Are protein-protein interfaces special regions on a protein’s surface?

Algorithmic approaches to protein-protein interaction site prediction

(2015) Tristan T Aumentado-Armstrong et al.   Algorithms for Molecular Biology

Predicting protein interface residues using easily accessible on-line resources

(2015) S. Maheshwari et al.   BRIEFINGS IN BIOINFORMATICS

Insights into Disease-Associated Mutations in the Human Proteome through Protein Structural Analysis

(2015) Mu Gao et al.   STRUCTURE

Comprehensive prediction of drug-protein interactions and side effects for the human proteome

(2015) Hongyi Zhou et al.   Scientific Reports

HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements

(2014) Yih-Chii Hwang et al.   BIOINFORMATICS

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers

(2014) B. G. Pierce et al.   BIOINFORMATICS

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

PRISM: a web server and repository for prediction of protein–protein interactions and modeling their 3D complexes

(2014) Alper Baspinar et al.   NUCLEIC ACIDS RESEARCH

Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces

(2014) Tanggis Bohnuud et al.   PLoS Computational Biology

APoc: large-scale identification of similar protein pockets

(2013) Mu Gao et al.   BIOINFORMATICS

Coarse Grained Normal Mode Analysis vs. Refined Gaussian Network Model for Protein Residue-Level Structural Fluctuations

(2013) Jun-Koo Park et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Towards a detailed atlas of protein–protein interactions

(2013) Roberto Mosca et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Interplay of physics and evolution in the likely origin of protein biochemical function

(2013) Jeffrey Skolnick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

COFACTOR: an accurate comparative algorithm for structure-based protein function annotation

(2012) Ambrish Roy et al.   NUCLEIC ACIDS RESEARCH

HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores

(2012) Martin H. Schaefer et al.   PLoS One

Prediction of Protein-Protein Interaction Sites by Random Forest Algorithm with mRMR and IFS

(2012) Bi-Qing Li et al.   PLoS One

The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation

(2012) M. Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Challenges for the prediction of macromolecular interactions

(2011) Mark N Wass et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM

(2011) Nurcan Tuncbag et al.   Nature Protocols

Prescont: Predicting protein-protein interfaces utilizing four residue properties

(2011) Hermann Zellner et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-Protein Complex Structure Predictions by Multimeric Threading and Template Recombination

(2011) Srayanta Mukherjee et al.   STRUCTURE

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

(2010) Jinrui Xu et al.   BIOINFORMATICS

Conserved residue clusters at protein-protein interfaces and their use in binding site identification

(2010) Mainak Guharoy et al.   BMC BIOINFORMATICS

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

Protein interface conservation across structure space

(2010) Q. C. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FINDSITE: a combined evolution/structure-based approach to protein function prediction

(2009) J. Skolnick et al.   BRIEFINGS IN BIOINFORMATICS

The continuity of protein structure space is an intrinsic property of proteins

(2009) J. Skolnick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Building and assessing atomic models of proteins from structural templates: Learning and benchmarks

(2009) Brinda Kizhakke Vallat et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of Protein–Protein Interaction Sites in Sequences and 3D Structures by Random Forests

(2009) Mile Šikić et al.   PLoS Computational Biology

Principles of Protein−Protein Interactions: What are the Preferred Ways For Proteins To Interact?

(2008) Ozlem Keskin et al.   CHEMICAL REVIEWS

An empirical framework for binary interactome mapping

(2008) Kavitha Venkatesan et al.   NATURE METHODS

Probing the origin of tubulin rigidity with molecular simulations

(2008) R. I. Dima et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimating the size of the human interactome

(2008) M. P. H. Stumpf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

M-TASSER: An Algorithm for Protein Quaternary Structure Prediction

(2007) Huiling Chen et al.   BIOPHYSICAL JOURNAL