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

https://doi.org/10.1021/ci3005786
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inferredcites →https://doi.org/10.1002/(sici)1097-0134(199612)26:4<363::aid-prot1>3.0.co;2-dopenalex-snapshot
Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures
inferredcites →https://doi.org/10.1002/(sici)1097-0134(19990101)34:1<17::aid-prot3>3.0.co;2-1openalex-snapshot
The particle concept: placing discrete water molecules during protein-ligand docking predictions
inferredcites →https://doi.org/10.1002/anie.200900481openalex-snapshot
The Thermodynamic Influence of Trapped Water Molecules on a Protein–Ligand Interaction
inferredcites →https://doi.org/10.1002/anie.200904410openalex-snapshot
Molecular Recognition at the Active Site of Catechol‐O‐Methyltransferase: Energetically Favorable Replacement of a Water Molecule Imported by a Bisubstrate Inhibitor
inferredcites →https://doi.org/10.1002/anie.201208561openalex-snapshot
Dissecting the Hydrophobic Effect on the Molecular Level: The Role of Water, Enthalpy, and Entropy in Ligand Binding to Thermolysin
inferredcites →https://doi.org/10.1002/bip.20893openalex-snapshot
Cluster analysis of hydration waters around the active sites of bacterial alanine racemase using a 2‐ns MD simulation
inferredcites →https://doi.org/10.1002/cmdc.201000533openalex-snapshot
Contribution of Explicit Solvent Effects to the Binding Affinity of Small‐Molecule Inhibitors in Blood Coagulation Factor Serine Proteases
inferredcites →https://doi.org/10.1002/jcc.21306openalex-snapshot
Drug efficiency indices for improvement of molecular docking scoring functions
inferredcites →https://doi.org/10.1002/jcc.23170openalex-snapshot
Water PMF for predicting the properties of water molecules in protein binding site
inferredcites →https://doi.org/10.1002/minf.201000007openalex-snapshot
Free Energy Calculations of Mutations Involving a Tightly Bound Water Molecule and Ligand Substitutions in a Ligand‐Protein Complex
inferredcites →https://doi.org/10.1002/minf.201100086openalex-snapshot
A Role for Hydration in Interleukin‐2 Inducible T Cell Kinase (Itk) Selectivity
inferredcites →https://doi.org/10.1002/minf.201100094openalex-snapshot
Disease‐Specific Differentiation Between Drugs and Non‐Drugs Using Principal Component Analysis of Their Molecular Descriptor Space
inferredcites →https://doi.org/10.1002/pro.177openalex-snapshot
High‐energy water sites determine peptide binding affinity and specificity of PDZ domains
inferredcites →https://doi.org/10.1002/prot.20274openalex-snapshot
Solvation influences flap collapse in HIV‐1 protease
inferredcites →https://doi.org/10.1002/qsar.200810174openalex-snapshot
Docking and Virtual Screening Using Distributed Grid Technology
inferredcites →https://doi.org/10.1002/wcms.18openalex-snapshot
Outstanding challenges in protein–ligand docking and structure‐based virtual screening
inferredcites →https://doi.org/10.1006/jmbi.1996.0746openalex-snapshot
Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm
inferredcites →https://doi.org/10.1006/jmbi.1998.2439openalex-snapshot
The atomic structure of protein-protein recognition sites 1 1Edited by A. R. Fersht
inferredcites →https://doi.org/10.1006/jmbi.1999.2929openalex-snapshot
Crystallographic and Calorimetric Analysis of Peptide Binding to OppA Protein
inferredcites →https://doi.org/10.1007/s00894-003-0129-xopenalex-snapshot
WaterScore: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes
inferredcites →https://doi.org/10.1007/s00894-005-0063-1openalex-snapshot
The effect of a tightly bound water molecule on scaffold diversity in the computer-aided de novo ligand design of CDK2 inhibitors
inferredcites →https://doi.org/10.1016/j.biochi.2006.06.006openalex-snapshot
A molecular dynamics simulation study of an aminoglycoside/A-site RNA complex: conformational and hydration patterns
inferredcites →https://doi.org/10.1016/j.bmcl.2012.04.004openalex-snapshot
Investigation of the binding pocket of human hematopoietic prostaglandin (PG) D2 synthase (hH-PGDS): A tale of two waters
inferredcites →https://doi.org/10.1016/j.drudis.2006.05.012openalex-snapshot
Virtual ligand screening: strategies, perspectives and limitations
inferredcites →https://doi.org/10.1016/j.drudis.2008.06.006openalex-snapshot
Limitations and lessons in the use of X-ray structural information in drug design
inferredcites →https://doi.org/10.1016/j.jmb.2003.12.030openalex-snapshot
Thermodynamic Dissection of the Binding Energetics of Proline-rich Peptides to the Abl-SH3 Domain: Implications for Rational Ligand Design
inferredcites →https://doi.org/10.1016/j.jmb.2008.07.062openalex-snapshot
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inferredcites →https://doi.org/10.1016/j.jmb.2010.02.007openalex-snapshot
Non-additivity of Functional Group Contributions in Protein–Ligand Binding: A Comprehensive Study by Crystallography and Isothermal Titration Calorimetry
inferredcites →https://doi.org/10.1016/j.str.2009.02.010openalex-snapshot
Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”
inferredcites →https://doi.org/10.1016/s1074-5521(02)00186-2openalex-snapshot
Structure-Activity Analysis of the Purine Binding Site of Human Liver Glycogen Phosphorylase
inferredcites →https://doi.org/10.1016/s1359-6446(04)03069-7openalex-snapshot
Ligand efficiency: a useful metric for lead selection
inferredcites →https://doi.org/10.1021/ar9600087openalex-snapshot
How Water Provides the Impetus for Molecular Recognition in Aqueous Solution
inferredcites →https://doi.org/10.1021/bi301544kopenalex-snapshot
Further Studies on the Role of Water in R67 Dihydrofolate Reductase
inferredcites →https://doi.org/10.1021/ci049694bopenalex-snapshot
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inferredcites →https://doi.org/10.1021/ci200150popenalex-snapshot
AcquaAlta: A Directional Approach to the Solvation of Ligand–Protein Complexes
inferredcites →https://doi.org/10.1021/ci200203hopenalex-snapshot
Combined Approach Using Ligand Efficiency, Cross-Docking, and Antitarget Hits for Wild-Type and Drug-Resistant Y181C HIV-1 Reverse Transcriptase
inferredcites →https://doi.org/10.1021/ci200587hopenalex-snapshot
DrugLogit: Logistic Discrimination between Drugs and Nondrugs Including Disease-Specificity by Assigning Probabilities Based on Molecular Properties
inferredcites →https://doi.org/10.1021/ci6003527openalex-snapshot
Analysis of Ligand-Bound Water Molecules in High-Resolution Crystal Structures of Protein−Ligand Complexes
inferredcites →https://doi.org/10.1021/ci7004669openalex-snapshot
AIScore — Chemically Diverse Empirical Scoring Function Employing Quantum Chemical Binding Energies of Hydrogen-Bonded Complexes
inferredcites →https://doi.org/10.1021/ci800242zopenalex-snapshot
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inferredcites →https://doi.org/10.1021/ci900497dopenalex-snapshot
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inferredcites →https://doi.org/10.1021/ct1003077openalex-snapshot
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inferredcites →https://doi.org/10.1021/ja0377908openalex-snapshot
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inferredcites →https://doi.org/10.1021/ja049701copenalex-snapshot
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inferredcites →https://doi.org/10.1021/ja066980qopenalex-snapshot
Classification of Water Molecules in Protein Binding Sites
inferredcites →https://doi.org/10.1021/ja0771033openalex-snapshot
Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding
inferredcites →https://doi.org/10.1021/ja202972mopenalex-snapshot
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inferredcites →https://doi.org/10.1021/ja9059156openalex-snapshot
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inferredcites →https://doi.org/10.1021/ja9738539openalex-snapshot
Computational Alchemy To Calculate Absolute Protein−Ligand Binding Free Energy
inferredcites →https://doi.org/10.1021/jm00017a020openalex-snapshot
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inferredcites →https://doi.org/10.1021/jm048957qopenalex-snapshot
The PDBbind Database: Methodologies and Updates
inferredcites →https://doi.org/10.1021/jm050543popenalex-snapshot
Modeling Water Molecules in Protein−Ligand Docking Using GOLD
inferredcites →https://doi.org/10.1021/jm0611915openalex-snapshot
Synthesis, Crystal Structure, and Activity of Pyrazole-Based Inhibitors of p38 Kinase
inferredcites →https://doi.org/10.1021/jm061305copenalex-snapshot
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inferredcites →https://doi.org/10.1021/jm100112jopenalex-snapshot
A Medicinal Chemist’s Guide to Molecular Interactions
inferredcites →https://doi.org/10.1021/jm1013693openalex-snapshot
Synopsis of Some Recent Tactical Application of Bioisosteres in Drug Design
inferredcites →https://doi.org/10.1021/jm2000085openalex-snapshot
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inferredcites →https://doi.org/10.1021/jm2005145openalex-snapshot
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inferredcites →https://doi.org/10.1021/jm300337qopenalex-snapshot
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inferredcites →https://doi.org/10.1021/jm701023hopenalex-snapshot
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inferredcites →https://doi.org/10.1021/jm8006239openalex-snapshot
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inferredcites →https://doi.org/10.1021/jm901241eopenalex-snapshot
Escape from Flatland: Increasing Saturation as an Approach to Improving Clinical Success
inferredcites →https://doi.org/10.1021/jo701443copenalex-snapshot
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inferredcites →https://doi.org/10.1021/jp0477912openalex-snapshot
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inferredcites →https://doi.org/10.1021/jp104209wopenalex-snapshot
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inferredcites →https://doi.org/10.1021/jp2024654openalex-snapshot
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inferredcites →https://doi.org/10.1021/jp709766copenalex-snapshot
Microwave Catalysis through Rotationally Hot Reactive Species
inferredcites →https://doi.org/10.1021/jp9047456openalex-snapshot
Prediction of the Water Content in Protein Binding Sites
inferredcites →https://doi.org/10.1021/jp9712213openalex-snapshot
Orientational Disorder and Entropy of Water in Protein Cavities
inferredcites →https://doi.org/10.1021/jp9723574openalex-snapshot
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inferredcites →https://doi.org/10.1023/a:1008763405023openalex-snapshot
Calculating partition coefficient by atom-additive method
inferredcites →https://doi.org/10.1023/b:jcam.0000030032.81753.b4openalex-snapshot
The effect of tightly bound water molecules on the structural interpretation of ligand-derived pharmacophore models
inferredcites →https://doi.org/10.1038/nchembio.155openalex-snapshot
Molecular docking and ligand specificity in fragment-based inhibitor discovery
inferredcites →https://doi.org/10.1038/nrd2445openalex-snapshot
The influence of drug-like concepts on decision-making in medicinal chemistry
inferredcites →https://doi.org/10.1038/nrd3701openalex-snapshot
Finding the sweet spot: the role of nature and nurture in medicinal chemistry
inferredcites →https://doi.org/10.1038/nsb1296-998openalex-snapshot
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inferredcites →https://doi.org/10.1063/1.4732514openalex-snapshot
Individual degrees of freedom and the solvation properties of water
inferredcites →https://doi.org/10.1071/ch04161openalex-snapshot
The Role of Virtual Screening in Computer Aided Structure-Based Drug Design
inferredcites →https://doi.org/10.1073/pnas.0610202104openalex-snapshot
Motifs for molecular recognition exploiting hydrophobic enclosure in protein–ligand binding
inferredcites →https://doi.org/10.1073/pnas.1016793108openalex-snapshot
Ligand binding to protein-binding pockets with wet and dry regions
inferredcites →https://doi.org/10.1073/pnas.1114107108openalex-snapshot
Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase
inferredcites →https://doi.org/10.1073/pnas.96.18.9997openalex-snapshot
The maximal affinity of ligands
inferredcites →https://doi.org/10.1074/jbc.274.44.31272openalex-snapshot
Thermodynamic Analyses Reveal Role of Water Release in Epitope Recognition by a Monoclonal Antibody against the Human Guanylyl Cyclase C Receptor
inferredcites →https://doi.org/10.1080/1062936x.2013.773373openalex-snapshot
Drugs, non-drugs, and disease category specificity: organ effects by ligand pharmacology1
inferredcites →https://doi.org/10.1093/bioinformatics/btm431openalex-snapshot
Structure-based calculation of drug efficiency indices
inferredcites →https://doi.org/10.1093/bioinformatics/btq100openalex-snapshot
ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1093/nar/gkj067openalex-snapshot
DrugBank: a comprehensive resource for in silico drug discovery and exploration
inferredcites →https://doi.org/10.1093/protein/gzr036openalex-snapshot
Systematic placement of structural water molecules for improved scoring of protein-ligand interactions
inferredcites →https://doi.org/10.1096/fasebj.10.1.8566551openalex-snapshot
Forces contributing to the conformational stability of proteins
inferredcites →https://doi.org/10.1107/97809553602060000892openalex-snapshot
Protein–ligand interactions
inferredcites →https://doi.org/10.1111/j.1747-0285.2007.00545.xopenalex-snapshot
Prediction of Solvation Sites at the Interface of Src SH2 Domain Complexes Using Molecular Dynamics Simulations
inferredcites →https://doi.org/10.1126/science.264.5159.670openalex-snapshot
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inferredcites →https://doi.org/10.1126/science.8278812openalex-snapshot
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inferredcites →https://doi.org/10.1371/journal.pone.0024712openalex-snapshot
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inferredcites →https://doi.org/10.1371/journal.pone.0032036openalex-snapshot
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inferredcites →https://doi.org/10.1517/17460441.2010.497534openalex-snapshot
De novodesign: balancing novelty and confined chemical space
inferredcites →https://doi.org/10.1517/17460441.2011.534452openalex-snapshot
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inferredcites →https://doi.org/10.1517/17460441.3.8.841openalex-snapshot
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inferredcites →https://doi.org/10.1529/biophysj.105.065524openalex-snapshot
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inferredcites →https://doi.org/10.2174/092986706776873005openalex-snapshot
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inferredcites →https://doi.org/10.2174/092986712799945021openalex-snapshot
Molecular Property Filters Describing Pharmacokinetics and Drug Binding
inferredcites →https://doi.org/10.2174/156802610790232288openalex-snapshot
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inferredcites →https://doi.org/10.2174/156802610790232305openalex-snapshot
Computational Approaches for Fragment-Based and De Novo Design
inferredcites →https://doi.org/10.2174/156802611795589610openalex-snapshot
Modulators of Protein-Protein Interactions – Novel Approaches in Targeting Protein Kinases and Other Pharmaceutically Relevant Biomolecules
inferredcites →https://doi.org/10.2174/157340909789054694openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/2211-5463.12201openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/ange.201408487openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/anie.201408487openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/cphc.202500765openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.23714openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-4-431-56919-0_3openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-014-9740-4openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-019-00239-3openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s11030-024-11075-5openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.abb.2015.08.002openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.abb.2019.02.002openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.addr.2022.114310openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.asoc.2019.105509openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.bmc.2016.04.018openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.bmc.2025.118419openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.bmcl.2018.05.061openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.cbi.2023.110568openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.jmgm.2018.04.011openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.jmgm.2026.109329openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.jnoncrysol.2014.07.017openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.analchem.6c02162openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01266openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.2c01610openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.5c01188openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00642openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00545openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00645openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00109openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jctc.5b00839openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jctc.5b00939openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jmedchem.7b00057openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jmedchem.7b00366openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acsomega.2c03421openalex-snapshot
Design of Anti-infectious Agents from Lawsone in a Three-Component Reaction with Aldehydes and Isocyanides
inferred← citeshttps://doi.org/10.1021/ci400367mopenalex-snapshot
Accounting for Target Flexibility and Water Molecules by Docking to Ensembles of Target Structures: The HCV NS5B Palm Site I Inhibitors Case Study
inferred← citeshttps://doi.org/10.1021/ci500299hopenalex-snapshot
Docking Ligands into Flexible and Solvated Macromolecules. 7. Impact of Protein Flexibility and Water Molecules on Docking-Based Virtual Screening Accuracy
inferred← citeshttps://doi.org/10.1021/ci500300uopenalex-snapshot
Improving the Use of Ranking in Virtual Screening against HIV-1 Integrase with Triangular Numbers and Including Ligand Profiling with Antitargets
inferred← citeshttps://doi.org/10.1021/jacs.5b07940openalex-snapshot
Water Sites, Networks, And Free Energies with Grand Canonical Monte Carlo
inferred← citeshttps://doi.org/10.1021/jp502213yopenalex-snapshot
An Investigation of G-Quadruplex Structural Polymorphism in the Human Telomere Using a Combined Approach of Hydrodynamic Bead Modeling and Molecular Dynamics Simulation
inferred← citeshttps://doi.org/10.1039/c6cp02645aopenalex-snapshot
The solvation structure of alprazolam
inferred← citeshttps://doi.org/10.1039/c7ra04435fopenalex-snapshot
Micro-solvation of tyrosine-kinase inhibitor AG1478 explored with fluorescence spectroscopy and computational chemistry
inferred← citeshttps://doi.org/10.1039/c8cp04118kopenalex-snapshot
Effective lead optimization targeting the displacement of bridging receptor–ligand water molecules
inferred← citeshttps://doi.org/10.1039/d2md00044jopenalex-snapshot
N -1,2,3-Triazole–isatin derivatives: anti-proliferation effects and target identification in solid tumour cell lines
inferred← citeshttps://doi.org/10.1073/pnas.1703781114openalex-snapshot
Water is an active matrix of life for cell and molecular biology
inferred← citeshttps://doi.org/10.1080/07391102.2016.1273136openalex-snapshot
Role of structural water for prediction of cation binding sites in apoproteins
inferred← citeshttps://doi.org/10.1080/17460441.2023.2267015openalex-snapshot
The application of WaterMap-guided structure-based virtual screening in novel drug discovery
inferred← citeshttps://doi.org/10.1093/bib/bbae145openalex-snapshot
A new paradigm for applying deep learning to protein–ligand interaction prediction
inferred← citeshttps://doi.org/10.1093/bioinformatics/btv093openalex-snapshot
Mobility-based prediction of hydration structures of protein surfaces
inferred← citeshttps://doi.org/10.1093/bioinformatics/btv411openalex-snapshot
WATCLUST: a tool for improving the design of drugs based on protein-water interactions
inferred← citeshttps://doi.org/10.1093/glycob/cwu102openalex-snapshot
Using crystallographic water properties for the analysis and prediction of lectin-carbohydrate complex structures
inferred← citeshttps://doi.org/10.1111/febs.14405openalex-snapshot
Architecture and hydration of the arginine‐binding site of neuropilin‐1
inferred← citeshttps://doi.org/10.1155/2014/257040openalex-snapshot
Peptide-Ligand Binding Modeling of siRNA with Cell-Penetrating Peptides
inferred← citeshttps://doi.org/10.12691/ajmo-1-3-7openalex-snapshot
How to Calculate Binding Constants for Drug Discovery Studies
inferred← citeshttps://doi.org/10.1371/journal.pone.0134444openalex-snapshot
Similarities between the Binding Sites of SB-206553 at Serotonin Type 2 and Alpha7 Acetylcholine Nicotinic Receptors: Rationale for Its Polypharmacological Profile
inferred← citeshttps://doi.org/10.18297/etd/799openalex-snapshot
Biophysical and computational investigations into G-quadruplex structural polymorphism and interaction with small molecules.
inferred← citeshttps://doi.org/10.21203/rs.3.rs-981656/v1openalex-snapshot
WaterSwap Analysis, a Computation-based Method for the Discovery of Effective and Stable Binding Compounds for Mutant EGFR Inhibition
inferred← citeshttps://doi.org/10.2174/0109298673334469241017053508openalex-snapshot
Developing Generalizable Scoring Functions for Molecular Docking: Challenges and Perspectives
inferred← citeshttps://doi.org/10.2174/0929867325666180514110824openalex-snapshot
Advances in the Treatment of Explicit Water Molecules in Docking and Binding Free Energy Calculations
inferred← citeshttps://doi.org/10.2174/0929867331666230913165219openalex-snapshot
Three Decades of Targeting Falcipains to Develop Antiplasmodial Agents: What have we Learned and What can be Done Next?
inferred← citeshttps://doi.org/10.2174/1568026622666220726114407openalex-snapshot
The Role of Water Network Chemistry in Proteins: A Structural Bioinformatics Perspective in Drug Discovery and Development
inferred← citeshttps://doi.org/10.2174/1570180819666220613094708openalex-snapshot
Discovery, Design, and Development of Effective and Stable Binding Compounds for Mutant EGFR Inhibition
inferred← citeshttps://doi.org/10.2174/9798898812164125080007openalex-snapshot
Advances in Quantum Mechanical Methods for the Computation of Protein-Ligand Binding Free Energy
inferred← citeshttps://doi.org/10.3389/fchem.2018.00043openalex-snapshot
An Efficient Implementation of the Nwat-MMGBSA Method to Rescore Docking Results in Medium-Throughput Virtual Screenings
inferred← citeshttps://doi.org/10.3389/fchem.2021.753002openalex-snapshot
OnionNet-2: A Convolutional Neural Network Model for Predicting Protein-Ligand Binding Affinity Based on Residue-Atom Contacting Shells
inferred← citeshttps://doi.org/10.3389/fmolb.2025.1668400openalex-snapshot
Molecular mechanisms and computational insights into human SGLTs: advancing toward selective SGLT1 inhibition
inferred← citeshttps://doi.org/10.3390/books978-3-03897-615-8openalex-snapshot
Molecular Modeling in Drug Design
inferred← citeshttps://doi.org/10.3390/molecules21050589openalex-snapshot
Arginase Flavonoid Anti-Leishmanial in Silico Inhibitors Flagged against Anti-Targets
inferred← citeshttps://doi.org/10.3390/molecules23123269openalex-snapshot
Solvents to Fragments to Drugs: MD Applications in Drug Design
inferred← citeshttps://doi.org/10.70675/fd9e129cz6025z4906z80f0za62f611b75a0openalex-snapshot
Solvatation de systèmes d'intérêt pharmaceutique : apports de la théorie de la fonctionnelle de la densité moléculaire
inferred← citeshttps://doi.org/10.7498/aps.68.20181273openalex-snapshot
Research progress of molecular structure and dynamics of biological water
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