Related references
Note: Only part of the references are listed.Developing end-point methods for absolute binding free energy calculation using the Boltzmann-quasiharmonic model
Lauren Wickstrom et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2022)
Quantitative FRET (qFRET) Technology for the Determination of Protein-Protein Interaction Affinity in Solution
Jiayu Liao et al.
MOLECULES (2021)
A Bit Stickier, a Bit Slower, a Lot Stiffer: Specific vs. Nonspecific Binding of Gal4 to DNA
Thomas Carzaniga et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)
Native or Non-Native Protein-Protein Docking Models? Molecular Dynamics to the Rescue
Zuzana Jandova et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)
Slowdown of Water Dynamics from the Top to the Bottom of the GroEL Cavity
Nicolas Macro et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2021)
Moving pictures: Reassessing docking experiments with a dynamic view of protein interfaces
Chantal Prevost et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2021)
Computational prediction of protein-protein binding affinities
Till Siebenmorgen et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2020)
Performance of human and server prediction inCAPRIrounds 38-45
Rui Duan et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2020)
SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation
Justina Jankauskaite et al.
BIOINFORMATICS (2019)
Atomic-level characterization of protein-protein association
Albert C. Pan et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
TTClust: A Versatile Molecular Simulation Trajectory Clustering Program with Graphical Summaries
Thibault Tubiana et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2018)
Recent Developments and Applications of the MMPBSA Method
Changhao Wang et al.
FRONTIERS IN MOLECULAR BIOSCIENCES (2018)
Flexibility vs Preorganization: Direct Comparison of Binding Kinetics for a Disordered Peptide and Its Exact Preorganized Analogues
A. S. Saglam et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2017)
Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling
Nuria Plattner et al.
NATURE CHEMISTRY (2017)
Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations
Fabian Paul et al.
NATURE COMMUNICATIONS (2017)
Water Dynamics in the Hydration Shells of Biomolecules
Damien Laage et al.
CHEMICAL REVIEWS (2017)
Mapping, modeling, and characterization of protein-protein interactions on a proteomic scale
T. M. Cafarelli et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2017)
Engineering cell signaling modulators from native protein-protein interactions
Wei Zhang et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2017)
Dynamics and recognition within a protein-DNA complex: a molecular dynamics study of the SKN-1/DNA interaction
Loic Etheve et al.
NUCLEIC ACIDS RESEARCH (2016)
Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan
Vytautas Gapsys et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2016)
New Computational Approach for External Entropy in Protein-Protein Binding
Song-Ho Chong et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Computational Methods for Configurational Entropy Using Internal and Cartesian Coordinates
Simon Hikiri et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Anomalous Dynamics of Water Confined in Protein-Protein and Protein-DNA Interfaces
Song-Ho Chong et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2016)
Protein-DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors
Loic Etheve et al.
NUCLEIC ACIDS RESEARCH (2016)
DockQ: A Quality Measure for Protein-Protein Docking Models
Sankar Basu et al.
PLOS ONE (2016)
Peptide Binding to a PDZ Domain by Electrostatic Steering via Nonnative Salt Bridges
Nicolas Bloechliger et al.
BIOPHYSICAL JOURNAL (2015)
Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin
Julian E. Fuchs et al.
PLOS ONE (2015)
Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding
Luciano A. Abriata et al.
SCIENTIFIC REPORTS (2015)
cocor: A Comprehensive Solution for the Statistical Comparison of Correlations
Birk Diedenhofen et al.
PLOS ONE (2015)
Ward's Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward's Criterion?
Fionn Murtagh et al.
JOURNAL OF CLASSIFICATION (2014)
Intuitive, but not simple: Including explicit water molecules in protein-protein docking simulations improves model quality
Hardik I. Parikh et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2014)
Molecular origins of binding affinity: seeking the Archimedean point
Panagiotis L. Kastritis et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2013)
On the binding affinity of macromolecular interactions: daring to ask why proteins interact
Panagiotis L. Kastritis et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2013)
Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody
Aaron G. Schmidt et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Free-energy landscape of protein oligomerization from atomistic simulations
Alessandro Barducci et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations
Tingjun Hou et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)
Thermodynamic Properties of Water Molecules at a Protein Protein Interaction Surface
David J. Huggins et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values
Chresten R. Sondergaard et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions
Mats H. M. Olsson et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Calculation of Configurational Entropy with a Boltzmann-Quasiharmonic Model: The Origin of High-Affinity Protein-Ligand Binding
Kyle W. Harpole et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2011)
A structure-based benchmark for protein-protein binding affinity
Panagiotis L. Kastritis et al.
PROTEIN SCIENCE (2011)
Adhesive water networks facilitate binding of protein interfaces
Mazen Ahmad et al.
NATURE COMMUNICATIONS (2011)
A Simple Definition of Structural Regions in Proteins and Its Use in Analyzing Interface Evolution
Emmanuel D. Levy
JOURNAL OF MOLECULAR BIOLOGY (2010)
Protein-protein docking benchmark version 4.0
Howook Hwang et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)
Improved side-chain torsion potentials for the Amber ff99SB protein force field
Kresten Lindorff-Larsen et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)
Transient Protein-Protein Interactions: Structural, Functional, and Network Properties
James R. Perkins et al.
STRUCTURE (2010)
Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model
Devleena Shivakumar et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Mechanism of fast peptide recognition by SH3 domains
Mazen Ahmad et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2008)
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
Berk Hess et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)
Protein interactions in human genetic diseases
Benjamin Schuster-Bockler et al.
GENOME BIOLOGY (2008)
Structural basis for ubiquitin-mediated dimerization and activation of the ubiquitin protein ligase Cbl-b
Pascal Peschard et al.
MOLECULAR CELL (2007)
Canonical sampling through velocity rescaling
Giovanni Bussi et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Deciphering protein-protein interactions. Part I. Experimental techniques and databases
Benjamin A. Shoemaker et al.
PLOS COMPUTATIONAL BIOLOGY (2007)
Comparison of multiple amber force fields and development of improved protein backbone parameters
Viktor Hornak et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)
Solvated docking: introducing water into the modelling of biomolecular complexes
Aalt D. J. van Dijk et al.
BIOINFORMATICS (2006)
ProFace: a server for the analysis of the physicochemical features of protein-protein interfaces
Rudra P. Saha et al.
BMC STRUCTURAL BIOLOGY (2006)
GROMACS: Fast, flexible, and free
D Van der Spoel et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
Hydration of protein-protein interfaces
F Rodier et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)
New methodologies for measuring protein interactions in vivo and in vitro
J Piehler
CURRENT OPINION IN STRUCTURAL BIOLOGY (2005)
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
TJ Dolinsky et al.
NUCLEIC ACIDS RESEARCH (2004)
Convergent mechanisms for recognition of divergent cytokines by the shared signaling receptor gp130
MJ Boulanger et al.
MOLECULAR CELL (2003)
On the nonpolar hydration free energy of proteins: Surface area and continuum solvent models for the solute-solvent interaction energy
RM Levy et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)
Role of water mediated interactions in protein-protein recognition landscapes
GA Papoian et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)
Continuum solvent modeling of nonpolar solvation: Improvement by separating surface area dependent cavity and dispersion contributions
M Zacharias
JOURNAL OF PHYSICAL CHEMISTRY A (2003)
Dissecting protein-protein recognition sites
P Chakrabarti et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2002)
Novel recognition mode between Vav and Grb2 SH3 domains
M Nishida et al.
EMBO JOURNAL (2001)
GROMACS 3.0: a package for molecular simulation and trajectory analysis
E Lindahl et al.
JOURNAL OF MOLECULAR MODELING (2001)
Implications of macromolecular crowding for protein assembly
AP Minton
CURRENT OPINION IN STRUCTURAL BIOLOGY (2000)
The Protein Data Bank
HM Berman et al.
NUCLEIC ACIDS RESEARCH (2000)
Specificity in protein-protein interactions: The structural basis for dual recognition in endonuclease colicin-immunity protein complexes
UC Kuhlmann et al.
JOURNAL OF MOLECULAR BIOLOGY (2000)
Share Paper
