A multiscale approach to predicting affinity changes in protein-protein interfaces

Predicting the Impact of Missense Mutations on Protein–Protein Binding Affinity

(2014) Minghui Li et al.   Journal of Chemical Theory and Computation

mCSM: predicting the effects of mutations in proteins using graph-based signatures

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

Intermolecular Contact Potentials for Protein–Protein Interactions Extracted from Binding Free Energy Changes upon Mutation

(2013) Iain H. Moal et al.   Journal of Chemical Theory and Computation

Fast fitting to low resolution density maps: elucidating large-scale motions of the ribosome

(2013) Samuel Coulbourn Flores   NUCLEIC ACIDS RESEARCH

BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations

(2013) Yves Dehouck et al.   NUCLEIC ACIDS RESEARCH

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

(2013) Rocco Moretti et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models

(2012) Iain H. Moal et al.   BIOINFORMATICS

Multiscale modeling of macromolecular biosystems

(2012) S. C. Flores et al.   BRIEFINGS IN BIOINFORMATICS

Modeling and design by hierarchical natural moves

(2012) A. Y. L. Sim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast Flexible Modeling of RNA Structure Using Internal Coordinates

(2010) S. C. Flores et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Accounting for conformational entropy in predicting binding free energies of protein-protein interactions

(2010) Hetunandan Kamisetty et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Role of conformational sampling in computing mutation-induced changes in protein structure and stability

(2010) Elizabeth H. Kellogg et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Structural Dynamics and Energetics of an Immunodominant T Cell Receptor Are Programmed by Its Vβ Domain

(2008) Jeffrey Ishizuka et al.   IMMUNITY

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Experimental and Computational Analyses of the Energetic Basis for Dual Recognition of Immunity Proteins by Colicin Endonucleases

(2008) Anthony H. Keeble et al.   JOURNAL OF MOLECULAR BIOLOGY

Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction

(2008) Colin A. Smith et al.   JOURNAL OF MOLECULAR BIOLOGY

Predicting free energy changes using structural ensembles

(2008) Alexander Benedix et al.   NATURE METHODS