Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures

Predicting protein interface residues using easily accessible on-line resources

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

Exploring the potential of global protein–protein docking: an overview and critical assessment of current programs for automatic ab initio docking

(2015) Sheng-You Huang   DRUG DISCOVERY TODAY

Prediction of protein-protein interaction sites from weakly homologous template structures using meta-threading and machine learning

(2015) Surabhi Maheshwari et al.   JOURNAL OF MOLECULAR RECOGNITION

Scoring docking conformations using predicted protein interfaces

(2014) Reyhaneh Esmaielbeiki et al.   BMC BIOINFORMATICS

Search strategies and evaluation in protein–protein docking: principles, advances and challenges

(2014) Sheng-You Huang   DRUG DISCOVERY TODAY

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

Scoring functions for protein–protein interactions

(2013) Iain H Moal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

DOT2: Macromolecular docking with improved biophysical models

(2013) Victoria A. Roberts et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

How to Use Not-Always-Reliable Binding Site Information in Protein-Protein Docking Prediction

(2013) Lin Li et al.   PLoS One

A Critical Assessment of Information-guided Protein–Protein Docking Predictions

(2012) Edward S. C. Shih et al.   MOLECULAR & CELLULAR PROTEOMICS

eThread: A Highly Optimized Machine Learning-Based Approach to Meta-Threading and the Modeling of Protein Tertiary Structures

(2012) Michal Brylinski et al.   PLoS One

Scoring protein interaction decoys using exposed residues (SPIDER): A novel multibody interaction scoring function based on frequent geometric patterns of interfacial residues

(2012) Raed Khashan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

LIBSVM

(2012) Chih-Chung Chang et al.   ACM Transactions on Intelligent Systems and Technology

DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking

(2011) Shiyong Liu et al.   BMC BIOINFORMATICS

Prediction of protein-binding areas by small-world residue networks and application to docking

(2011) Carles Pons et al.   BMC BIOINFORMATICS

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK

(2011) Sjoerd J. de Vries et al.   PLoS One

On the use of distance constraints in protein-protein docking computations

(2011) Edward S. C. Shih et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement

(2011) Nurcan Tuncbag et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2010) Mu Gao et al.   BIOINFORMATICS

Discovery of Modulators of Protein-Protein Interactions: Current Approaches and Limitations

(2010) Lidio M.C. Meireles et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

New measures for estimating surface complementarity and packing at protein-protein interfaces

(2010) Pralay Mitra et al.   FEBS LETTERS

Building Macromolecular Assemblies by Information-driven Docking

(2010) Ezgi Karaca et al.   MOLECULAR & CELLULAR PROTEOMICS

Interactome under construction

(2010) Laura Bonetta   NATURE

The HADDOCK web server for data-driven biomolecular docking

(2010) Sjoerd J de Vries et al.   Nature Protocols

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

Performance of ZDOCK and ZRANK in CAPRI rounds 13-19

(2010) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Docking by structural similarity at protein-protein interfaces

(2010) Rohita Sinha et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Docking and scoring protein interactions: CAPRI 2009

(2010) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-protein docking benchmark version 4.0

(2010) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Blind predictions of protein interfaces by docking calculations in CAPRI

(2010) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

(2009) Shashi Pandit et al.   BMC BIOINFORMATICS

Protein-protein docking using region-based 3D Zernike descriptors

(2009) Vishwesh Venkatraman et al.   BMC BIOINFORMATICS

Evolution of Protein Binding Modes in Homooligomers

(2009) Judith E. Dayhoff et al.   JOURNAL OF MOLECULAR BIOLOGY

Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling

(2009) Stefan Engelen et al.   PLoS Computational Biology

Integrating Diverse Data for Structure Determination of Macromolecular Assemblies

(2008) Frank Alber et al.   Annual Review of Biochemistry

Amino acid network and its scoring application in protein–protein docking

(2008) Shan Chang et al.   BIOPHYSICAL CHEMISTRY

Recent Progress and Future Directions in Protein-Protein Docking

(2008) David Ritchie   CURRENT PROTEIN & PEPTIDE SCIENCE

Using protein binding site prediction to improve protein docking

(2008) Bingding Huang et al.   GENE

Assembly reflects evolution of protein complexes

(2008) Emmanuel D. Levy et al.   NATURE

The RosettaDock server for local protein-protein docking

(2008) S. Lyskov et al.   NUCLEIC ACIDS RESEARCH

An iterative knowledge-based scoring function for protein-protein recognition

(2008) Sheng-You Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Principles of flexible protein-protein docking

(2008) Nelly Andrusier et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-protein docking benchmark version 3.0

(2008) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS