Dissecting water binding sites at protein–protein interfaces: a lesson from the atomic structures in the Protein Data Bank

No abstract is available for this paper.

• Publication year

  2019

• Venue

  Journal of Biomolecular Structure and Dynamics

• Publication date

  2019-03-01

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1080/07391102.2018.1453379PMID 29546800
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Recognition dynamics of dopamine to human Monoamine oxidase B: role of Leu171/Gln206 and conserved water molecules in the active site cavity

  2018cited by this paper
• Computational protein structure refinement: almost there, yet still so far to go

  2017cited by this paper
• Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces.

  2016cited by this paper
• Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.

  2015influential reference
• Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors

  2015cited by this paper
• Molecular architecture of protein-RNA recognition sites

  2015cited by this paper
• Probing binding hot spots at protein–RNA recognition sites

  2015cited by this paper
• Prediction of Water Binding to Protein Hydration Sites with a Discrete, Semiexplicit Solvent Model.

  2015cited by this paper
• The role of water in protein's behavior: The two dynamical crossovers studied by NMR and FTIR techniques

  2014cited by this paper
• Hydration of protein–RNA recognition sites

  2014influential reference
• Intuitive, but not simple: Including explicit water molecules in protein–protein docking simulations improves model quality

  2014cited by this paper
• Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation

  2014cited by this paper
• Solvated protein–protein docking using Kyte‐Doolittle‐based water preferences

  2013cited by this paper
• Molecular signatures of G-protein-coupled receptors

  2013cited by this paper
• Explicit treatment of water molecules in data-driven protein-protein docking: the solvated HADDOCKing approach.

  2012cited by this paper
• The Newest View on Protein Folding: Stoichiometric and Spatial Unity in Structural and Functional Diversity

  2011cited by this paper
• Backbones of folded proteins reveal novel invariant amino acid neighborhoods.

  2011cited by this paper
• A Stoichiometry Driven Universal Spatial Organization of Backbones of Folded Proteins: Are there Chargaff's Rules for Protein Folding?

  2010cited by this paper
• Calculations of the Free Energy of Interaction of the c-Fos-c-Jun Coiled Coil: Effects of the Solvation Model and the Inclusion of Polarization Effects

  2010cited by this paper
• Hydrophobic Interactions and Dewetting between Plates with Hydrophobic and Hydrophilic Domains

  2008cited by this paper
• Solvent dramatically affects protein structure refinement

  2008cited by this paper
• Cavities and Atomic Packing in Protein Structures and Interfaces

  2008cited by this paper
• Water as an active constituent in cell biology.

  2008cited by this paper
• On the contribution of water-mediated interactions to protein-complex stability.

  2008cited by this paper
• Protein-protein docking with backbone flexibility.

  2007cited by this paper
• A Mathematical Theory of Communication

  2006influential reference
• Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface.

  2006cited by this paper
• Flexible protein-protein docking.

  2006cited by this paper
• Solvated docking: introducing water into the modelling of biomolecular complexes

  2006cited by this paper
• Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues.

  2005cited by this paper
• Conservation and relative importance of residues across protein-protein interfaces

  2005cited by this paper
• Binding mode prediction of cytochrome p450 and thymidine kinase protein-ligand complexes by consideration of water and rescoring in automated docking.

  2005cited by this paper
• Accounting for loop flexibility during protein–protein docking

  2005cited by this paper
• Hydration of protein–protein interfaces

  2005influential reference
• A “solvated rotamer” approach to modeling water‐mediated hydrogen bonds at protein–protein interfaces

  2005cited by this paper
• Water and proteins: a love-hate relationship.

  2004cited by this paper
• Role of water mediated interactions in protein-protein recognition landscapes.

  2003cited by this paper
• Protein folding: could hydrophobic collapse be coupled with hydrogen‐bond formation?

  2003cited by this paper
• Amino acid?base interactions: a three-dimensional analysis of protein?DNA interactions at an atomic level

  2001cited by this paper
• The Protein Data Bank

  2000cited by this paper
• Water in enzyme reactions: biophysical aspects of hydration-dehydration processes

  2000cited by this paper
• How many water molecules can be detected by protein crystallography?

  1999cited by this paper
• How many water molecules can be detected by protein crystallography?

  1999cited by this paper
• Rapid refinement of protein interfaces incorporating solvation: application to the docking problem.

  1998cited by this paper
• Packing at the protein-water interface.

  1996cited by this paper
• The HSSP database of protein structure-sequence alignments.

  1994cited by this paper
• Bound water molecules and conformational stabilization help mediate an antigen-antibody association.

  1994cited by this paper
• Cavities and packing at protein interfaces

  1994cited by this paper
• Satisfying hydrogen bonding potential in proteins.

  1994cited by this paper
• Prediction of protein secondary structure at better than 70% accuracy.

  1993cited by this paper
• The HSSP data base of protein structure-sequence alignments

  1993cited by this paper
• Small rearrangements in structures of Fv and Fab fragments of antibody D 1.3 on antigen binding

  1990cited by this paper
• Distributions of water around amino acid residues in proteins.

  1988cited by this paper
• Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features

  1983cited by this paper
• The interpretation of protein structures: estimation of static accessibility.

  1971cited by this paper
• Some factors in the interpretation of protein denaturation.

  1959cited by this paper
• Free Volume and Entropy in Condensed Systems III. Entropy in Binary Liquid Mixtures; Partial Molal Entropy in Dilute Solutions; Structure and Thermodynamics in Aqueous Electrolytes

  1945cited by this paper
• Electronic Reprint Biological Crystallography the Protein Data Bank Biological Crystallography the Protein Data Bank

  year unknowncited by this paper

• WatCon: A Python Tool for Analysis of Conserved Water Networks Across Protein Families

  2025cites this paper
• Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA–ligand interactions

  2024cites this paper
• Advanced computational tools for quantitative analysis of protein–nucleic acid interfaces

  2022cites this paper
• Higher Affinity Antibodies Bind With Lower Hydration and Flexibility in Large Scale Simulations

  2022cites this paper
• Protein Engineering in the Design of Protein–Protein Interactions: SARS-CoV-2 Inhibitors as a Test Case

  2021cites this paper
• Soft regions of protein surface are potent for stable dimer formation

  2020cites this paper
• A structure-based model for the prediction of protein–RNA binding affinity

  2019cites this paper