Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles

PCalign: a method to quantify physicochemical similarity of protein-protein interfaces

(2015) Shanshan Cheng et al.   BMC BIOINFORMATICS

Comment on ‘protein–protein binding affinity prediction from amino acid sequence’

(2014) Iain H. Moal et al.   BIOINFORMATICS

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

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

Proteins Feel More Than They See: Fine-Tuning of Binding Affinity by Properties of the Non-Interacting Surface

(2014) Panagiotis L. Kastritis et al.   JOURNAL OF MOLECULAR BIOLOGY

Non-Redundant Unique Interface Structures as Templates for Modeling Protein Interactions

(2014) Engin Cukuroglu et al.   PLoS One

Combining Structural Modeling with Ensemble Machine Learning to Accurately Predict Protein Fold Stability and Binding Affinity Effects upon Mutation

(2014) Niklas Berliner et al.   PLoS One

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

(2014) Daniel F. A. R. Dourado et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Buried and Accessible Surface Area Control Intrinsic Protein Flexibility

(2013) Joseph A. Marsh   JOURNAL OF MOLECULAR BIOLOGY

EvoDesign: de novo protein design based on structural and evolutionary profiles

(2013) Pralay Mitra et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Yves Dehouck et al.   NUCLEIC ACIDS RESEARCH

Applying Physics-Based Scoring to Calculate Free Energies of Binding for Single Amino Acid Mutations in Protein-Protein Complexes

(2013) Hege Beard et al.   PLoS One

Coupling mutagenesis and parallel deep sequencing to probe essential residues in a genome or gene

(2013) William P. Robins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improving ranking of models for protein complexes with side chain modeling and atomic potentials

(2013) Shruthi Viswanath et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

An Evolution-Based Approach to De Novo Protein Design and Case Study on Mycobacterium tuberculosis

(2013) Pralay Mitra et al.   PLoS Computational Biology

Energetics of oligomeric protein folding and association

(2012) Colleen M. Doyle et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

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

(2012) Iain H. Moal et al.   BIOINFORMATICS

Computational Prediction of Protein Hot Spot Residues

(2012) John Kenneth Morrow et al.   CURRENT PHARMACEUTICAL DESIGN

A Strategy Based on Protein–Protein Interface Motifs May Help in Identifying Drug Off-Targets

(2012) H. Billur Engin et al.   Journal of Chemical Information and Modeling

On the binding affinity of macromolecular interactions: daring to ask why proteins interact

(2012) P. L. Kastritis et al.   Journal of the Royal Society Interface

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing

(2012) Timothy A Whitehead et al.   NATURE BIOTECHNOLOGY

Experimental support for the foldability-function tradeoff hypothesis: Segregation of the folding nucleus and functional regions in fibroblast growth factor-1

(2012) Liam Longo et al.   PROTEIN SCIENCE

A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds

(2012) P. Benjamin Stranges et al.   PROTEIN SCIENCE

Versatility and Invariance in the Evolution of Homologous Heteromeric Interfaces

(2012) Jessica Andreani et al.   PLoS Computational Biology

Anchored Design of Protein-Protein Interfaces

(2011) Steven M. Lewis et al.   PLoS One

Characterization of Protein-Protein Interaction Interfaces from a Single Species

(2011) David Talavera et al.   PLoS One

Restricted sidechain plasticity in the structures of native proteins and complexes

(2011) Sarel J. Fleishman et al.   PROTEIN SCIENCE

Computational protein design with explicit consideration of surface hydrophobic patches

(2011) Ron Jacak et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

iAlign: a method for the structural comparison of protein–protein interfaces

(2010) Mu Gao et al.   BIOINFORMATICS

Exposing the co-adaptive potential of protein–protein interfaces through computational sequence design

(2010) Menachem Fromer et al.   BIOINFORMATICS

How significant is a protein structure similarity with TM-score = 0.5?

(2010) Jinrui Xu et al.   BIOINFORMATICS

Computational Design of Protein Interfaces with Receptor Flexibility

(2010) Samy Meroueh et al.   BIOPHYSICAL JOURNAL

A Simple Definition of Structural Regions in Proteins and Its Use in Analyzing Interface Evolution

(2010) Emmanuel D. Levy   JOURNAL OF MOLECULAR BIOLOGY

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

Validation of Coevolving Residue Algorithms via Pipeline Sensitivity Analysis: ELSC and OMES and ZNMI, Oh My!

(2010) Christopher A. Brown et al.   PLoS One

The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction

(2010) N. A. G. Meenan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected

(2010) M. Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming

(2009) Srayanta Mukherjee et al.   NUCLEIC ACIDS RESEARCH

PIE—Efficient filters and coarse grained potentials for unbound protein–protein docking

(2009) D. V. S. Ravikant et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

DOCKGROUND protein-protein docking decoy set

(2008) S. Liu et al.   BIOINFORMATICS

Predicting free energy changes using structural ensembles

(2008) Alexander Benedix et al.   NATURE METHODS

Prediction of Protein-Protein Interface Sequence Diversity Using Flexible Backbone Computational Protein Design

(2008) Elisabeth L. Humphris et al.   STRUCTURE

Phylogenetic Signal, Evolutionary Process, and Rate

(2008) Liam J. Revell et al.   SYSTEMATIC BIOLOGY