserted-by":"crossref","first-page":"742","DOI":"10.1021\/ci100050t","volume":"50","author":"D Rogers","year":"2010","unstructured":"Rogers D, Hahn M (2010) Extended-connectivity fingerprints. J Chem Inf Model 50:742\u2013754","journal-title":"J Chem Inf Model"},{"key":"9923_CR79","doi-asserted-by":"crossref","first-page":"5912","DOI":"10.1021\/jm050362n","volume":"49","author":"GL Warren","year":"2006","unstructured":"Warren GL, Andrews CW, Capelli AM, Clarke B, LaLonde J, Lambert MH, Lindvall M, Nevins N, Semus SF, Senger S, Tedesco G, Wall ID, Woolven JM, Peishoff CE, Head MS (2006) A critical assessment of docking programs and scoring functions. J Med Chem 49:5912\u20135931","journal-title":"J Med Chem"},{"key":"9923_CR80","doi-asserted-by":"crossref","first-page":"742","DOI":"10.1002\/jcc.21643","volume":"32","author":"D Plewczynski","year":"2011","unstructured":"Plewczynski D, Lazniewski M, Augustyniak R, Ginalski K (2011) Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database. J Comput Chem 32:742\u2013755","journal-title":"J Comput Chem"},{"key":"9923_CR81","doi-asserted-by":"crossref","first-page":"1432","DOI":"10.1021\/ci100161z","volume":"50","author":"T Tuccinardi","year":"2010","unstructured":"Tuccinardi T, Botta M, Giordano A, Martinelli A (2010) Protein kinases: docking and homology modeling reliability. J Chem Inf Model 50:1432\u20131441","journal-title":"J Chem Inf Model"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-016-9923-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s10822-016-9923-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-016-9923-2","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,18]],"date-time":"2024-06-18T03:25:46Z","timestamp":1718681146000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10822-016-9923-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,6]]},"references-count":81,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2016,6]]}},"alternative-id":["9923"],"URL":"https:\/\/doi.org\/10.1007\/s10822-016-9923-2","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"value":"0920-654X","type":"print"},{"value":"1573-4951","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,6]]}}}