Protein–protein interaction networks studies and importance of 3D structure knowledge

Dissecting Disease Inheritance Modes in a Three-Dimensional Protein Network Challenges the “Guilt-by-Association” Principle

(2013) Yu Guo et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes

(2013) Romain A. Studer et al.   BIOCHEMICAL JOURNAL

INstruct: a database of high-quality 3D structurally resolved protein interactome networks

(2013) Michael J. Meyer et al.   BIOINFORMATICS

Allostery in Disease and in Drug Discovery

(2013) Ruth Nussinov et al.   CELL

Protein–protein interactions as druggable targets: recent technological advances

(2013) Alicia P Higueruelo et al.   CURRENT OPINION IN PHARMACOLOGY

Molecular Mechanisms of Disease-Causing Missense Mutations

(2013) Shannon Stefl et al.   JOURNAL OF MOLECULAR BIOLOGY

Inhibition of α-helix-mediated protein–protein interactions using designed molecules

(2013) Valeria Azzarito et al.   Nature Chemistry

Reproducibility restored—on toward the human interactome

(2013) Pascal Braun   NATURE METHODS

Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS

(2013) Markku Varjosalo et al.   NATURE METHODS

Emerging methods in protein co-evolution

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

Structure and dynamics of molecular networks: A novel paradigm of drug discovery

(2013) Peter Csermely et al.   PHARMACOLOGY & THERAPEUTICS

Cancer Missense Mutations Alter Binding Properties of Proteins and Their Interaction Networks

(2013) Hafumi Nishi et al.   PLoS One

Protein Modeling: What Happened to the “Protein Structure Gap”?

(2013) Torsten Schwede   STRUCTURE

A Census of Human Soluble Protein Complexes

(2012) Pierre C. Havugimana et al.   CELL

Oncogenic Mutations Counteract Intrinsic Disorder in the EGFR Kinase and Promote Receptor Dimerization

(2012) Yibing Shan et al.   CELL

Constructing structural networks of signaling pathways on the proteome scale

(2012) Guray Kuzu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A Strategy Based on Protein–Protein Interface Motifs May Help in Identifying Drug Off-Targets

(2012) H. Billur Engin et al.   Journal of Chemical Information and Modeling

Protein interactions in 3D: From interface evolution to drug discovery

(2012) Christof Winter et al.   JOURNAL OF STRUCTURAL BIOLOGY

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

(2012) P. L. Kastritis et al.   Journal of the Royal Society Interface

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

(2012) Qiangfeng Cliff Zhang et al.   NATURE

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

(2012) Xiujuan Wang et al.   NATURE BIOTECHNOLOGY

Interactome3D: adding structural details to protein networks

(2012) Roberto Mosca et al.   NATURE METHODS

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

(2012) Sandra Orchard et al.   NATURE METHODS

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

(2012) Tony E. Lewis et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2013 update

(2012) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

B-RAF Mutant Alleles Associated with Langerhans Cell Histiocytosis, a Granulomatous Pediatric Disease

(2012) Takeshi Satoh et al.   PLoS One

Templates are available to model nearly all complexes of structurally characterized proteins

(2012) P. J. Kundrotas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational structural analysis of protein interactions and networks

(2012) Yogesh Hooda et al.   PROTEOMICS

Molecular interaction databases

(2012) Sandra Orchard   PROTEOMICS

An integrated analysis of germline and somatic, genetic and epigenetic alterations at 9p21.3 in glioblastoma

(2011) Junjie Feng et al.   CANCER

Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs

(2011) Alessia David et al.   HUMAN MUTATION

Distinct Roles of Overlapping and Non-overlapping Regions of Hub Protein Interfaces in Recognition of Multiple Partners

(2011) Bhaskar Dasgupta et al.   JOURNAL OF MOLECULAR 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

The IntAct molecular interaction database in 2012

(2011) S. Kerrien et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Genetic dissection of the biotic stress response using a genome-scale gene network for rice

(2011) I. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Surface-based protein binding pocket similarity

(2011) Russell Spitzer et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

KFC2: A knowledge-based hot spot prediction method based on interface solvation, atomic density, and plasticity features

(2011) Xiaolei Zhu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Evidence for Network Evolution in an Arabidopsis Interactome Map

(2011) et al.   SCIENCE

A Targeted siRNA Screen Identifies Regulators of Cdc42 Activity at the Natural Killer Cell Immunological Synapse

(2011) L. M. Carlin et al.   Science Signaling

Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets

(2010) Hsiang Ho et al.   BMC Systems Biology

Hub Promiscuity in Protein-Protein Interaction Networks

(2010) Ashwini Patil et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Ten-year trends in hospital admissions for adverse drug reactions in England 1999–2009

(2010) Tai-Yin Wu et al.   JOURNAL OF THE ROYAL SOCIETY OF MEDICINE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

3did: identification and classification of domain-based interactions of known three-dimensional structure

(2010) A. Stein et al.   NUCLEIC ACIDS RESEARCH

FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking

(2010) E. Mashiach 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

Protein annotation and modelling servers at University College London

(2010) D. W. A. Buchan et al.   NUCLEIC ACIDS RESEARCH

Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected

(2010) M. Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Evolution of biomolecular networks — lessons from metabolic and protein interactions

(2009) Takuji Yamada et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Gene3D: merging structure and function for a Thousand genomes

(2009) Jonathan Lees et al.   NUCLEIC ACIDS RESEARCH

MINT, the molecular interaction database: 2009 update

(2009) Arnaud Ceol et al.   NUCLEIC ACIDS RESEARCH

Exploring functional roles of multibinding protein interfaces

(2009) Manoj Tyagi et al.   PROTEIN SCIENCE

Human Cancer Protein-Protein Interaction Network: A Structural Perspective

(2009) Gozde Kar et al.   PLoS Computational Biology

Topological properties of protein interaction networks from a structural perspective

(2008) Attila Gursoy et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

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

(2008) Ozlem Keskin et al.   CHEMICAL REVIEWS

Protein-protein interaction networks and biology—what's the connection?

(2008) Luke Hakes et al.   NATURE BIOTECHNOLOGY

An experimentally derived confidence score for binary protein-protein interactions

(2008) Pascal Braun et al.   NATURE METHODS

Activation of tyrosine kinases by mutation of the gatekeeper threonine

(2008) Mohammad Azam et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design

(2008) J. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimating the size of the human interactome

(2008) M. P. H. Stumpf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network properties of genes harboring inherited disease mutations

(2008) I. Feldman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phosphorylation Networks Regulating JNK Activity in Diverse Genetic Backgrounds

(2008) C. Bakal et al.   SCIENCE

From Genotype to Phenotype: Systems Biology Meets Natural Variation

(2008) P. N. Benfey et al.   SCIENCE

Low duplicability and network fragility of cancer genes

(2008) Davide Rambaldi et al.   TRENDS IN GENETICS

Protein interactions in human genetic diseases

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

Identification of transient hub proteins and the possible structural basis for their multiple interactions

(2007) Miho Higurashi et al.   PROTEIN SCIENCE