Predicting Protein–Protein Interactions from the Molecular to the Proteome Level

Cytoscape: A software Environment for integrated models of biomolecular interaction networks

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The Protein Data Bank

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STRING v10: protein–protein interaction networks, integrated over the tree of life

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Inference of macromolecular assemblies from crystalline state.

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Alternative isoform regulation in human tissue transcriptomes

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A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae

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STRING v9.1: protein-protein interaction networks, with increased coverage and integration

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A comprehensive two-hybrid analysis to explore the yeast protein interactome

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Human Protein Reference Database--2009 update

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PatchDock and SymmDock: servers for rigid and symmetric docking

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The FoldX web server: an online force field

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Principles of protein-protein interactions

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Intrinsically disordered protein

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The Database of Interacting Proteins: 2004 update

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A draft map of the human proteome

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Classification of Intrinsically Disordered Regions and Proteins

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Protein structure prediction and analysis using the Robetta server

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Anatomy of hot spots in protein interfaces

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A Hot Spot of Binding Energy in a Hormone-Receptor Interface

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Reaching for high-hanging fruit in drug discovery at protein–protein interfaces

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Crystal structure of the ribosome at 5.5 Å resolution

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The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

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

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Mass-spectrometry-based draft of the human proteome

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

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Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

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Uncovering disease-disease relationships through the incomplete interactome

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

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The HADDOCK web server for data-driven biomolecular docking

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A Proteome-Scale Map of the Human Interactome Network

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CORUM: the comprehensive resource of mammalian protein complexes—2009

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The crystal structure of the asymmetric GroEL–GroES–(ADP)7 chaperonin complex

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Conservation of gene order: a fingerprint of proteins that physically interact.

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Protein interaction maps for complete genomes based on gene fusion events

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MINT, the molecular interaction database: 2012 update

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Identification of direct residue contacts in protein–protein interaction by message passing

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Predicting protein–protein interactions based only on sequences information

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A human phenome-interactome network of protein complexes implicated in genetic disorders

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Diversity of protein–protein interactions

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Ensembl 2014

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An empirical framework for binary interactome mapping

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The BioGRID interaction database: 2015 update

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ClusPro: an automated docking and discrimination method for the prediction of protein complexes

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Estimating the size of the human interactome

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A simple physical model for binding energy hot spots in protein–protein complexes

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Native mass spectrometry: a bridge between interactomics and structural biology

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Global landscape of HIV–human protein complexes

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Methods for the detection and analysis of protein–protein interactions

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

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FireDock: Fast interaction refinement in molecular docking

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ConsensusPathDB: toward a more complete picture of cell biology

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Relating Whole-Genome Expression Data with Protein-Protein InteractionsPreprint

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Reactome: a knowledge base of biologic pathways and processes

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The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins

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Book Review: Pattern Recognition and Machine Learning

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Scoring residue conservation

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PDBsum: a web-based database of summaries and analyses of all PDB structures

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Visualization of omics data for systems biology

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Protein–protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces

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The RosettaDock server for local protein-protein docking

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Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae

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Exploiting indirect neighbours and topological weight to predict protein function from protein–protein interactions

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The MIPS mammalian protein–protein interaction database

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Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

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Similarity of phylogenetic trees as indicator of protein–protein interaction

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On the binding affinity of macromolecular interactions: daring to ask why proteins interact

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Hot Regions in Protein–Protein Interactions: The Organization and Contribution of Structurally Conserved Hot Spot Residues

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Sequence co-evolution gives 3D contacts and structures of protein complexes

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Interactome3D: adding structural details to protein networks

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Protein–protein docking benchmark version 4.0

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Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights

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ZRANK: Reranking protein docking predictions with an optimized energy function

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A dissection of specific and non-specific protein-protein interfaces.

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Probing Native Protein Structures by Chemical Cross-linking, Mass Spectrometry, and Bioinformatics

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An experimentally derived confidence score for binary protein-protein interactions

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ProMate: A Structure Based Prediction Program to Identify the Location of Protein–Protein Binding Sites

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Functional topology in a network of protein interactions

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Updates to the integrated protein-protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2

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Mass Spectrometry–Based Proteomics and Network Biology

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ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions

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How complete are current yeast and human protein-interaction networks?

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Assessing experimentally derived interactions in a small world

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Structure, function, and evolution of transient and obligate protein–protein interactions

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pyDock: Electrostatics and desolvation for effective scoring of rigid‐body protein–protein docking

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HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores

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Phosphorylation in protein-protein binding: effect on stability and function

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Protein-Protein Docking: From Interaction to Interactome

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A structure‐based benchmark for protein–protein binding affinity

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3did: a catalog of domain-based interactions of known three-dimensional structure

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Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2

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Computational alanine scanning of the 1:1 human growth hormone–receptor complex

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PDBsum additions

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SwarmDock: a server for flexible protein–protein docking

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Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity

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SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models

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Dissecting subunit interfaces in homodimeric proteins

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