Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination

D Cappel, 2017, Calculating Water Thermodynamics in the Binding Site of Proteins—Applications of WaterMap to Drug Discovery, Curr Top Med Chem, 17, 2586, 10.2174/1568026617666170414141452

K Lindorff-Larsen, 2011, How fast-folding proteins fold, Science, 334, 517, 10.1126/science.1208351

DL Mobley, 2007, Predicting absolute ligand binding free energies to a simple model site, Journal of molecular biology, 371, 1118, 10.1016/j.jmb.2007.06.002

WC Still, 1990, Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics, J Am Chem Soc, 112, 6127, 10.1021/ja00172a038

KA Beauchamp, 2012, Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements, J Chem Theory Comput, 8, 1409, 10.1021/ct2007814

DJ Huggins, 2011, Systematic placement of structural water molecules for improved scoring of protein-ligand interactions, Protein engineering, design & selection: PEDS, 24, 777, 10.1093/protein/gzr036

G Lemmon, 2013, Towards ligand docking including explicit interface water molecules, PloS one, 8, e67536, 10.1371/journal.pone.0067536

HI Parikh, 2014, Intuitive, but not simple: including explicit water molecules in protein-protein docking simulations improves model quality, Proteins, 82, 916, 10.1002/prot.24466

GA Ross, 2012, Rapid and accurate prediction and scoring of water molecules in protein binding sites, PloS one, 7, e32036, 10.1371/journal.pone.0032036

AD van Dijk, 2006, Solvated docking: introducing water into the modelling of biomolecular complexes, Bioinformatics, 22, 2340, 10.1093/bioinformatics/btl395

T Young, 2007, Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding, Proceedings of the National Academy of Sciences of the United States of America, 104, 808, 10.1073/pnas.0610202104

L Jiang, 2005, A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces, Proteins, 58, 893, 10.1002/prot.20347

RF Alford, 2017, The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design, J Chem Theory Comput, 13, 3031, 10.1021/acs.jctc.7b00125

H Park, 2016, Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules, J Chem Theory Comput, 12, 6201, 10.1021/acs.jctc.6b00819

F Rodier, 2005, Hydration of protein-protein interfaces, Proteins, 60, 36, 10.1002/prot.20478

Case DA, Ben-Shalom I. Y., Brozell S. R., Cerutti D. S., Cheatham, T. E. III, Cruzeiro V. W. D., Darden T. A., Duke R. E., Ghoreishi D., Gilson M. K., Gohlke H., Goetz A. W., Greene D., Harris R., Homeyer N., Izadi S., Kovalenko A., Kurtzman T., Lee T. S., LeGrand S., Li P., Lin C., Liu J., Luchko T., Luo R., Mermelstein D. J., Merz K. M., Miao Y., Monard G., Nguyen C., Nguyen H., Omelyan I., Onufriev A., Pan F., Qi R., Roe D. R., Roitberg A., Sagui C., Schott-Verdugo S., Shen J., Simmerling C. L., Smith J., Salomon-Ferrer R., Swails J., Walker R. C., Wang J., Wei H., Wolf R. M., Wu X., Xiao L., York D. M. and Kollman P. A. AMBER 2018. University of California, San Francisco2018.

E Nittinger, 2019, Water molecules in protein-ligand interfaces. Evaluation of software tools and SAR comparison, Journal of computer-aided molecular design, 33, 307, 10.1007/s10822-019-00187-y

MF Lensink, 2014, Blind prediction of interfacial water positions in CAPRI, Proteins, 82, 620, 10.1002/prot.24439

R Chen, 2003, ZDOCK: an initial-stage protein-docking algorithm, Proteins, 52, 80, 10.1002/prot.10389

JJ Gray, 2003, Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations, Journal of molecular biology, 331, 281, 10.1016/S0022-2836(03)00670-3

J Meiler, 2006, ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility, Proteins, 65, 538, 10.1002/prot.21086

Z Wang, 2016, Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: the prediction accuracy of sampling power and scoring power, Phys Chem Chem Phys, 18, 12964, 10.1039/C6CP01555G

MJ Hartshorn, 2007, Diverse, high-quality test set for the validation of protein-ligand docking performance, Journal of medicinal chemistry, 50, 726, 10.1021/jm061277y

O Korb, 2009, Empirical scoring functions for advanced protein-ligand docking with PLANTS, J Chem Inf Model, 49, 84, 10.1021/ci800298z

A Leaver-Fay, 2005, An adaptive dynamic programming algorithm for the side chain placement problem., Pac Symp Biocomput, 16

MJ O'Meara, 2015, Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta, J Chem Theory Comput, 11, 609, 10.1021/ct500864r

S Li, 2013, Probing the role of interfacial waters in protein-DNA recognition using a hybrid implicit/explicit solvation model, Proteins, 81, 1318, 10.1002/prot.24272

JC Mitchell, 2008, Sampling Rotation Groups by Successive Orthogonal Images, Siam J Sci Comput, 30, 525, 10.1137/030601879

C Yanover, 2011, Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers, Nucleic acids research, 39, 4564, 10.1093/nar/gkr048

A Leaver-Fay, 2011, ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules, Methods Enzymol, 487, 545, 10.1016/B978-0-12-381270-4.00019-6

H Hwang, 2010, Protein-protein docking benchmark version 4.0, Proteins, 78, 3111, 10.1002/prot.22830

ML Benson, 2008, Binding MOAD, a high-quality protein-ligand database, Nucleic acids research, 36, D674, 10.1093/nar/gkm911

D Beglov, 1997, An integral equation to describe the solvation of polar molecules in liquid water, The journal of physical chemistry B, 101, 7821, 10.1021/jp971083h

T Luchko, 2010, Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber, J Chem Theory Comput, 6, 607, 10.1021/ct900460m

DJ Sindhikara, 2012, Placevent: an algorithm for prediction of explicit solvent atom distribution-application to HIV-1 protease and F-ATP synthase, J Comput Chem, 33, 1536, 10.1002/jcc.22984

Z Li, 2005, The effect of water displacement on binding thermodynamics: concanavalin A. The journal of physical chemistry, B, 109, 662

EF Pettersen, 2004, UCSF Chimera—a visualization system for exploratory research and analysis, J Comput Chem, 25, 1605, 10.1002/jcc.20084

O. T. GNU Parallel—The Command-Lune Power Tool.; login: The USENIX Magazine2011.