Shedding light on important waters for drug design: simulations versus grid-based methods.

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

Sastry, G. M., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-013-9644-8 · Cited by 6,130 · see citing works

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins.

Harder, E. D., Damm, W., Maple, J., Wu, C., Reboul, M., Xiang, J.-Y., Wang, L.-L., Lupyan, D., Dahlgren, M. K., Knight, J. L., et al. (2016) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5b00864 · Cited by 2,826 · see citing works

Enhanced sampling techniques in molecular dynamics simulations of biological systems

Bernardi, R. C., Melo, M. C. R., & Schulten, K. (2015) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2014.10.019 · Cited by 757 · see citing works

Motifs for molecular recognition exploiting hydrophobic enclosure in protein–ligand binding

Young, T. K., Abel, R., Kim, B., Berne, B. J., & Friesner, R. A. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0610202104 · Cited by 697 · see citing works

Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding

Abel, R., Young, T. K., Farid, R., Berne, B. J., & Friesner, R. A. (2008) · Journal of the American Chemical Society · doi:10.1021/ja0771033 · Cited by 682 · see citing works

The Entropic Cost of Bound Water in Crystals and Biomolecules

Dunitz, J. D. (1994) · Science · doi:10.1126/science.264.5159.670 · Cited by 577 · see citing works

Proceedings of the 2006 ACM/IEEE conference on Supercomputing - SC '06

(2006) · doi:10.1145/1188455 · Cited by 528 · see citing works

Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design

Ladbury, J. E. (1996) · Chemistry & Biology · doi:10.1016/s1074-5521(96)90164-7 · Cited by 521 · see citing works

An Integral Equation To Describe the Solvation of Polar Molecules in Liquid Water

Beglov, D. B., & Roux, B. (1997) · The Journal of Physical Chemistry B · doi:10.1021/jp971083h · Cited by 517 · see citing works

Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase

Snyder, P. W., Mecinović, J., Moustakas, D. T., Thomas, S. W., Harder, M., Mack, E. T., Lockett, M. R., Heroux, A., Sherman, W., & Whitesides, G. M. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1114107108 · Cited by 358 · see citing works

Inhomogeneous Fluid Approach to Solvation Thermodynamics. 1. Theory

Lazaridis, T. (1998) · The Journal of Physical Chemistry B · doi:10.1021/jp9723574 · Cited by 334 · see citing works

Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril.

Nguyen, C., Young, T., & Gilson, M. (2012) · Journal of Chemical Physics · doi:10.1063/1.4733951 · Cited by 305 · see citing works

Energetics of Displacing Water Molecules from Protein Binding Sites: Consequences for Ligand Optimization

Michel, J., Tirado‐Rives, J., & Jorgensen, W. L. (2009) · Journal of the American Chemical Society · doi:10.1021/ja906058w · Cited by 258 · see citing works

How Can Hydrophobic Association Be Enthalpy Driven?

Setny, P., Baron, R., & McCammon, J. A. (2010) · Journal of Chemical Theory and Computation · doi:10.1021/ct1003077 · Cited by 234 · see citing works

Perspective: Alchemical free energy calculations for drug discovery.

Mobley, D., & Klimovich, P. V. (2012) · Journal of Chemical Physics · doi:10.1063/1.4769292 · Cited by 232 · see citing works

Fragment-Based Drug Discovery Applied to Hsp90. Discovery of Two Lead Series with High Ligand Efficiency

Murray, C. W., Carr, M. G., Callaghan, O., Chessari, G., Congreve, M., Cowan, S., Coyle, J. E., Downham, R., Figueroa, E., Frederickson, M., et al. (2010) · Journal of Medicinal Chemistry · doi:10.1021/jm100059d · Cited by 186 · see citing works

The Role of Water Molecules in Computational Drug Design

de Beer, S., Vermeulen, N., & Oostenbrink, C. (2010) · Current Topics in Medicinal Chemistry · doi:10.2174/156802610790232288 · Cited by 173 · see citing works

Analysis of Ligand-Bound Water Molecules in High-Resolution Crystal Structures of Protein−Ligand Complexes

Lu, Y., Wang, R., Yang, C., & Wang, S. (2007) · Journal of Chemical Information and Modeling · doi:10.1021/ci6003527 · Cited by 172 · see citing works

Discovery of Clinical Candidate 1-{[(2 S ,3 S ,4 S )-3-Ethyl-4-fluoro-5-oxopyrrolidin-2-yl]methoxy}-7-methoxyisoquinoline-6-carboxamide (PF-06650833), a Potent, Selective Inhibitor of Interleukin-1 Receptor Associated Kinase 4 (IRAK4), by Fragment-Based Drug Design

Lee, K. L., Ambler, C. M., Anderson, D. R., Boscoe, B. P., Bree, A. G., Brodfuehrer, J., Chang, J. S., Choi, C., Chung, S., Curran, K. J., et al. (2017) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.7b00231 · Cited by 162 · see citing works

Discovery of 2-[[2-Ethyl-6-[4-[2-(3-hydroxyazetidin-1-yl)-2-oxoethyl]piperazin-1-yl]-8-methylimidazo[1,2- a ]pyridin-3-yl]methylamino]-4-(4-fluorophenyl)thiazole-5-carbonitrile (GLPG1690), a First-in-Class Autotaxin Inhibitor Undergoing Clinical Evaluation for the Treatment of Idiopathic Pulmonary Fibrosis

Desroy, N., Housseman, C., Bock, X., Joncour, A., Bienvenu, N., Cherel, L., Labeguere, V., Rondet, E., Peixoto, C., Grassot, J., et al. (2017) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.7b00032 · Cited by 148 · see citing works

A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free Energies

Truchon, J., Pettitt, B. M., & Labute, P. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct4009359 · Cited by 145 · see citing works

Is it the shape of the cavity, or the shape of the water in the cavity?

Snyder, P. W., Lockett, M. R., Moustakas, D. T., & Whitesides, G. M. (2013) · The European Physical Journal Special Topics · doi:10.1140/epjst/e2013-01818-y · Cited by 141 · see citing works

Thermodynamic Contributions of the Ordered Water Molecule in HIV-1 Protease

Li, Z., & Lazaridis, T. (2003) · Journal of the American Chemical Society · doi:10.1021/ja0299203 · Cited by 124 · see citing works

Water Sites, Networks, And Free Energies with Grand Canonical Monte Carlo

Ross, G. A., Bodnarchuk, M. S., & Essex, J. W. (2015) · Journal of the American Chemical Society · doi:10.1021/jacs.5b07940 · Cited by 122 · see citing works

Hydration Site Thermodynamics Explain SARs for Triazolylpurines Analogues Binding to the A2A Receptor

Higgs, C. J., Beuming, T., & Sherman, W. (2010) · ACS Medicinal Chemistry Letters · doi:10.1021/ml100008s · Cited by 102 · see citing works

High end GPCR design: crafted ligand design and druggability analysis using protein structure, lipophilic hotspots and explicit water networks

Mason, J. S., Bortolato, A., Weiss, D. R., et al. (2013) · In Silico Pharmacology · doi:10.1186/2193-9616-1-23 · Cited by 86 · see citing works

A Strategy for the Incorporation of Water Molecules Present in a Ligand Binding Site into a Three-Dimensional Quantitative Structure−Activity Relationship Analysis

Pastor, M., Cruciani, G., & Watson, K. A. (1997) · Journal of Medicinal Chemistry · doi:10.1021/jm970273d · Cited by 85 · see citing works

Water, water, everywhere… It’s time to stop and think.

Bodnarchuk, M. S. (2016) · Drug Discovery Today · doi:10.1016/j.drudis.2016.05.009 · Cited by 81 · see citing works

Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP

Bayden, A. S., Moustakas, D. T., Joseph‐McCarthy, D., & Lamb, M. L. (2015) · Journal of Chemical Information and Modeling · doi:10.1021/ci500746d · Cited by 80 · see citing works

Testing inhomogeneous solvation theory in structure-based ligand discovery

Balius, T. E., Fischer, M. M., Stein, R. M., Adler, T. B., Nguyen, C. N., Cruz, A., Gilson, M. K., Kurtzman, T., & Shoichet, B. K. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1703287114 · Cited by 80 · see citing works

Hydration Properties of Ligands and Drugs in Protein Binding Sites: Tightly-Bound, Bridging Water Molecules and Their Effects and Consequences on Molecular Design Strategies

García‐Sosa, A. T. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci3005786 · Cited by 79 · see citing works

Rational Design of Thermodynamic and Kinetic Binding Profiles by Optimizing Surface Water Networks Coating Protein-Bound Ligands

Krimmer, S. G., Cramer, J., Betz, M., Fridh, V., Karlsson, R., Heine, A., & Klebe, G. (2016) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.6b00998 · Cited by 79 · see citing works

Molecular fields in drug discovery: getting old or reaching maturity?

Cross, S., & Cruciani, G. (2009) · Drug Discovery Today · doi:10.1016/j.drudis.2008.12.006 · Cited by 70 · see citing works

A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins

Wade, R. C., Mazor, M. H., McCammon, J. A., et al. (1991) · Biopolymers · doi:10.1002/bip.360310802 · Cited by 69 · see citing works

Discovery, Structure–Activity Relationship, and Binding Mode of an Imidazo[1,2-a]pyridine Series of Autotaxin Inhibitors

Joncour, A., Desroy, N., Housseman, C., et al. (2017) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.7b00647 · Cited by 61 · see citing works

Assessing the Accuracy of Inhomogeneous Fluid Solvation Theory in Predicting Hydration Free Energies of Simple Solutes

Huggins, D. J., & Payne, M. C. (2013) · The Journal of Physical Chemistry B · doi:10.1021/jp4042233 · Cited by 39 · see citing works

Identifying targets for bioreductive agents: Using GRID to predict selective binding regions of proteins

Reynolds, C. A., Wade, R. C., & Goodford, P. J. (1989) · Journal of Molecular Graphics · doi:10.1016/s0263-7855(89)80013-x · Cited by 37 · see citing works

Active-Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process

Miao, Y., & Baudry, J. Y. (2011) · Biophysical Journal · doi:10.1016/j.bpj.2011.08.020 · Cited by 23 · see citing works

A Perspective on Water Site Prediction Methods for Structure Based Drug Design

Graves, A. P., Wall, I. D., Edge, C., Woolven, J. M., Cui, G., Gall, A. L., Hong, X., Raha, K., & Manas, E. S. (2017) · Current Topics in Medicinal Chemistry · doi:10.2174/1568026617666170427095035 · Cited by 14 · see citing works

Empirical scoring functions for structure-based virtual screening: applications, critical aspects, and challenges

Guedes, I. A., Pereira, F. S. S., & Dardenne, L. E. (2018) · Frontiers in Pharmacology · doi:10.3389/fphar.2018.01089 · Cited by 331 · see citing works

ИСПОЛЬЗОВAНИЕ ПОТЕНЦИAЛA СОЦИAЛЬНЫХ ПAРТНЕРОВ В ПОДГОТОВКЕ БУДУЩИХ ПЕДAГОГОВ

Атабекова, Б. Б. (2024) · Habaršy. Pedagogika ġylymdary seriâsy · doi:10.51889/2959-5762.2023.80.4.019

Susquehanna Chorale Spring Concert "Roots and Wings"

Hawkins, D. (2017)

Using DataGrid Control to Realize DataBase of Querying in VB6.0

Hu, S. (2000) · Modern Computer

Study and Two Types of Typical Usage of DataGrid Web Server Control

Hai-tao, L. (2005) · Modern Computer

STKVS: secure technique for keyframes-based video summarization model

Saini, P., Berwal, K., Kashid, S., et al. (2024) · Multimedia Tools and Applications · doi:10.1007/s11042-024-18909-2 · Cited by 10 · see citing works