• Morris Kragh posted an update 3 months ago

    J Med Chem 42:5100?109 Warren GL, Andrews CW, Capelli AM, Clarke B, LaLonde J, Lambert MH, Lindvall M, Nevins N, Semus SF, Senger S et al (2006) A crucial assessment of docking applications and scoring functions. J Med Chem 49:5912?931 Keseru GM (2001) A virtual high throughput screen for high affinity cytochrome P450cam substrates. Implications for in silico prediction of drug metabolism. J Comput Aided Mol Des 15:649?57 Huang N, Shoichet BK, Irwin JJ (2006) Benchmarking sets for molecular docking. J Med Chem 49:6789?801 Cross JB, Thompson DC, Rai BK, Baber JC, Fan KY, Hu Y, Humblet C (2009) Comparison of various molecular docking applications: pose prediction and virtual screening accuracy. J Chem Inf Model 49:1455?474 Fan H, Irwin JJ, Webb BM, Klebe G, Shoichet BK, Sali A (2009) Molecular docking screens making use of comparative models of proteins. J Chem Inf Model 49:2512?527 Spitzer R, Jain AN (2012) Surflexdock: docking benchmarks and true globe application. J Comput Aided Mol Des 26:687?99 Liebeschuetz JW, Cole JC, Korb O (2012) Pose prediction and virtual screening overall performance of GOLD scoring functions within a standardized test. J Comput Aided Mol Des 26:737?48 Neves MA, Totrov M, Abagyan R (2012) Docking and scoring with ICM: the benchmarking benefits and techniques for improvement. J Comput Aided Mol Des 26:675?86 Schneider N, Lange G, Hindle S, Klein R, Rarey M (2013) A constant description of HYdrogen bond and DEhydration energies in protein ligand complexes: techniques behind the HYDE SART.S23506 scoring function. J Comput Aided Mol Des 27:15?9 Hawkins Pc, Warren GL, Skillman AG, Nicholls A (2008) The way to do an evaluation: pitfalls and traps. J Comput Aided Mol Des 22:179?90 Good AC, Oprea TI (2008) Optimization of CAMD methods three. Virtual screening enrichment studies: a support or hindrance in tool selection? J Comput Aided Mol Des 22:169?78 Irwin JJ (2008) Community benchmarks for virtual screening. J Comput Aided Mol Des 22:193?99 Mysinger MM, Carchia M, Irwin s12889-015-2195-2 JJ, Shoichet BK (2012) Directory of valuable decoys, enhanced (DUDE): greater ligands and decoys for greater bench marking. J Med Chem 55:6582?594 Chen YC (2015) Beware of docking! Trends Pharmacol Sci 36:78?5 Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Ozanimod Improvement and validation of a genetic algorithm for versatile docking. J Mol Biol 267:727?48 Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK et al (2004) Glide: a new method for rapid, accurate docking and scoring. 1. Method and assessment of dock ing accuracy. J Med Chem 47:1739?749 Jain AN (2003) Surflex: fully automatic flexible molecular docking employing a molecular similaritybased search engine. J Med Chem 46:499?11 Rarey M, Kramer B, Lengauer T, Klebe G (1996) A fast flexible dock ing technique making use of an incremental construction algorithm. J Mol Biol 261:470?89 Truchon JF, Bayly CI (2007) Evaluating virtual screening solutions: great and negative metrics for the “early recognition” trouble. J Chem Inf Model 47:488?08 Chaput L, MartinezSanz J, Quiniou E, Rigolet P, Saettel N, Mouawad L (2016) vSDC: a approach to improve early recognition in virtual screening when limited experimental sources are readily available.