Progress and challenges in predicting protein interfaces

Antibody informatics for drug discovery

(2014) Hiroki Shirai et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Improving B-cell epitope prediction and its application to global antibody-antigen docking

(2014) Konrad Krawczyk et al.   BIOINFORMATICS

Efficient prediction of human protein-protein interactions at a global scale

(2014) Andrew Schoenrock et al.   BMC BIOINFORMATICS

Transient protein-protein interface prediction: datasets, features, algorithms, and the RAD-T predictor

(2014) Calem J Bendell et al.   BMC BIOINFORMATICS

Scoring docking conformations using predicted protein interfaces

(2014) Reyhaneh Esmaielbeiki et al.   BMC BIOINFORMATICS

CRF-based models of protein surfaces improve protein-protein interaction site predictions

(2014) Zhijie Dong et al.   BMC BIOINFORMATICS

FreeContact: fast and free software for protein contact prediction from residue co-evolution

(2014) László Kaján et al.   BMC BIOINFORMATICS

Integrative computational modeling of protein interactions

(2014) João P. G. L. M. Rodrigues et al.   FEBS Journal

SEPPA 2.0—more refined server to predict spatial epitope considering species of immune host and subcellular localization of protein antigen

(2014) Tao Qi et al.   NUCLEIC ACIDS RESEARCH

Origins of specificity and affinity in antibody–protein interactions

(2014) Hung-Pin Peng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An overview of recent advances in structural bioinformatics of protein–protein interactions and a guide to their principles

(2014) Govindarajan Sudha et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Using a Combined Computational-Experimental Approach to Predict Antibody-Specific B Cell Epitopes

(2014) Inbal Sela-Culang et al.   STRUCTURE

InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution

(2013) Jessica Andreani et al.   BIOINFORMATICS

Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server

(2013) Pier Paolo Olimpieri et al.   BIOINFORMATICS

Evaluating template-based and template-free protein-protein complex structure prediction

(2013) T. Vreven et al.   BRIEFINGS IN BIOINFORMATICS

Bioinformatics Resources and Tools for Conformational B-Cell Epitope Prediction

(2013) Pingping Sun et al.   Computational and Mathematical Methods in Medicine

Low-resolution structural modeling of protein interactome

(2013) Ilya A Vakser   CURRENT OPINION IN STRUCTURAL BIOLOGY

One Size Does Not Fit All: The Limits of Structure-Based Models in Drug Discovery

(2013) Gregory A. Ross et al.   Journal of Chemical Theory and Computation

Antibody and Antigen Contact Residues Define Epitope and Paratope Size and Structure

(2013) J. W. Stave et al.   JOURNAL OF IMMUNOLOGY

Residue-Level Prediction of HIV-1 Antibody Epitopes Based on Neutralization of Diverse Viral Strains

(2013) G.-Y. Chuang et al.   JOURNAL OF VIROLOGY

Antibodies to watch in 2014

(2013) Janice M Reichert   mAbs

Emerging methods in protein co-evolution

(2013) David de Juan et al.   NATURE REVIEWS GENETICS

SAbDab: the structural antibody database

(2013) James Dunbar et al.   NUCLEIC ACIDS RESEARCH

metaPIS: A Sequence-based Meta-server for Protein Interaction Site Prediction

(2013) Junfeng Huang et al.   PROTEIN AND PEPTIDE LETTERS

The indistinguishability of epitopes from protein surface is explained by the distinct binding preferences of each of the six antigen-binding loops

(2013) Vered Kunik et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Antibody i-Patch prediction of the antibody binding site improves rigid local antibody-antigen docking

(2013) K. Krawczyk et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Binding interface prediction by combining protein-protein docking results

(2013) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

DockRank: Ranking docked conformations using partner-specific sequence homology-based protein interface prediction

(2013) Li C. Xue et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Docking, scoring, and affinity prediction in CAPRI

(2013) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

PAIRpred: Partner-specific prediction of interacting residues from sequence and structure

(2013) Fayyaz ul Amir Afsar Minhas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structural analysis and epitope prediction of HCV E1 protein isolated in Pakistan: an in-silico approach

(2013) Sobia Idrees et al.   Virology Journal

A holistic in silico approach to predict functional sites in protein structures

(2012) Joan Segura et al.   BIOINFORMATICS

Protein-protein binding site identification by enumerating the configurations

(2012) Fei Guo et al.   BMC BIOINFORMATICS

Predicting protein-protein interface residues using local surface structural similarity

(2012) Rafael A Jordan et al.   BMC BIOINFORMATICS

A novel method for prediction of protein interaction sites based on integrated RBF neural networks

(2012) Yuehui Chen et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Detection of Outlier Residues for Improving Interface Prediction in Protein Heterocomplexes

(2012) Peng Chen et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Structure-based prediction of protein–protein interactions on a genome-wide scale

(2012) Qiangfeng Cliff Zhang et al.   NATURE

Immune epitope database analysis resource

(2012) Y. Kim et al.   NUCLEIC ACIDS RESEARCH

PrePPI: a structure-informed database of protein–protein interactions

(2012) Qiangfeng Cliff Zhang et al.   NUCLEIC ACIDS RESEARCH

Homology Inference of Protein-Protein Interactions via Conserved Binding Sites

(2012) Manoj Tyagi 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

Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking

(2012) Jens Vindahl Kringelum et al.   PLoS Computational Biology

Structural Consensus among Antibodies Defines the Antigen Binding Site

(2012) Vered Kunik et al.   PLoS Computational Biology

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

(2011) David T. Jones et al.   BIOINFORMATICS

HomPPI: a class of sequence homology based protein-protein interface prediction methods

(2011) Li C Xue et al.   BMC BIOINFORMATICS

Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi diagrams

(2011) Joan Segura et al.   BMC BIOINFORMATICS

Binding Site Prediction for Protein-Protein Interactions and Novel Motif Discovery using Re-occurring Polypeptide Sequences

(2011) Adam Amos-Binks et al.   BMC BIOINFORMATICS

Antibody-Specified B-Cell Epitope Prediction in Line with the Principle of Context-Awareness

(2011) Liang Zhao et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Prediction of protein–protein interaction sites using patch-based residue characterization

(2011) Zhijun Qiu et al.   JOURNAL OF THEORETICAL BIOLOGY

Towards the prediction of protein interaction partners using physical docking

(2011) M. N. Wass et al.   Molecular Systems Biology

IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins

(2011) B. A. Shoemaker et al.   NUCLEIC ACIDS RESEARCH

PredUs: a web server for predicting protein interfaces using structural neighbors

(2011) Q. C. Zhang et al.   NUCLEIC ACIDS RESEARCH

A database of immunoglobulins with integrated tools: DIGIT

(2011) A. Chailyan et al.   NUCLEIC ACIDS RESEARCH

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

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

Characterization of Protein-Protein Interaction Interfaces from a Single Species

(2011) David Talavera et al.   PLoS One

Partner-Aware Prediction of Interacting Residues in Protein-Protein Complexes from Sequence Data

(2011) Shandar Ahmad et al.   PLoS One

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prescont: Predicting protein-protein interfaces utilizing four residue properties

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

Prediction of protein binding sites and hot spots

(2011) Juan Fernández-Recio   Wiley Interdisciplinary Reviews-Computational Molecular Science

ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment

(2010) Janez Konc et al.   BIOINFORMATICS

Applying the Naïve Bayes classifier with kernel density estimation to the prediction of protein–protein interaction sites

(2010) Yoichi Murakami et al.   BIOINFORMATICS

Sequence-based identification of interface residues by an integrative profile combining hydrophobic and evolutionary information

(2010) Peng Chen et al.   BMC BIOINFORMATICS

EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results

(2010) Shide Liang et al.   BMC BIOINFORMATICS

Protein−Protein Binding Site Prediction by Local Structural Alignment

(2010) Nejc Carl et al.   Journal of Chemical Information and Modeling

An Integrated View of Molecular Coevolution in Protein-Protein Interactions

(2010) S. C. Lovell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Anti-HLA-E mAb 3D12 mimics MEM-E/02 in binding to HLA-B and HLA-C alleles: Web-tools validate the immunogenic epitopes of HLA-E recognized by the antibodies

(2010) Mepur H. Ravindranath et al.   MOLECULAR IMMUNOLOGY

ProBiS: a web server for detection of structurally similar protein binding sites

(2010) J. Konc et al.   NUCLEIC ACIDS RESEARCH

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

(2010) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

IEDB-3D: structural data within the immune epitope database

(2010) J. Ponomarenko et al.   NUCLEIC ACIDS RESEARCH

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

Protein interactions and ligand binding: From protein subfamilies to functional specificity

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

Use of amino acid composition to predict epitope residues of individual antibodies

(2010) Shinji Soga et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Protein-protein docking benchmark version 4.0

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

i-Patch: Interprotein contact prediction using local network information

(2010) Rebecca Hamer 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

Mining for the antibody-antigen interacting associations that predict the B cell epitopes

(2010) Liang Zhao et al.   BMC STRUCTURAL BIOLOGY

Beauty Is in the Eye of the Beholder: Proteins Can Recognize Binding Sites of Homologous Proteins in More than One Way

(2010) Juliette Martin   PLoS Computational Biology

Accuracy of Protein-Protein Binding Sites in High-Throughput Template-Based Modeling

(2010) Petras J. Kundrotas et al.   PLoS Computational Biology

Sequence-based prediction of protein interaction sites with an integrative method

(2009) Xue-wen Chen et al.   BIOINFORMATICS

Prediction of protein binding sites in protein structures using hidden Markov support vector machine

(2009) Bin Liu et al.   BMC BIOINFORMATICS

Prediction of protein-protein interaction sites using an ensemble method

(2009) Lei Deng et al.   BMC BIOINFORMATICS

Epitopia: a web-server for predicting B-cell epitopes

(2009) Nimrod D Rubinstein et al.   BMC BIOINFORMATICS

Prediction of antigenic epitopes on protein surfaces by consensus scoring

(2009) Shide Liang et al.   BMC BIOINFORMATICS

A survey of available tools and web servers for analysis of protein-protein interactions and interfaces

(2009) N. Tuncbag et al.   BRIEFINGS IN BIOINFORMATICS

Progress and challenges in predicting protein-protein interaction sites

(2009) I. Ezkurdia et al.   BRIEFINGS IN BIOINFORMATICS

A simple and efficient method for predicting protein-protein interaction sites

(2009) R.H. Higa et al.   GENETICS AND MOLECULAR RESEARCH

Inferred Biomolecular Interaction Server—a web server to analyze and predict protein interacting partners and binding sites

(2009) Benjamin A. Shoemaker et al.   NUCLEIC ACIDS RESEARCH

IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF

(2009) François Ehrenmann et al.   NUCLEIC ACIDS RESEARCH

AntigenDB: an immunoinformatics database of pathogen antigens

(2009) Hifzur Rahman Ansari et al.   NUCLEIC ACIDS RESEARCH

SEPPA: a computational server for spatial epitope prediction of protein antigens

(2009) Jing Sun et al.   NUCLEIC ACIDS RESEARCH

The Immune Epitope Database 2.0

(2009) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

Structural relationships among proteins with different global topologies and their implications for function annotation strategies

(2009) D. Petrey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Stefan Engelen et al.   PLoS Computational Biology

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

(2009) Mile Šikić et al.   PLoS Computational Biology

PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure

(2008) Michael J. Sweredoski et al.   BIOINFORMATICS

Prediction of protein-protein binding site by using core interface residue and support vector machine

(2008) Nan Li et al.   BMC BIOINFORMATICS

PEPOP: Computational design of immunogenic peptides

(2008) Violaine Moreau et al.   BMC BIOINFORMATICS

ElliPro: a new structure-based tool for the prediction of antibody epitopes

(2008) Julia Ponomarenko et al.   BMC BIOINFORMATICS

How Proteins Get in Touch: Interface Prediction in the Study of Biomolecular Complexes

(2008) Sjoerd de Vries et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Using protein binding site prediction to improve protein docking

(2008) Bingding Huang et al.   GENE

Protein Surface Conservation in Binding Sites

(2008) Nejc Carl et al.   Journal of Chemical Information and Modeling

Protein-protein docking benchmark version 3.0

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

Side-chain conformational entropy at protein-protein interfaces

(2002) Christian Cole et al.   PROTEIN SCIENCE