{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,21]],"date-time":"2026-06-21T07:04:38Z","timestamp":1782025478196,"version":"3.54.5"},"reference-count":61,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2015,5,15]],"date-time":"2015-05-15T00:00:00Z","timestamp":1431648000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Cheminform"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/s13321-015-0067-5","type":"journal-article","created":{"date-parts":[[2015,5,14]],"date-time":"2015-05-14T16:25:18Z","timestamp":1431620718000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":214,"title":["Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets"],"prefix":"10.1186","volume":"7","author":[{"given":"Wei P.","family":"Feinstein","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michal","family":"Brylinski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2015,5,15]]},"reference":[{"issue":"3","key":"67_CR1","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1016\/j.sbi.2005.05.011","volume":"15","author":"J Moult","year":"2005","unstructured":"Moult J. A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr Opin Struct Biol. 2005;15(3):285\u20139.","journal-title":"Curr Opin Struct Biol"},{"issue":"Suppl 9","key":"67_CR2","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1002\/prot.22588","volume":"77","author":"Y Zhang","year":"2009","unstructured":"Zhang Y. I-TASSER: fully automated protein structure prediction in CASP8. Proteins. 2009;77 Suppl 9:100\u201313.","journal-title":"Proteins"},{"issue":"11","key":"67_CR3","doi-asserted-by":"publisher","first-page":"e50200","DOI":"10.1371\/journal.pone.0050200","volume":"7","author":"M Brylinski","year":"2012","unstructured":"Brylinski M, Lingam D. eThread: a highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures. PLoS One. 2012;7(11):e50200.","journal-title":"PLoS One"},{"issue":"4","key":"67_CR4","doi-asserted-by":"publisher","first-page":"725","DOI":"10.1038\/nprot.2010.5","volume":"5","author":"A Roy","year":"2010","unstructured":"Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc. 2010;5(4):725\u201338.","journal-title":"Nat Protoc"},{"key":"67_CR5","doi-asserted-by":"publisher","first-page":"118","DOI":"10.3389\/fgene.2013.00118","volume":"4","author":"M Brylinski","year":"2013","unstructured":"Brylinski M. Unleashing the power of meta-threading for evolution\/structure-based function inference of proteins. Front Genet. 2013;4:118.","journal-title":"Front Genet"},{"issue":"Database issue","key":"67_CR6","doi-asserted-by":"publisher","first-page":"D230","DOI":"10.1093\/nar\/gkh008","volume":"32","author":"J Kopp","year":"2004","unstructured":"Kopp J, Schwede T. The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models. Nucleic Acids Res. 2004;32(Database issue):D230\u20134.","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"67_CR7","doi-asserted-by":"publisher","first-page":"e1000585","DOI":"10.1371\/journal.pcbi.1000585","volume":"5","author":"JA Capra","year":"2009","unstructured":"Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Comput Biol. 2009;5(12):e1000585.","journal-title":"PLoS Comput Biol"},{"issue":"15","key":"67_CR8","doi-asserted-by":"publisher","first-page":"2083","DOI":"10.1093\/bioinformatics\/btr331","volume":"27","author":"Z Zhang","year":"2011","unstructured":"Zhang Z, Li Y, Lin B, Schroeder M, Huang B. Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction. Bioinformatics. 2011;27(15):2083\u20138.","journal-title":"Bioinformatics"},{"issue":"6","key":"67_CR9","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1007\/s10822-013-9663-5","volume":"27","author":"M Brylinski","year":"2013","unstructured":"Brylinski M, Feinstein WP. eFindSite: improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. J Comput Aided Mol Des. 2013;27(6):551\u201367.","journal-title":"J Comput Aided Mol Des"},{"issue":"5","key":"67_CR10","doi-asserted-by":"publisher","first-page":"395","DOI":"10.2174\/138920306778559386","volume":"7","author":"AT Laurie","year":"2006","unstructured":"Laurie AT, Jackson RM. Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening. Curr Protein Pept Sci. 2006;7(5):395\u2013406.","journal-title":"Curr Protein Pept Sci"},{"issue":"4","key":"67_CR11","doi-asserted-by":"publisher","first-page":"381","DOI":"10.2174\/138920307781369391","volume":"8","author":"BO Villoutreix","year":"2007","unstructured":"Villoutreix BO, Renault N, Lagorce D, Sperandio O, Montes M, Miteva MA. Free resources to assist structure-based virtual ligand screening experiments. Curr Protein Pept Sci. 2007;8(4):381\u2013411.","journal-title":"Curr Protein Pept Sci"},{"issue":"3","key":"67_CR12","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1016\/S0014-827X(02)01211-9","volume":"57","author":"C Sotriffer","year":"2002","unstructured":"Sotriffer C, Klebe G. Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design. Farmaco. 2002;57(3):243\u201351.","journal-title":"Farmaco"},{"issue":"11","key":"67_CR13","doi-asserted-by":"publisher","first-page":"935","DOI":"10.1038\/nrd1549","volume":"3","author":"DB Kitchen","year":"2004","unstructured":"Kitchen DB, Decornez H, Furr JR, Bajorath J. Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov. 2004;3(11):935\u201349.","journal-title":"Nat Rev Drug Discov"},{"issue":"1","key":"67_CR14","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1016\/S1359-6446(01)02091-8","volume":"7","author":"G Schneider","year":"2002","unstructured":"Schneider G, Bohm HJ. Virtual screening and fast automated docking methods. Drug Discov Today. 2002;7(1):64\u201370.","journal-title":"Drug Discov Today"},{"issue":"7019","key":"67_CR15","doi-asserted-by":"publisher","first-page":"862","DOI":"10.1038\/nature03197","volume":"432","author":"BK Shoichet","year":"2004","unstructured":"Shoichet BK. Virtual screening of chemical libraries. Nature. 2004;432(7019):862\u20135.","journal-title":"Nature"},{"issue":"5","key":"67_CR16","doi-asserted-by":"publisher","first-page":"2130","DOI":"10.1039\/c2cs35357a","volume":"42","author":"DL Ma","year":"2013","unstructured":"Ma DL, Chan DS, Leung CH. Drug repositioning by structure-based virtual screening. Chem Soc Rev. 2013;42(5):2130\u201341.","journal-title":"Chem Soc Rev"},{"issue":"2","key":"67_CR17","first-page":"239","volume":"17","author":"YY Li","year":"2006","unstructured":"Li YY, An J, Jones SJ. A large-scale computational approach to drug repositioning. Genome Informatics Int Conference Genome Informatics. 2006;17(2):239\u201347.","journal-title":"Genome Informatics Int Conference Genome Informatics"},{"issue":"7","key":"67_CR18","doi-asserted-by":"publisher","first-page":"e1000423","DOI":"10.1371\/journal.pcbi.1000423","volume":"5","author":"SL Kinnings","year":"2009","unstructured":"Kinnings SL, Liu N, Buchmeier N, Tonge PJ, Xie L, Bourne PE. Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis. PLoS Comput Biol. 2009;5(7):e1000423.","journal-title":"PLoS Comput Biol"},{"issue":"2","key":"67_CR19","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1002\/1097-0134(20010501)43:2<217::AID-PROT1032>3.0.CO;2-G","volume":"43","author":"YZ Chen","year":"2001","unstructured":"Chen YZ, Zhi DG. Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule. Proteins. 2001;43(2):217\u201326.","journal-title":"Proteins"},{"issue":"11","key":"67_CR20","doi-asserted-by":"publisher","first-page":"3596","DOI":"10.1016\/j.bmc.2012.03.072","volume":"20","author":"G Lauro","year":"2012","unstructured":"Lauro G, Masullo M, Piacente S, Riccio R, Bifulco G. Inverse Virtual Screening allows the discovery of the biological activity of natural compounds. Bioorg Med Chem. 2012;20(11):3596\u2013602.","journal-title":"Bioorg Med Chem"},{"key":"67_CR21","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1146\/annurev.biophys.32.110601.142532","volume":"32","author":"N Brooijmans","year":"2003","unstructured":"Brooijmans N, Kuntz ID. Molecular recognition and docking algorithms. Annu Rev Biophys Biomol Struct. 2003;32:335\u201373.","journal-title":"Annu Rev Biophys Biomol Struct"},{"issue":"5","key":"67_CR22","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1002\/jmr.2266","volume":"26","author":"E Yuriev","year":"2013","unstructured":"Yuriev E, Ramsland PA. Latest developments in molecular docking: 2010\u20132011 in review. J Mol Recog JMR. 2013;26(5):215\u201339.","journal-title":"J Mol Recog JMR"},{"issue":"14","key":"67_CR23","doi-asserted-by":"publisher","first-page":"2540","DOI":"10.1002\/jcc.21545","volume":"31","author":"JA Feng","year":"2010","unstructured":"Feng JA, Marshall GR. SKATE: a docking program that decouples systematic sampling from scoring. J Comput Chem. 2010;31(14):2540\u201354.","journal-title":"J Comput Chem"},{"issue":"3","key":"67_CR24","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1002\/prot.340130304","volume":"13","author":"TN Hart","year":"1992","unstructured":"Hart TN, Read RJ. A multiple-start Monte Carlo docking method. Proteins. 1992;13(3):206\u201322.","journal-title":"Proteins"},{"key":"67_CR25","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1007\/978-3-540-79450-9_37","volume":"4983","author":"R \u00d6rd\u00f6g","year":"2008","unstructured":"\u00d6rd\u00f6g R, Grolmusz V. Evaluating genetic algorithms in protein-ligand docking. Bioinformatics Res Applications. 2008;4983:402\u201313.","journal-title":"Bioinformatics Res Applications"},{"issue":"2","key":"67_CR26","doi-asserted-by":"publisher","first-page":"228","DOI":"10.1002\/(SICI)1097-0134(19991101)37:2<228::AID-PROT8>3.0.CO;2-8","volume":"37","author":"B Kramer","year":"1999","unstructured":"Kramer B, Rarey M, Lengauer T. Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking. Proteins. 1999;37(2):228\u201341.","journal-title":"Proteins"},{"issue":"9","key":"67_CR27","doi-asserted-by":"publisher","first-page":"1623","DOI":"10.1021\/ci100218t","volume":"50","author":"F Ding","year":"2010","unstructured":"Ding F, Yin S, Dokholyan NV. Rapid flexible docking using a stochastic rotamer library of ligands. J Chem Inf Model. 2010;50(9):1623\u201332.","journal-title":"J Chem Inf Model"},{"issue":"13","key":"67_CR28","doi-asserted-by":"publisher","first-page":"1549","DOI":"10.1002\/jcc.10306","volume":"24","author":"G Wu","year":"2003","unstructured":"Wu G, Robertson DH, Brooks 3rd CL, Vieth M. Detailed analysis of grid-based molecular docking: a case study of CDOCKER-A CHARMm-based MD docking algorithm. J Comput Chem. 2003;24(13):1549\u201362.","journal-title":"J Comput Chem"},{"issue":"11","key":"67_CR29","doi-asserted-by":"publisher","first-page":"2682","DOI":"10.1016\/j.bpj.2010.02.034","volume":"98","author":"E Stjernschantz","year":"2010","unstructured":"Stjernschantz E, Oostenbrink C. Improved ligand-protein binding affinity predictions using multiple binding modes. Biophys J. 2010;98(11):2682\u201391.","journal-title":"Biophys J"},{"issue":"7","key":"67_CR30","doi-asserted-by":"publisher","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, et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem. 2004;47(7):1739\u201349.","journal-title":"J Med Chem"},{"issue":"16","key":"67_CR31","doi-asserted-by":"publisher","first-page":"2785","DOI":"10.1002\/jcc.21256","volume":"30","author":"GM Morris","year":"2009","unstructured":"Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, et al. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009;30(16):2785\u201391.","journal-title":"J Comput Chem"},{"issue":"20","key":"67_CR32","doi-asserted-by":"publisher","first-page":"6296","DOI":"10.1021\/jm050436v","volume":"48","author":"HF Velec","year":"2005","unstructured":"Velec HF, Gohlke H, Klebe G. DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction. J Med Chem. 2005;48(20):6296\u2013303.","journal-title":"J Med Chem"},{"issue":"10","key":"67_CR33","doi-asserted-by":"publisher","first-page":"2731","DOI":"10.1021\/ci200274q","volume":"51","author":"G Neudert","year":"2011","unstructured":"Neudert G, Klebe G. DSX: a knowledge-based scoring function for the assessment of protein-ligand complexes. J Chem Inf Model. 2011;51(10):2731\u201345.","journal-title":"J Chem Inf Model"},{"issue":"2","key":"67_CR34","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcc.21334","volume":"31","author":"O Trott","year":"2010","unstructured":"Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010;31(2):455\u201361.","journal-title":"J Comput Chem"},{"issue":"4","key":"67_CR35","doi-asserted-by":"publisher","first-page":"609","DOI":"10.1002\/prot.10465","volume":"52","author":"ML Verdonk","year":"2003","unstructured":"Verdonk ML, Cole JC, Hartshorn MJ, Murray CW, Taylor RD. Improved protein-ligand docking using GOLD. Proteins. 2003;52(4):609\u201323.","journal-title":"Proteins"},{"issue":"4","key":"67_CR36","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003571","volume":"10","author":"S Ruiz-Carmona","year":"2014","unstructured":"Ruiz-Carmona S, Alvarez-Garcia D, Foloppe N, Garmendia-Doval AB, Juhos S, Schmidtke P, et al. rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids. PLoS Comput Biol. 2014;10(4), e1003571.","journal-title":"PLoS Comput Biol"},{"issue":"6","key":"67_CR37","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1007\/s10822-011-9533-y","volume":"26","author":"R Spitzer","year":"2012","unstructured":"Spitzer R, Jain AN. Surflex-Dock: Docking benchmarks and real-world application. J Comput Aided Mol Des. 2012;26(6):687\u201399.","journal-title":"J Comput Aided Mol Des"},{"issue":"3","key":"67_CR38","doi-asserted-by":"publisher","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. A fast flexible docking method using an incremental construction algorithm. J Mol Biol. 1996;261(3):470\u201389.","journal-title":"J Mol Biol"},{"issue":"3","key":"67_CR39","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1021\/ci100436p","volume":"51","author":"M McGann","year":"2011","unstructured":"McGann M. FRED pose prediction and virtual screening accuracy. J Chem Inf Model. 2011;51(3):578\u201396.","journal-title":"J Chem Inf Model"},{"issue":"5","key":"67_CR40","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1023\/A:1011115820450","volume":"15","author":"TJ Ewing","year":"2001","unstructured":"Ewing TJ, Makino S, Skillman AG, Kuntz ID. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aided Mol Des. 2001;15(5):411\u201328.","journal-title":"J Comput Aided Mol Des"},{"issue":"8","key":"67_CR41","doi-asserted-by":"publisher","first-page":"e11955","DOI":"10.1371\/journal.pone.0011955","volume":"5","author":"MW Chang","year":"2010","unstructured":"Chang MW, Ayeni C, Breuer S, Torbett BE. Virtual screening for HIV protease inhibitors: a comparison of AutoDock 4 and Vina. PLoS One. 2010;5(8):e11955.","journal-title":"PLoS One"},{"issue":"1\u20133","key":"67_CR42","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1016\/j.bpc.2010.01.011","volume":"150","author":"M Lape","year":"2010","unstructured":"Lape M, Elam C, Paula S. Comparison of current docking tools for the simulation of inhibitor binding by the transmembrane domain of the sarco\/endoplasmic reticulum calcium ATPase. Biophys Chem. 2010;150(1\u20133):88\u201397.","journal-title":"Biophys Chem"},{"issue":"4","key":"67_CR43","doi-asserted-by":"publisher","first-page":"642","DOI":"10.1002\/pro.351","volume":"19","author":"DA Jacques","year":"2010","unstructured":"Jacques DA, Trewhella J. Small-angle scattering for structural biology\u2013expanding the frontier while avoiding the pitfalls. Protein Sci. 2010;19(4):642\u201357.","journal-title":"Protein Sci"},{"issue":"4","key":"67_CR44","doi-asserted-by":"publisher","first-page":"701","DOI":"10.1134\/S0026893308040195","volume":"42","author":"M Lobanov","year":"2008","unstructured":"Lobanov M, Bogatyreva NS, Galzitskaia OV. [Radius of gyration is indicator of compactness of protein structure]. Mol Biol. 2008;42(4):701\u20136.","journal-title":"Mol Biol"},{"issue":"4","key":"67_CR45","doi-asserted-by":"publisher","first-page":"742","DOI":"10.1002\/jcc.21643","volume":"32","author":"D Plewczynski","year":"2011","unstructured":"Plewczynski D, Lazniewski M, Augustyniak R, Ginalski K. Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database. J Comput Chem. 2011;32(4):742\u201355.","journal-title":"J Comput Chem"},{"issue":"1","key":"67_CR46","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1214\/aoms\/1177730491","volume":"18","author":"HB Mann","year":"1947","unstructured":"Mann HB, Whitney DR. On a test of whether one of two random variables is stochastically larger than the other. Ann Math Stat. 1947;18(1):50\u201360.","journal-title":"Ann Math Stat"},{"issue":"6","key":"67_CR47","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. Biom Bull. 1945;1(6):80\u20133.","journal-title":"Biom Bull"},{"issue":"5066","key":"67_CR48","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1126\/science.1621098","volume":"257","author":"DK Wilson","year":"1992","unstructured":"Wilson DK, Bohren KM, Gabbay KH, Quiocho FA. An unlikely sugar substrate site in the 1.65 A structure of the human aldose reductase holoenzyme implicated in diabetic complications. Science. 1992;257(5066):81\u20134.","journal-title":"Science"},{"key":"67_CR49","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/1758-2946-3-33","volume":"3","author":"NM O'Boyle","year":"2011","unstructured":"O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open Babel: An open chemical toolbox. J Cheminformatics. 2011;3:33.","journal-title":"J Cheminformatics"},{"issue":"5","key":"67_CR50","doi-asserted-by":"publisher","first-page":"615","DOI":"10.1093\/bioinformatics\/btp035","volume":"25","author":"I Wallach","year":"2009","unstructured":"Wallach I, Lilien R. The protein-small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding. Bioinformatics. 2009;25(5):615\u201320.","journal-title":"Bioinformatics"},{"issue":"1","key":"67_CR51","doi-asserted-by":"publisher","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, et al. The protein data bank. Nucleic Acids Res. 2000;28(1):235\u201342.","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"67_CR52","doi-asserted-by":"publisher","first-page":"1589","DOI":"10.1093\/bioinformatics\/btg224","volume":"19","author":"G Wang","year":"2003","unstructured":"Wang G, Dunbrack Jr RL. PISCES: a protein sequence culling server. Bioinformatics. 2003;19(12):1589\u201391.","journal-title":"Bioinformatics"},{"issue":"4","key":"67_CR53","doi-asserted-by":"publisher","first-page":"702","DOI":"10.1002\/prot.20264","volume":"57","author":"Y Zhang","year":"2004","unstructured":"Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins. 2004;57(4):702\u201310.","journal-title":"Proteins"},{"key":"67_CR54","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1186\/1471-2105-9-531","volume":"9","author":"SB Pandit","year":"2008","unstructured":"Pandit SB, Skolnick J. Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score. BMC Bioinformatics. 2008;9:531.","journal-title":"BMC Bioinformatics"},{"issue":"23","key":"67_CR55","doi-asserted-by":"publisher","first-page":"6789","DOI":"10.1021\/jm0608356","volume":"49","author":"N Huang","year":"2006","unstructured":"Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem. 2006;49(23):6789\u2013801.","journal-title":"J Med Chem"},{"issue":"14","key":"67_CR56","doi-asserted-by":"publisher","first-page":"6582","DOI":"10.1021\/jm300687e","volume":"55","author":"MM Mysinger","year":"2012","unstructured":"Mysinger MM, Carchia M, Irwin JJ, Shoichet BK. Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. J Med Chem. 2012;55(14):6582\u201394.","journal-title":"J Med Chem"},{"issue":"10","key":"67_CR57","doi-asserted-by":"publisher","first-page":"2807","DOI":"10.1021\/ci500406k","volume":"54","author":"J Gabel","year":"2014","unstructured":"Gabel J, Desaphy J, Rognan D. Beware of machine learning-based scoring functions-on the danger of developing black boxes. J Chem Inf Model. 2014;54(10):2807\u201315.","journal-title":"J Chem Inf Model"},{"issue":"11","key":"67_CR58","doi-asserted-by":"publisher","first-page":"3198","DOI":"10.1021\/ci500299h","volume":"54","author":"E Therrien","year":"2014","unstructured":"Therrien E, Weill N, Tomberg A, Corbeil CR, Lee D, Moitessier N. Docking ligands into flexible and solvated macromolecules. 7. Impact of protein flexibility and water molecules on docking-based virtual screening accuracy. J Chem Inf Model. 2014;54(11):3198\u2013210.","journal-title":"J Chem Inf Model"},{"key":"67_CR59","doi-asserted-by":"publisher","first-page":"922","DOI":"10.1107\/S0567739476001873","volume":"32","author":"W Kabsch","year":"1976","unstructured":"Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Cryst A. 1976;32:922\u20133.","journal-title":"Acta Cryst A"},{"issue":"4","key":"67_CR60","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1093\/bioinformatics\/15.4.327","volume":"15","author":"V Sobolev","year":"1999","unstructured":"Sobolev V, Sorokine A, Prilusky J, Abola EE, Edelman M. Automated analysis of interatomic contacts in proteins. Bioinformatics. 1999;15(4):327\u201332.","journal-title":"Bioinformatics"},{"issue":"2","key":"67_CR61","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1021\/ci600426e","volume":"47","author":"JF Truchon","year":"2007","unstructured":"Truchon JF, Bayly CI. Evaluating virtual screening methods: good and bad metrics for the \"early recognition\" problem. J Chem Inf Model. 2007;47(2):488\u2013508.","journal-title":"J Chem Inf Model"}],"container-title":["Journal of Cheminformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-015-0067-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s13321-015-0067-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-015-0067-5","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-015-0067-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,8]],"date-time":"2024-06-08T23:56:39Z","timestamp":1717890999000},"score":1,"resource":{"primary":{"URL":"https:\/\/jcheminf.biomedcentral.com\/articles\/10.1186\/s13321-015-0067-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,5,15]]},"references-count":61,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["67"],"URL":"https:\/\/doi.org\/10.1186\/s13321-015-0067-5","relation":{},"ISSN":["1758-2946"],"issn-type":[{"value":"1758-2946","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,5,15]]},"assertion":[{"value":"20 December 2014","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 April 2015","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 May 2015","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"18"}}