Domain-mediated protein interaction prediction: From genome to network

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

(2012) Xiujuan Wang et al.   NATURE BIOTECHNOLOGY

Overview of the BioCreative III Workshop

(2011) Cecilia N Arighi et al.   BMC BIOINFORMATICS

Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis

(2011) Renu Goel et al.   Molecular BioSystems

The multiple-specificity landscape of modular peptide recognition domains

(2011) D. Gfeller et al.   Molecular Systems Biology

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

g:Profiler—a web server for functional interpretation of gene lists (2011 update)

(2011) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

Bringing order to protein disorder through comparative genomics and genetic interactions

(2011) Jeremy Bellay et al.   GENOME BIOLOGY

A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain–peptide interaction from primary sequence

(2010) Xiaojian Shao et al.   BIOINFORMATICS

Large-scale prediction of protein-protein interactions from structures

(2010) Martial Hue et al.   BMC BIOINFORMATICS

An improved method for scoring protein-protein interactions using semantic similarity within the Gene Ontology

(2010) Shobhit Jain et al.   BMC BIOINFORMATICS

Predicting protein-protein interactions in unbalanced data using the primary structure of proteins

(2010) Chi-Yuan Yu et al.   BMC BIOINFORMATICS

PDZ domains and their binding partners: structure, specificity, and modification

(2010) Ho-Jin Lee et al.   Cell Communication and Signaling

Structure-Based Prediction of the Peptide Sequence Space Recognized by Natural and Synthetic PDZ Domains

(2010) Colin A. Smith et al.   JOURNAL OF MOLECULAR BIOLOGY

A physical model for PDZ-domain/peptide interactions

(2010) Kristian Kaufmann et al.   JOURNAL OF MOLECULAR MODELING

Topological network alignment uncovers biological function and phylogeny

(2010) O. Kuchaiev et al.   Journal of the Royal Society Interface

A Novel Method to Detect Proteins Evolving at Correlated Rates: Identifying New Functional Relationships between Coevolving Proteins

(2010) Nathaniel L. Clark et al.   MOLECULAR BIOLOGY AND EVOLUTION

Deciphering the splicing code

(2010) Yoseph Barash et al.   NATURE

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Docking and scoring protein interactions: CAPRI 2009

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

Ranking Genes by Their Co-expression to Subsets of Pathway Members

(2009) Priit Adler et al.   Annals of the New York Academy of Sciences

Modeling Effects of Human Single Nucleotide Polymorphisms on Protein-Protein Interactions

(2009) Shaolei Teng et al.   BIOPHYSICAL JOURNAL

A structure filter for the Eukaryotic Linear Motif Resource

(2009) Allegra Via et al.   BMC BIOINFORMATICS

Protein structure prediction: when is it useful?

(2009) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structure-Based Prediction of the Saccharomyces cerevisiae SH3–Ligand Interactions

(2009) Gregorio Fernandez-Ballester et al.   JOURNAL OF MOLECULAR BIOLOGY

A machine learning based method for the prediction of G protein-coupled receptor-binding PDZ domain proteins

(2009) Hae-Seok Eo et al.   MOLECULES AND CELLS

Using genome-wide measurements for computational prediction of SH2–peptide interactions

(2009) Zeba Wunderlich et al.   NUCLEIC ACIDS RESEARCH

The Negatome database: a reference set of non-interacting protein pairs

(2009) Pawel Smialowski et al.   NUCLEIC ACIDS RESEARCH

Exploiting Amino Acid Composition for Predicting Protein-Protein Interactions

(2009) Sushmita Roy et al.   PLoS One

DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility

(2009) Iris Antes   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins

(2009) Raffi Tonikian et al.   PLOS BIOLOGY

Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data

(2008) Tao Xu et al.   BMC BIOINFORMATICS

iRefIndex: A consolidated protein interaction database with provenance

(2008) Sabry Razick et al.   BMC BIOINFORMATICS

PRINCESS, a Protein Interaction Confidence Evaluation System with Multiple Data Sources

(2008) Dong Li et al.   MOLECULAR & CELLULAR PROTEOMICS

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

Predicting PDZ domain–peptide interactions from primary sequences

(2008) Jiunn R Chen et al.   NATURE BIOTECHNOLOGY

Patterns of co-expression for protein complexes by size in Saccharomyces cerevisiae

(2008) Ching-Ti Liu et al.   NUCLEIC ACIDS RESEARCH

Using support vector machine combined with auto covariance to predict protein–protein interactions from protein sequences

(2008) Yanzhi Guo et al.   NUCLEIC ACIDS RESEARCH

McKusick's Online Mendelian Inheritance in Man (OMIM(R))

(2008) J. Amberger et al.   NUCLEIC ACIDS RESEARCH

Reactome knowledgebase of human biological pathways and processes

(2008) L. Matthews et al.   NUCLEIC ACIDS RESEARCH

Global alignment of multiple protein interaction networks with application to functional orthology detection

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

A Specificity Map for the PDZ Domain Family

(2008) Raffi Tonikian et al.   PLOS BIOLOGY

Genome-Wide Prediction of SH2 Domain Targets Using Structural Information and the FoldX Algorithm

(2008) Ignacio E. Sánchez et al.   PLoS Computational Biology

Protein interactions in human genetic diseases

(2008) Benjamin Schuster-Böckler et al.   GENOME BIOLOGY

Sequence-based prediction of protein-protein interactions by means of codon usage

(2008) Hamed Najafabadi et al.   GENOME BIOLOGY