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

scientific article published on December 1996

Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design is …
instance of (P31):
review articleQ7318358
scholarly articleQ13442814

External links are
P356DOI10.1016/S1074-5521(96)90164-7
P698PubMed publication ID9000013
P5875ResearchGate publication ID14208413

P2093author name stringLadbury JE
P2860cites workSubstrate specificity and affinity of a protein modulated by bound water moleculesQ27728486
Design of inhibitors of glycogen phosphorylase: a study of alpha- and beta-C-glucosides and 1-thio-beta-D-glucose compoundsQ27731317
The structural basis of sequence-independent peptide binding by OppA proteinQ27731418
Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitorsQ27731528
The role of water in sequence-independent ligand binding by an oligopeptide transporter proteinQ27734061
Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbonsQ27861091
A computational procedure for determining energetically favorable binding sites on biologically important macromoleculesQ30406755
Structure-based drug design: progress, results and challengesQ30419784
Side-chain conformational entropy in protein foldingQ34732367
Internal water molecules and H‐bonding in biological macromolecules: A review of structural features with functional implicationsQ35222975
Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculationsQ36696201
Acquisition and use of calorimetric data for prediction of the thermodynamics of ligand-binding and folding reactions of proteinsQ36705468
A thermodynamic study of the trp repressor-operator interactionQ38308023
A possible involvement of solvent-induced interactions in drug designQ38359999
Hydrogen bonding in globular proteinsQ40188265
Water: now you see it, now you don'tQ40700389
What makes a binding site a binding site?Q41071994
Win some, lose some: enthalpy-entropy compensation in weak intermolecular interactionsQ41651485
Analysis of protein main-chain solvation as a function of secondary structureQ42039571
Water-mediated protein-DNA interactions: the relationship of thermodynamics to structural detailQ42183781
Buried waters and internal cavities in monomeric proteinsQ42844341
Distributions of water around amino acid residues in proteinsQ47643805
The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measuresQ52410091
Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins.Q53903013
The Entropic Cost of Bound Water in Crystals and BiomoleculesQ56524513
Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bondsQ57975324
Protein hydration in aqueous solutionQ68053669
Small rearrangements in structures of Fv and Fab fragments of antibody D1.3 on antigen bindingQ68564328
The effect of water activity on the association constant and the enthalpy of reaction between lysozyme and the specific antibodies D1.3 and D44.1.Q71301569
Atomic and residue hydrophilicity in the context of folded protein structuresQ71374330
Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactionsQ71491557
Hydration in drug design. 2. Influence of local site surface shape on water bindingQ71491560
P433issue12
P921main subjectprotein designQ410814
ligand bindingQ61659151
P304page(s)973-980
P577publication date1996-12-01
P1433published inChemistry and BiologyQ15758410
P1476titleJust add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design
P478volume3

Reverse relations

cites work (P2860)
Q388261813D-Lab: a collaborative web-based platform for molecular modeling
Q93141195A Fragmenting Protocol with Explicit Hydration for Calculation of Binding Enthalpies of Target-Ligand Complexes at a Quantum Mechanical Level
Q46845410A balancing act between net uptake of water during dihydrofolate binding and net release of water upon NADPH binding in R67 dihydrofolate reductase
Q48054359A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge.
Q27680722A conserved water-mediated hydrogen bond network defines bosutinib's kinase selectivity
Q37719514A medicinal chemist's guide to molecular interactions
Q37302264A short guide for molecular dynamics simulations of RNA systems.
Q34494894A solvated ligand rotamer approach and its application in computational protein design
Q36260709Accessing gap-junction channel structure-function relationships through molecular modeling and simulations
Q38014544Accounting for water molecules in drug design
Q37609374Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1.
Q56452754Adding calorimetric data to decision making in lead discovery: a hot tip
Q42069286Analysis of factors influencing hydration site prediction based on molecular dynamics simulations
Q84275293Analysis of structural water and CH···π interactions in HIV-1 protease and PTP1B complexes using a hydrogen bond prediction tool, HBPredicT
Q33683156Analysis of the binding surfaces of proteins
Q38071408Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap
Q47342876AquaMMapS: an alternative tool to monitor the role of water molecules during protein-ligand association.
Q51304233AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking.
Q57976077Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling
Q64966935Binding Affinity via Docking: Fact and Fiction.
Q42319095Binding Pose Flip Explained via Enthalpic and Entropic Contributions.
Q77130211Binding of the natural killer cell inhibitory receptor Ly49A to its major histocompatibility complex class I ligand. Crucial contacts include both H-2Dd AND beta 2-microglobulin
Q42183649Biophysical studies of the c-MYC NHE III1 promoter: model quadruplex interactions with a cationic porphyrin
Q42139627Break in the heat capacity change at 303 K for complex binding of netropsin to AATT containing hairpin DNA constructs
Q56794650Calculation of the reaction field due to off-center point multipoles
Q42183057Characterization of a novel water pocket inside the human Cx26 hemichannel structure
Q36280688Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity
Q42263771Combining solvent thermodynamic profiles with functionality maps of the Hsp90 binding site to predict the displacement of water molecules
Q93039507Comparative study of the interactions between fungal transcription factor nuclear localization sequences with mammalian and fungal importin-alpha
Q39024147Computational analysis of BACE1-ligand complex crystal structures and linear discriminant analysis for identification of BACE1 inhibitors with anti P-glycoprotein binding property
Q21092524Computational analysis of phosphopeptide binding to the polo-box domain of the mitotic kinase PLK1 using molecular dynamics simulation
Q26997089Computational methods in drug discovery
Q39731372Conservation of structure and function among tyrosine recombinases: homology-based modeling of the lambda integrase core-binding domain
Q27618712Conserved water molecules in a large family of microbial ribonucleases
Q42619215Contribution of proton linkage to the thermodynamic stability of the major cold-shock protein of Escherichia coli CspA.
Q48254643Designing dual inhibitors of Mdm2/MdmX: Unexpected coupling of water with gatekeeper Y100/99.
Q62648677Development of a QSAR Model for Binding of Tripeptides and Tripeptidomimetics to the Human Intestinal Di-/Tripeptide Transporter hPEPT1
Q30391536Dissecting the Influence of Protein Flexibility on the Location and Thermodynamic Profile of Explicit Water Molecules in Protein-Ligand Binding
Q30928104Dominant Alcohol-Protein Interaction via Hydration-Enabled Enthalpy-Driven Binding Mechanism
Q47617691Doxorubicin hinders DNA condensation promoted by the protein bovine serum albumin (BSA).
Q36980659Dynamics of conserved waters in human Hsp90: implications for drug design
Q37439036Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization
Q27636521Engineering inhibitors highly selective for the S1 sites of Ser190 trypsin-like serine protease drug targets
Q41099155Enthalpic and Entropic Contributions to Hydrophobicity
Q38737287Estimation of kinetic and thermodynamic ligand-binding parameters using computational strategies
Q77475375Exploring computational lead optimisation with affinity constants obtained by surface plasmon resonance for the interaction of PorA epitope peptides with antibody against Neisseria meningitidis
Q27684227FGFR1 Kinase Inhibitors: Close Regioisomers Adopt Divergent Binding Modes and Display Distinct Biophysical Signatures
Q63246733Flavonoids as Putative Epi-Modulators: Insight into Their Binding Mode with BRD4 Bromodomains Using Molecular Docking and Dynamics
Q90442534Fluorescence enhancement of a ligand-activated fluorescent protein induced by collective noncovalent interactions
Q30156028Free Energy Calculations of Mutations Involving a Tightly Bound Water Molecule and Ligand Substitutions in a Ligand-Protein Complex.
Q27681407From lin-benzoguanines to lin-benzohypoxanthines as ligands for Zymomonas mobilis tRNA-guanine transglycosylase: replacement of protein-ligand hydrogen bonding by importing water clusters
Q36299668Gain-of-function mutations in the MEC-4 DEG/ENaC sensory mechanotransduction channel alter gating and drug blockade
Q27658273Gaining ligand selectivity in thyroid hormone receptors via entropy
Q28387381Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril
Q38356209Heat capacity changes in carbohydrates and protein-carbohydrate complexes.
Q43278152High-affinity inhibitors of tRNA-guanine transglycosylase replacing the function of a structural water cluster
Q27682233High-resolution crystal structure of HA33 of botulinum neurotoxin type B progenitor toxin complex
Q27680274High-resolution crystal structure of Streptococcus pyogenes β-NAD + glycohydrolase in complex with its endogenous inhibitor IFS reveals a highly water-rich interface
Q90022265How Ligand Binding Affects the Dynamical Transition Temperature in Proteins
Q41965081How and when does an anticancer drug leave its binding site?
Q39280041How does a drug molecule find its target binding site?
Q35606825Hydration changes accompanying the binding of minor groove ligands with DNA.
Q33229875Hydration changes in the association of Hoechst 33258 with DNA.
Q37145520Hydration of drug-DNA complexes: greater water uptake for adriamycin compared to daunomycin
Q42854419Hydration of protein-RNA recognition sites
Q37636509Hydrophobic hydration of poly-N-isopropyl acrylamide: a matter of the mean energetic state of water
Q47384926Identification of Conserved Water Sites in Protein Structures for Drug Design.
Q89429512Identification of a Water-Coordinating HER2 Inhibitor by Virtual Screening Using Similarity-Based Scoring
Q90375092Inclusion of enclosed hydration effects in the binding free energy estimation of dopamine D3 receptor complexes
Q35045753Inclusion of multiple fragment types in the site identification by ligand competitive saturation (SILCS) approach
Q90871426Incorporating Explicit Water Molecules and Ligand Conformation Stability in Machine-Learning Scoring Functions
Q90441881Increasing the affinity of an O-antigen polysaccharide binding site in Shigella flexneri bacteriophage Sf6 tailspike protein
Q28346496Influence of Glu-376 --> Gln mutation on enthalpy and heat capacity changes for the binding of slightly altered ligands to medium chain acyl-CoA dehydrogenase
Q27671778Inhibition of Bacterial Dihydrofolate Reductase by 6-Alkyl-2,4-diaminopyrimidines
Q45422409Interaction between a 1998 human influenza virus N2 neuraminidase and monoclonal antibody Mem5.
Q30010103Interfacial water molecules in SH3 interactions: Getting the full picture on polyproline recognition by protein-protein interaction domains
Q58769381Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes
Q56452981Isothermal titration calorimetry: application to structure-based drug design
Q31134461Isothermal titration calorimetry: experimental design, data analysis, and probing macromolecule/ligand binding and kinetic interactions
Q56815991Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo
Q59795950Ligand Binding Free Energies with Adaptive Water Networks: Two-Dimensional Grand Canonical Alchemical Perturbations
Q32014468Mass spectrometric and thermodynamic studies reveal the role of water molecules in complexes formed between SH2 domains and tyrosyl phosphopeptides
Q37395452Microcalorimetry: a response to challenges in modern biotechnology.
Q58491302Modelling of carbohydrate–aromatic interactions: ab initio energetics and force field performance
Q91801506Molecular Docking Guided Grid-Independent Descriptor Analysis to Probe the Impact of Water Molecules on Conformational Changes of hERG Inhibitors in Drug Trapping Phenomenon
Q38842249Molecular Shape and the Hydrophobic Effect
Q60185466Molecular design using electrostatic interactions. Part 4: Synthesis and properties of flexible tetrapodand tetracations derived from naphthalene. Role of structured water in the electrostatic binding of polyanion guests: a model for interactions in
Q60998748Molecular dynamics of Mycobacterium tuberculosis KasA: implications for inhibitor and substrate binding and consequences for drug design
Q41385158Molecular dynamics of water-mediated interactions of a linear benzimidazole-biphenyl diamidine with the DNA minor groove
Q57821066Molecular dynamics simulation reveals the possible druggable of USP7
Q46794956Molecular dynamics study of Pseudomonas aeruginosa lectin-II complexed with monosaccharides
Q38272394Molecular mimicry of substrate oxygen atoms by water molecules in the beta-amylase active site.
Q38335784Molecular recognition in chemical and biological systems
Q54549089Multiple drugs and multiple targets: an analysis of the electrostatic determinants of binding between non-nucleoside HIV-1 reverse transcriptase inhibitors and variants of HIV-1 RT.
Q28834483Multivalent display of minimal Clostridium difficile glycan epitopes mimics antigenic properties of larger glycans
Q52610195New insights on repellent recognition by Anopheles gambiae odorant-binding protein 1.
Q56875890On the structure of water and chloride ion interactions with a peptide backbone in solution
Q92372738Pharmacophoric Site Identification and Inhibitor Design for Autotaxin
Q41834356Phosphinic peptides, the first potent inhibitors of astacin, behave as extremely slow-binding inhibitors
Q51377144Placevent: an algorithm for prediction of explicit solvent atom distribution-application to HIV-1 protease and F-ATP synthase.
Q47225368Prediction of ordered water molecules in protein binding sites from molecular dynamics simulations: The impact of ligand binding on hydration networks.
Q30495095Prediction of the water content in protein binding sites
Q82299173Preferential affinity of the components of liquid mixtures at a rigid non-polar surface: enthalpic and entropic driving forces
Q50237585Protein-fluctuation-induced water-pore formation in ion channel voltage-sensor translocation across a lipid bilayer membrane.
Q57889797Protonation linked equilibria and apparent affinity constants: the thermodynamic profile of the α-chymotrypsin–proflavin interaction
Q42739559Quantifying water-mediated protein-ligand interactions in a glutamate receptor: a DFT study
Q26865357Rational approaches to improving selectivity in drug design
Q27696473Replacement of water molecules in a phosphate binding site by furanoside-appended lin-benzoguanine ligands of tRNA-guanine transglycosylase (TGT)
Q99611207Repurposing drugs for treatment of SARS-CoV-2 infection: computational design insights into mechanisms of action
Q27666303Rigid-body Ligand Recognition Drives Cytotoxic T-lymphocyte Antigen 4 (CTLA-4) Receptor Triggering
Q90059259Role of Displacing Confined Solvent in the Conformational Equilibrium of β-Cyclodextrin
Q54598455Role of bridging water molecules in GSK3β-inhibitor complexes: insights from QM/MM, MD, and molecular docking studies.
Q36120365Role of water and steric constraints in the kinetics of cavity-ligand unbinding
Q27679166Roles for Ordered and Bulk Solvent in Ligand Recognition and Docking in Two Related Cavities
Q90108447STACKED - Solvation Theory of Aromatic Complexes as Key for Estimating Drug Binding
Q74633107Scoring functions: a view from the bench
Q57831754Simulation studies of the protein-water interface. I. Properties at the molecular resolution
Q46202746Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.
Q41339143Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST.
Q48049114Solvent effects on ligand binding to a serine protease
Q60960514Solvents to Fragments to Drugs: MD Applications in Drug Design
Q36761394Spatial Decomposition of Translational Water-Water Correlation Entropy in Binding Pockets
Q36710407Spectral gap optimization of order parameters for sampling complex molecular systems
Q41785296Strategic targeting of multiple water-mediated interactions: a concise and rational structure-based design approach to potent and selective MMP-13 inhibitors
Q27641047Structural consequences of target epitope-directed functional alteration of an antibody. The case of anti-hen lysozyme antibody, HyHEL-10
Q27651627Structural coupling between FKBP12 and buried water
Q28071559Structure-Based Reverse Vaccinology Failed in the Case of HIV Because it Disregarded Accepted Immunological Theory
Q36252997Structure-activity relationships for the binding of polymyxins with human α-1-acid glycoprotein
Q83397092Study of intermolecular contacts in the proline-rich homeodomain (PRH)-DNA complex using molecular dynamics simulations
Q27679528Substrate specificity of fluoroacetate dehalogenase: an insight from crystallographic analysis, fluorescence spectroscopy, and theoretical computations
Q42401762Synthesis of urea picket porphyrins and their use in the elucidation of the role buried solvent plays in the selectivity and stoichiometry of anion binding receptors
Q77328526TCR binding to peptide-MHC stabilizes a flexible recognition interface
Q47155050The Binding Mode of the Sonic Hedgehog Inhibitor Robotnikinin, a Combined Docking and QM/MM MD Study
Q27675776The Carbohydrate-Binding Site in Galectin-3 Is Preorganized To Recognize a Sugarlike Framework of Oxygens: Ultra-High-Resolution Structures and Water Dynamics
Q35203619The Hydractinia echinata test-system. III: Structure-toxicity relationship study of some azo-, azo-anilide, and diazonium salt derivatives.
Q47270961The Role of Interfacial Water in Protein-Ligand Binding: Insights from the Indirect Solvent Mediated Potential of Mean Force.
Q39113611The SAMPL4 hydration challenge: evaluation of partial charge sets with explicit-water molecular dynamics simulations
Q27649703The Structure of Clostridium perfringens NanI Sialidase and Its Catalytic Intermediates
Q28546951The Structure of the T190M Mutant of Murine α-Dystroglycan at High Resolution: Insight into the Molecular Basis of a Primary Dystroglycanopathy
Q44679907The creation of proton hopping from a drug-receptor encounter
Q36964787The electrostatic response of water to neutral polar solutes: implications for continuum solvent modeling
Q74259529The how and why of protein-carbohydrate interaction: a primer to the theoretical concept and a guide to application in drug design
Q27639993The role of hydrogen bonding via interfacial water molecules in antigen-antibody complexation. The HyHEL-10-HEL interaction
Q57943293The role of water in host-guest interaction
Q73009412The thermodynamics of protein-protein recognition as characterized by a combination of volumetric and calorimetric techniques: the binding of turkey ovomucoid third domain to alpha-chymotrypsin
Q27697923The water network in galectin-3 ligand binding site guides inhibitor design
Q38269524Thermodynamic analysis of the binding of component enzymes in the assembly of the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus.
Q34120049Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization
Q24644503Thermodynamic consequences of disrupting a water-mediated hydrogen bond network in a protein:pheromone complex
Q33874099Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa.
Q30374518Thermodynamics of antibody-antigen interaction revealed by mutation analysis of antibody variable regions.
Q30697899Thermodynamics of drug-DNA interactions
Q35877480Thermodynamics of protein-ligand interactions: history, presence, and future aspects
Q92127242Topological Water Network Analysis Around Amino Acids
Q37014096Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go.
Q36910544Triazole resistance mediated by mutations of a conserved active site tyrosine in fungal lanosterol 14α-demethylase
Q52023426Utilising structural knowledge in drug design strategies: applications using Relibase.
Q27758213Visualisation of extensive water ribbons and networks in a DNA minor-groove drug complex
Q30401473WATsite2.0 with PyMOL Plugin: Hydration Site Prediction and Visualization
Q42407198WATsite: hydration site prediction program with PyMOL interface
Q37072904Water and proteins: a love-hate relationship
Q48431415Water and side-chain embedded π-turns.
Q36715297Water at biomolecular binding interfaces
Q92917819Water in protein hydration and ligand recognition
Q48013457Water is an active matrix of life for cell and molecular biology
Q27681384Water makes the difference: rearrangement of water solvation layer triggers non-additivity of functional group contributions in protein-ligand binding
Q36290001Waterdock 2.0: Water placement prediction for Holo-structures with a pymol plugin
Q47097147What contributes to an effective mannose recognition domain?
Q50626015What has virtual screening ever done for drug discovery?
Q35254711sc-PDB: a 3D-database of ligandable binding sites--10 years on

Search more.