Water at biomolecular binding interfaces (Q36715297)

15 August 2017

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title

Water at biomolecular binding interfaces (English)

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15 August 2017

Zheng Li

1

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PubMed ID

17242738

15 August 2017

Themis Lazaridis

series ordinal

2

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PubMed ID

17242738

15 August 2017

language of work or name

English

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publication date

24 November 2006

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Physical Chemistry Chemical Physics

15 August 2017

9

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based on heuristic

inferred from page(s)

published in

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15 August 2017

9

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15 August 2017

5

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15 August 2017

573-581

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Crystal structure of trp repressor/operator complex at atomic resolution

15 August 2017

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Substrate specificity and affinity of a protein modulated by bound water molecules

21 January 2018

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X-ray structure of a monomeric cyclophilin A-cyclosporin A crystal complex at 2.1 A resolution

21 January 2018

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2.2 A refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MnATP and a peptide inhibitor.

21 January 2018

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Bound water molecules and conformational stabilization help mediate an antigen-antibody association

21 January 2018

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The structural basis of sequence-independent peptide binding by OppA protein

21 January 2018

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The entropic penalty of ordered water accounts for weaker binding of the antibiotic novobiocin to a resistant mutant of DNA gyrase: a thermodynamic and crystallographic study

21 January 2018

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Peptide binding in OppA, the crystal structures of the periplasmic oligopeptide binding protein in the unliganded form and in complex with lysyllysine

21 January 2018

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Conserved water molecules contribute to the extensive network of interactions at the active site of protein kinase A

21 January 2018

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GTP plus water mimic ATP in the active site of protein kinase CK2

21 January 2018

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Conserved positions for ribose recognition: importance of water bridging interactions among ATP, ADP and FAD-protein complexes

21 January 2018

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The atomic structure of protein-protein recognition sites

21 January 2018

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Water: now you see it, now you don't

21 January 2018

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

21 January 2018

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Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition

21 January 2018

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The role of water in protein-DNA recognition

21 January 2018

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Structure of HIV-1 protease with KNI-272, a tight-binding transition-state analog containing allophenylnorstatine

21 January 2018

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Structure of a G48H mutant of HIV-1 protease explains how glycine-48 replacements produce mutants resistant to inhibitor drugs

21 January 2018

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Hydrophilic peptides derived from the transframe region of Gag-Pol inhibit the HIV-1 protease

21 January 2018

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Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors

21 January 2018

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Improved cyclic urea inhibitors of the HIV-1 protease: synthesis, potency, resistance profile, human pharmacokinetics and X-ray crystal structure of DMP 450

21 January 2018

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Structure-based design of potent inhibitors of scytalone dehydratase: displacement of a water molecule from the active site

21 January 2018

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Solution Structure of FKBP, a Rotamase Enzyme and Receptor for FK506 and Rapamycin

21 January 2018

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Enthalpy of hydrogen bond formation in a protein-ligand binding reaction

21 January 2018

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Statistical and molecular dynamics studies of buried waters in globular proteins

21 January 2018

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Involvement of water in carbohydrate-protein binding.

21 January 2018

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The role of water molecules in the structure-based design of (5-hydroxynorvaline)-2-cyclosporin: synthesis, biological activity, and crystallographic analysis with cyclophilin A

21 January 2018

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Thermodynamic consequences of disrupting a water-mediated hydrogen bond network in a protein:pheromone complex

21 January 2018

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Anatomy of an antibody molecule: structure, kinetics, thermodynamics and mutational studies of the antilysozyme antibody D1.3.

21 January 2018

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The role of hydrogen bonding via interfacial water molecules in antigen-antibody complexation. The HyHEL-10-HEL interaction

21 January 2018

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Structure of an antibody-lysozyme complex unexpected effect of conservative mutation

21 January 2018

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Design of inhibitors of glycogen phosphorylase: a study of alpha- and beta-C-glucosides and 1-thio-beta-D-glucose compounds

21 January 2018

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A mutational analysis of binding interactions in an antigen-antibody protein-protein complex

21 January 2018

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Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme

21 January 2018

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Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and X-ray analysis of six Ser --> Ala mutants

21 January 2018

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Molecular recognition mediated by bound water. A mechanism for star activity of the restriction endonuclease EcoRI

21 January 2018

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Role of hydration in the binding of lac repressor to DNA.

21 January 2018

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Heat capacity effects of water molecules and ions at a protein-DNA interface

21 January 2018

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A thermodynamic study of the trp repressor-operator interaction

21 January 2018

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Application and limitations of X-ray crystallographic data in structure-based ligand and drug design

21 January 2018

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Modelling of solvent positions around polar groups in proteins.

21 January 2018

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A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

21 January 2018

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

21 January 2018

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Simple, Intuitive Calculations of Free Energy of Binding for Protein−Ligand Complexes. 3. The Free Energy Contribution of Structural Water Molecules in HIV-1 Protease Complexes

21 January 2018

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Functionality maps of binding sites: a multiple copy simultaneous search method

21 January 2018

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SuperStar: a knowledge-based approach for identifying interaction sites in proteins.

21 January 2018

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Algorithms for computational solvent mapping of proteins

21 January 2018

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Prediction of water and metal binding sites and their affinities by using the Fold-X force field

21 January 2018

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WaterScore: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes.

21 January 2018

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Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock

21 January 2018

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Structure-based prediction of free energy changes of binding of PTP1B inhibitors

21 January 2018

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Comparative evaluation of 11 scoring functions for molecular docking

21 January 2018

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The effect of tightly bound water molecules on the structural interpretation of ligand-derived pharmacophore models.

21 January 2018

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Binding mode prediction of cytochrome p450 and thymidine kinase protein-ligand complexes by consideration of water and rescoring in automated docking.

21 January 2018

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Modeling water molecules in protein-ligand docking using GOLD.

21 January 2018

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Mapping the energetics of water-protein and water-ligand interactions with the "natural" HINT forcefield: predictive tools for characterizing the roles of water in biomolecules

21 January 2018

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Water: How to evaluate its contribution in protein-ligand interactions

21 January 2018

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De novo ligand design with explicit water molecules: an application to bacterial neuraminidase.

21 January 2018

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Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy

21 January 2018

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Docking of aminoglycosides to hydrated and flexible RNA.

21 January 2018

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Methodology and problems of protein-ligand docking: case study of dihydroorotate dehydrogenase, thymidine kinase, and phosphodiesterase 4.

21 January 2018

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GEMDOCK: a generic evolutionary method for molecular docking.

21 January 2018

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Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase.

21 January 2018

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A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces

21 January 2018

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Role of water mediated interactions in protein-protein recognition landscapes

21 January 2018

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Water in protein structure prediction

21 January 2018

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Role of topology, nonadditivity, and water-mediated interactions in predicting the structures of alpha/beta proteins.

21 January 2018

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The Entropic Cost of Bound Water in Crystals and Biomolecules

21 January 2018

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MHC-peptide binding is assisted by bound water molecules.

21 January 2018

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Protein stability and ligand binding: new paradigms from in-silico experiments

21 January 2018

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Quantifying the role of water in protein-carbohydrate interactions

21 January 2018

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

21 January 2018

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Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method.

21 January 2018

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Hydration free energies and entropies for water in protein interiors

21 January 2018

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Thermodynamic properties of internal water molecules in the hydrophobic cavity around the catalytic center of cytochrome c oxidase.

21 January 2018

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Glycogen phosphorylase inhibitors: a free energy perturbation analysis of glucopyranose spirohydantoin analogues

21 January 2018

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Determination of the interfacial water content in protein-protein complexes from free energy simulations

21 January 2018

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Thermodynamics of buried water clusters at a protein-ligand binding interface

21 January 2018

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Thermodynamics of protein folding: a microscopic view

21 January 2018

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Effective energy functions for protein structure prediction.

21 January 2018

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Effective energy function for proteins in solution

21 January 2018

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Analysis of a Water Mediated Protein−Protein Interactions within RNase T1†,‡

21 January 2018

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Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds

21 January 2018

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21 January 2018

Identifiers

DOI

10.1039/B612449F

1 reference

15 August 2017

1 reference

PubMed ID

17242738