TY - JOUR AU - Lagarde, N. AU - Zagury, J. F. AU - Montes, M. PY - 2015 DA - 2015// TI - Benchmarking data sets for the evaluation of virtual ligand screening methods: review and perspectives JO - J Chem Inf Model VL - 55 UR - https://doi.org/10.1021/acs.jcim.5b00090 DO - 10.1021/acs.jcim.5b00090 ID - Lagarde2015 ER - TY - JOUR AU - Plewczynski, D. AU - Lazniewski, M. AU - Augustyniak, R. AU - Ginalski, K. PY - 2011 DA - 2011// TI - Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database JO - J Comput Chem VL - 32 UR - https://doi.org/10.1002/jcc.21643 DO - 10.1002/jcc.21643 ID - Plewczynski2011 ER - TY - JOUR AU - Kellenberger, E. AU - Rodrigo, J. AU - Muller, P. AU - Rognan, D. PY - 2004 DA - 2004// TI - Comparative evaluation of eight docking tools for docking and virtual screening accuracy JO - Proteins VL - 57 UR - https://doi.org/10.1002/prot.20149 DO - 10.1002/prot.20149 ID - Kellenberger2004 ER - TY - JOUR AU - Charifson, P. S. AU - Corkery, J. J. AU - Murcko, M. A. AU - Walters, W. P. PY - 1999 DA - 1999// TI - Consensus scoring: a method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins JO - J Med Chem VL - 42 UR - https://doi.org/10.1021/jm990352k DO - 10.1021/jm990352k ID - Charifson1999 ER - TY - JOUR AU - Warren, G. L. AU - Andrews, C. W. AU - Capelli, A. -. M. AU - Clarke, B. AU - LaLonde, J. AU - Lambert, M. H. AU - Lindvall, M. AU - Nevins, N. AU - Semus, S. F. AU - Senger, S. PY - 2006 DA - 2006// TI - A critical assessment of docking programs and scoring functions JO - J Med Chem VL - 49 UR - https://doi.org/10.1021/jm050362n DO - 10.1021/jm050362n ID - Warren2006 ER - TY - JOUR AU - Keseru, G. M. PY - 2001 DA - 2001// TI - A virtual high throughput screen for high affinity cytochrome P450cam substrates. Implications for in silico prediction of drug metabolism JO - J Comput Aided Mol Des VL - 15 UR - https://doi.org/10.1023/A:1011911204383 DO - 10.1023/A:1011911204383 ID - Keseru2001 ER - TY - JOUR AU - Huang, N. AU - Shoichet, B. K. AU - Irwin, J. J. PY - 2006 DA - 2006// TI - Benchmarking sets for molecular docking JO - J Med Chem VL - 49 UR - https://doi.org/10.1021/jm0608356 DO - 10.1021/jm0608356 ID - Huang2006 ER - TY - JOUR AU - Cross, J. B. AU - Thompson, D. C. AU - Rai, B. K. AU - Baber, J. C. AU - Fan, K. Y. AU - Hu, Y. AU - Humblet, C. PY - 2009 DA - 2009// TI - Comparison of several molecular docking programs: pose prediction and virtual screening accuracy JO - J Chem Inf Model VL - 49 UR - https://doi.org/10.1021/ci900056c DO - 10.1021/ci900056c ID - Cross2009 ER - TY - JOUR AU - Fan, H. AU - Irwin, J. J. AU - Webb, B. M. AU - Klebe, G. AU - Shoichet, B. K. AU - Sali, A. PY - 2009 DA - 2009// TI - Molecular docking screens using comparative models of proteins JO - J Chem Inf Model VL - 49 UR - https://doi.org/10.1021/ci9003706 DO - 10.1021/ci9003706 ID - Fan2009 ER - TY - JOUR AU - Spitzer, R. AU - Jain, A. N. PY - 2012 DA - 2012// TI - Surflex-dock: docking benchmarks and real-world application JO - J Comput Aided Mol Des VL - 26 UR - https://doi.org/10.1007/s10822-011-9533-y DO - 10.1007/s10822-011-9533-y ID - Spitzer2012 ER - TY - JOUR AU - Liebeschuetz, J. W. AU - Cole, J. C. AU - Korb, O. PY - 2012 DA - 2012// TI - Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test JO - J Comput Aided Mol Des VL - 26 UR - https://doi.org/10.1007/s10822-012-9551-4 DO - 10.1007/s10822-012-9551-4 ID - Liebeschuetz2012 ER - TY - JOUR AU - Neves, M. A. AU - Totrov, M. AU - Abagyan, R. PY - 2012 DA - 2012// TI - Docking and scoring with ICM: the benchmarking results and strategies for improvement JO - J Comput Aided Mol Des VL - 26 UR - https://doi.org/10.1007/s10822-012-9547-0 DO - 10.1007/s10822-012-9547-0 ID - Neves2012 ER - TY - JOUR AU - Schneider, N. AU - Lange, G. AU - Hindle, S. AU - Klein, R. AU - Rarey, M. PY - 2013 DA - 2013// TI - A consistent description of HYdrogen bond and DEhydration energies in protein-ligand complexes: methods behind the HYDE scoring function JO - J Comput Aided Mol Des VL - 27 UR - https://doi.org/10.1007/s10822-012-9626-2 DO - 10.1007/s10822-012-9626-2 ID - Schneider2013 ER - TY - JOUR AU - Hawkins, P. C. AU - Warren, G. L. AU - Skillman, A. G. AU - Nicholls, A. PY - 2008 DA - 2008// TI - How to do an evaluation: pitfalls and traps JO - J Comput Aided Mol Des VL - 22 UR - https://doi.org/10.1007/s10822-007-9166-3 DO - 10.1007/s10822-007-9166-3 ID - Hawkins2008 ER - TY - JOUR AU - Good, A. C. AU - Oprea, T. I. PY - 2008 DA - 2008// TI - Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection? JO - J Comput Aided Mol Des VL - 22 UR - https://doi.org/10.1007/s10822-007-9167-2 DO - 10.1007/s10822-007-9167-2 ID - Good2008 ER - TY - JOUR AU - Irwin, J. J. PY - 2008 DA - 2008// TI - Community benchmarks for virtual screening JO - J Comput Aided Mol Des VL - 22 UR - https://doi.org/10.1007/s10822-008-9189-4 DO - 10.1007/s10822-008-9189-4 ID - Irwin2008 ER - TY - JOUR AU - Mysinger, M. M. AU - Carchia, M. AU - Irwin, J. J. AU - Shoichet, B. K. PY - 2012 DA - 2012// TI - Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking JO - J Med Chem VL - 55 UR - https://doi.org/10.1021/jm300687e DO - 10.1021/jm300687e ID - Mysinger2012 ER - TY - JOUR AU - Chen, Y. C. PY - 2015 DA - 2015// TI - Beware of docking! JO - Trends Pharmacol Sci VL - 36 UR - https://doi.org/10.1016/j.tips.2014.12.001 DO - 10.1016/j.tips.2014.12.001 ID - Chen2015 ER - TY - JOUR AU - Jones, G. AU - Willett, P. AU - Glen, R. C. AU - Leach, A. R. AU - Taylor, R. PY - 1997 DA - 1997// TI - Development and validation of a genetic algorithm for flexible docking JO - J Mol Biol VL - 267 UR - https://doi.org/10.1006/jmbi.1996.0897 DO - 10.1006/jmbi.1996.0897 ID - Jones1997 ER - TY - JOUR AU - Friesner, R. A. AU - Banks, J. L. AU - Murphy, R. B. AU - Halgren, T. A. AU - Klicic, J. J. AU - Mainz, D. T. AU - Repasky, M. P. AU - Knoll, E. H. AU - Shelley, M. AU - Perry, J. K. PY - 2004 DA - 2004// TI - Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy JO - J Med Chem VL - 47 UR - https://doi.org/10.1021/jm0306430 DO - 10.1021/jm0306430 ID - Friesner2004 ER - TY - JOUR AU - Jain, A. N. PY - 2003 DA - 2003// TI - Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine JO - J Med Chem VL - 46 UR - https://doi.org/10.1021/jm020406h DO - 10.1021/jm020406h ID - Jain2003 ER - TY - JOUR AU - Rarey, M. AU - Kramer, B. AU - Lengauer, T. AU - Klebe, G. PY - 1996 DA - 1996// TI - A fast flexible docking method using an incremental construction algorithm JO - J Mol Biol VL - 261 UR - https://doi.org/10.1006/jmbi.1996.0477 DO - 10.1006/jmbi.1996.0477 ID - Rarey1996 ER - TY - JOUR AU - Truchon, J. F. AU - Bayly, C. I. PY - 2007 DA - 2007// TI - Evaluating virtual screening methods: good and bad metrics for the “early recognition” problem JO - J Chem Inf Model VL - 47 UR - https://doi.org/10.1021/ci600426e DO - 10.1021/ci600426e ID - Truchon2007 ER - TY - JOUR AU - Chaput, L. AU - Martinez-Sanz, J. AU - Quiniou, E. AU - Rigolet, P. AU - Saettel, N. AU - Mouawad, L. PY - 2016 DA - 2016// TI - vSDC: a method to improve early recognition in virtual screening when limited experimental resources are available JO - J Cheminform VL - 8 UR - https://doi.org/10.1186/s13321-016-0112-z DO - 10.1186/s13321-016-0112-z ID - Chaput2016 ER - TY - JOUR AU - Sievers, F. AU - Wilm, A. AU - Dineen, D. AU - Gibson, T. J. AU - Karplus, K. AU - Li, W. AU - Lopez, R. AU - McWilliam, H. AU - Remmert, M. AU - Soding, J. PY - 2014 DA - 2014// TI - Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega JO - Mol Syst Biol VL - 7 UR - https://doi.org/10.1038/msb.2011.75 DO - 10.1038/msb.2011.75 ID - Sievers2014 ER - TY - JOUR AU - Jones, G. AU - Willett, P. AU - Glen, R. C. AU - Leach, A. R. AU - Taylor, R. PY - 1997 DA - 1997// TI - Development and validation of a genetic algorithm for flexible docking JO - J Mol Biol VL - 267 UR - https://doi.org/10.1006/jmbi.1996.0897 DO - 10.1006/jmbi.1996.0897 ID - Jones1997 ER - TY - JOUR AU - Halgren, T. PY - 2007 DA - 2007// TI - New method for fast and accurate binding-site identification and analysis JO - Chem Biol Drug Des VL - 69 UR - https://doi.org/10.1111/j.1747-0285.2007.00483.x DO - 10.1111/j.1747-0285.2007.00483.x ID - Halgren2007 ER - TY - JOUR AU - Stahl, M. AU - Rarey, M. PY - 2001 DA - 2001// TI - Detailed analysis of scoring functions for virtual screening JO - J Med Chem VL - 44 UR - https://doi.org/10.1021/jm0003992 DO - 10.1021/jm0003992 ID - Stahl2001 ER - TY - JOUR AU - Schulz-Gasch, T. AU - Stahl, M. PY - 2003 DA - 2003// TI - Binding site characteristics in structure-based virtual screening: evaluation of current docking tools JO - J Mol Model VL - 9 UR - https://doi.org/10.1007/s00894-002-0112-y DO - 10.1007/s00894-002-0112-y ID - Schulz-Gasch2003 ER - TY - JOUR AU - Duan, J. AU - Dixon, S. L. AU - Lowrie, J. F. AU - Sherman, W. PY - 2010 DA - 2010// TI - Analysis and comparison of 2D fingerprints: insights into database screening performance using eight fingerprint methods JO - J Mol Graph Model VL - 29 UR - https://doi.org/10.1016/j.jmgm.2010.05.008 DO - 10.1016/j.jmgm.2010.05.008 ID - Duan2010 ER - TY - JOUR AU - Hall, L. H. AU - Kier, L. B. PY - 1995 DA - 1995// TI - Electrotopological state indices for atom types: a novel combination of electronic, topological, and valence State Information JO - J Chem Inf Comput Sci VL - 35 UR - https://doi.org/10.1021/ci00028a014 DO - 10.1021/ci00028a014 ID - Hall1995 ER - TY - STD TI - Tanimoto TT (1958) An elementary mathematical theory of classification and prediction. International Business Machines Corporation ID - ref32 ER - TY - JOUR AU - Cecchini, M. AU - Kolb, P. AU - Majeux, N. AU - Caflisch, A. PY - 2004 DA - 2004// TI - Automated docking of highly flexible ligands by genetic algorithms: a critical assessment JO - J Comput Chem VL - 25 UR - https://doi.org/10.1002/jcc.10384 DO - 10.1002/jcc.10384 ID - Cecchini2004 ER - TY - JOUR AU - Jones, G. AU - Willett, P. AU - Glen, R. C. PY - 1995 DA - 1995// TI - Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation JO - J Mol Biol VL - 245 UR - https://doi.org/10.1016/S0022-2836(95)80037-9 DO - 10.1016/S0022-2836(95)80037-9 ID - Jones1995 ER - TY - JOUR AU - Halgren, T. A. AU - Murphy, R. B. AU - Friesner, R. A. AU - Beard, H. S. AU - Frye, L. L. AU - Pollard, W. T. AU - Banks, J. L. PY - 2004 DA - 2004// TI - Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening JO - J Med Chem VL - 47 UR - https://doi.org/10.1021/jm030644s DO - 10.1021/jm030644s ID - Halgren2004 ER - TY - JOUR AU - Yabuuchi, H. AU - Niijima, S. AU - Takematsu, H. AU - Ida, T. AU - Hirokawa, T. AU - Hara, T. AU - Ogawa, T. AU - Minowa, Y. AU - Tsujimoto, G. AU - Okuno, Y. PY - 2011 DA - 2011// TI - Analysis of multiple compound-protein interactions reveals novel bioactive molecules JO - Mol Syst Biol VL - 7 UR - https://doi.org/10.1038/msb.2011.5 DO - 10.1038/msb.2011.5 ID - Yabuuchi2011 ER - TY - BOOK PY - 2014 DA - 2014// TI - R: A language and environment for statistical computing PB - R Foundation for Statistical Computing CY - Vienna ID - ref37 ER -