A computational framework for boosting confidence in high-throughput protein-protein interaction datasets

SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone

(2012) N. M. Daniels et al.   BIOINFORMATICS

Large-scale mapping of human protein interactome using structural complexes

(2012) Manoj Tyagi et al.   EMBO REPORTS

Dynamic Protein-Protein Interaction Wiring of the Human Spliceosome

(2012) Anna Hegele et al.   MOLECULAR CELL

Three-dimensional reconstruction of protein networks provides insight into human genetic disease

(2012) Xiujuan Wang et al.   NATURE BIOTECHNOLOGY

New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size

(2011) Laure Sambourg et al.   BMC BIOINFORMATICS

Challenges for the prediction of macromolecular interactions

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

Three-dimensional modeling of protein interactions and complexes is going ‘omics

(2011) Amelie Stein 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

Raptorx: Exploiting structure information for protein alignment by statistical inference

(2011) Jian Peng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2011) Srayanta Mukherjee et al.   STRUCTURE

Phosphorylation in Protein-Protein Binding: Effect on Stability and Function

(2011) Hafumi Nishi et al.   STRUCTURE

Activation Loop Phosphorylation of ERK3/ERK4 by Group I p21-activated Kinases (PAKs) Defines a Novel PAK-ERK3/4-MAPK-activated Protein Kinase 5 Signaling Pathway

(2010) Paul Déléris et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

iWRAP: An Interface Threading Approach with Application to Prediction of Cancer-Related Protein–Protein Interactions

(2010) Raghavendra Hosur et al.   JOURNAL OF MOLECULAR BIOLOGY

Predicting protein–protein interaction specificity through the integration of three-dimensional structural information and the evolutionary record of protein domains

(2010) Alejandro Panjkovich et al.   Molecular BioSystems

SAINT: probabilistic scoring of affinity purification–mass spectrometry data

(2010) Hyungwon Choi et al.   NATURE METHODS

A human MAP kinase interactome

(2010) Sourav Bandyopadhyay et al.   NATURE METHODS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Struct2Net: a web service to predict protein-protein interactions using a structure-based approach

(2010) R. Singh et al.   NUCLEIC ACIDS RESEARCH

ADAN: a database for prediction of protein-protein interaction of modular domains mediated by linear motifs

(2009) J. A. Encinar et al.   BIOINFORMATICS

hPDI: a database of experimental human protein-DNA interactions

(2009) Z. Xie et al.   BIOINFORMATICS

Augmented training of hidden Markov models to recognize remote homologs via simulated evolution

(2009) A. Kumar et al.   BIOINFORMATICS

Large-scale Proteomics Analysis of the Human Kinome

(2009) Felix S. Oppermann et al.   MOLECULAR & CELLULAR PROTEOMICS

Combining multiple positive training sets to generate confidence scores for protein–protein interactions

(2008) Jingkai Yu et al.   BIOINFORMATICS

Optimal contact map alignment of protein-protein interfaces

(2008) V. Pulim et al.   BIOINFORMATICS

Precision and recall estimates for two-hybrid screens

(2008) Hailiang Huang et al.   BIOINFORMATICS

Correlated Evolution of Interacting Proteins: Looking Behind the Mirrortree

(2008) Maricel G. Kann et al.   JOURNAL OF MOLECULAR BIOLOGY

Targeting the Human Cancer Pathway Protein Interaction Network by Structural Genomics

(2008) Yuanpeng Janet Huang et al.   MOLECULAR & CELLULAR PROTEOMICS

Cost-effective strategies for completing the interactome

(2008) Ariel S Schwartz et al.   NATURE METHODS

Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network

(2008) Nicolas Simonis et al.   NATURE METHODS

An experimentally derived confidence score for binary protein-protein interactions

(2008) Pascal Braun et al.   NATURE METHODS

Literature-curated protein interaction datasets

(2008) Michael E Cusick et al.   NATURE METHODS

A quantitative atlas of mitotic phosphorylation

(2008) N. Dephoure et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative assessment of the structural bias in protein-protein interaction assays

(2008) Åsa K. Björklund et al.   PROTEOMICS

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

(2008) H. Yu et al.   SCIENCE

LTHREADER: Prediction of extracellular ligand-receptor interactions in cytokines using localized threading

(2007) Vinay Pulim et al.   PROTEIN SCIENCE