Structural Bioinformatics of the Interactome

Deciphering the host-pathogen protein interface in chikungunya virus-mediated sickness

(2013) Jyoti Rana et al.   ARCHIVES OF VIROLOGY

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

(2013) Michael J. Meyer et al.   BIOINFORMATICS

Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding

(2013) Carlo Vittorio Cannistraci et al.   BIOINFORMATICS

Drug–target interaction prediction through domain-tuned network-based inference

(2013) Salvatore Alaimo et al.   BIOINFORMATICS

Predicting PDZ domain mediated protein interactions from structure

(2013) Shirley Hui et al.   BMC BIOINFORMATICS

Inferring homologous protein-protein interactions through pair position specific scoring matrix

(2013) Chun-Yu Lin et al.   BMC BIOINFORMATICS

Learning a peptide-protein binding affinity predictor with kernel ridge regression

(2013) Sébastien Giguère et al.   BMC BIOINFORMATICS

Prediction of protein-protein interactions from amino acid sequences with ensemble extreme learning machines and principal component analysis

(2013) Zhu-Hong You et al.   BMC BIOINFORMATICS

Pathogens Use Structural Mimicry of Native Host Ligands as a Mechanism for Host Receptor Engagement

(2013) Nir Drayman et al.   Cell Host & Microbe

Structural Systems Pharmacology: The Role of 3D Structures in Next-Generation Drug Development

(2013) Miquel Duran-Frigola et al.   CHEMISTRY & BIOLOGY

Assessment of high-confidence protein–protein interactome in yeast

(2013) Kubra Karagoz et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Compound promiscuity: what can we learn from current data?

(2013) Ye Hu et al.   DRUG DISCOVERY TODAY

Shifting from the single to the multitarget paradigm in drug discovery

(2013) José L. Medina-Franco et al.   DRUG DISCOVERY TODAY

Extracting a few functionally reproducible biomarkers to build robust subnetwork-based classifiers for the diagnosis of cancer

(2013) Lin Zhang et al.   GENE

PPIevo : Protein–protein interaction prediction from PSSM based evolutionary information

(2013) Javad Zahiri et al.   GENOMICS

Mapping Monomeric Threading to Protein–Protein Structure Prediction

(2013) Aysam Guerler et al.   Journal of Chemical Information and Modeling

A novel method based on new adaptive LVQ neural network for predicting protein–protein interactions from protein sequences

(2013) Abdulaziz Yousef et al.   JOURNAL OF THEORETICAL BIOLOGY

From Systems to Structure: Bridging Networks and Mechanism

(2013) James S. Fraser et al.   MOLECULAR CELL

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

Evaluation of Physical and Functional Protein-Protein Interaction Prediction Methods for Detecting Biological Pathways

(2013) Vijaykumar Yogesh Muley et al.   PLoS One

The Development of a Universal In Silico Predictor of Protein-Protein Interactions

(2013) Guilherme T. Valente et al.   PLoS One

Characterizing Genes with Distinct Methylation Patterns in the Context of Protein-Protein Interaction Network: Application to Human Brain Tissues

(2013) Yongsheng Li et al.   PLoS One

Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli

(2013) R. L. Chang et al.   SCIENCE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Cancer networks and beyond: Interpreting mutations using the human interactome and protein structure

(2013) Sakshi Gulati et al.   SEMINARS IN CANCER BIOLOGY

Targeting protein–protein interactions as an anticancer strategy

(2013) Andrei A. Ivanov et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Interpretation of Genomic Variants Using a Unified Biological Network Approach

(2013) Ekta Khurana et al.   PLoS Computational Biology

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

(2013) Raghavendra Hosur et al.   GENOME BIOLOGY

Bridging the Gap between Genotype and Phenotype via Network Approaches

(2013) Yoo-Ah Kim et al.   Frontiers in Genetics

Large-scale prediction of drug–target interactions using protein sequences and drug topological structures

(2012) Dong-Sheng Cao et al.   ANALYTICA CHIMICA ACTA

Human protein–protein interaction prediction by a novel sequence-based co-evolution method: co-evolutionary divergence

(2012) Chia Hsin Liu et al.   BIOINFORMATICS

Inferring high-confidence human protein-protein interactions

(2012) Xueping Yu et al.   BMC BIOINFORMATICS

Prediction of protein-protein interactions between viruses and human by an SVM model

(2012) Guangyu Cui et al.   BMC BIOINFORMATICS

Studying protein-protein interaction networks: a systems view on diseases

(2012) F. Jordan et al.   Briefings in Functional Genomics

Sequential Application of Anticancer Drugs Enhances Cell Death by Rewiring Apoptotic Signaling Networks

(2012) Michael J. Lee et al.   CELL

Constructing structural networks of signaling pathways on the proteome scale

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

Large-scale mapping of human protein interactome using structural complexes

(2012) Manoj Tyagi et al.   EMBO REPORTS

From protein interaction networks to novel therapeutic strategies

(2012) Samira Jaeger et al.   IUBMB LIFE

Transcriptional Network Analysis Identifies BACH1 as a Master Regulator of Breast Cancer Bone Metastasis

(2012) Yajun Liang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Analyzing Protein–Protein Interaction Networks

(2012) Gavin C. K. W. Koh et al.   JOURNAL OF PROTEOME RESEARCH

Enriching the human apoptosis pathway by predicting the structures of protein–protein complexes

(2012) Saliha Ece Acuner Ozbabacan et al.   JOURNAL OF STRUCTURAL BIOLOGY

Bioinformatics and variability in drug response: a protein structural perspective

(2012) J. L. Lahti et al.   Journal of the Royal Society Interface

Computational analysis of interactomes: Current and future perspectives for bioinformatics approaches to model the host–pathogen interaction space

(2012) Roland Arnold et al.   METHODS

Advances in integrative modeling of biomolecular complexes

(2012) Ezgi Karaca et al.   METHODS

Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions

(2012) David Ochoa et al.   Molecular BioSystems

Networks of ProteinProtein Interactions: From Uncertainty to Molecular Details

(2012) Javier Garcia-Garcia et al.   Molecular Informatics

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

Leveraging models of cell regulation and GWAS data in integrative network-based association studies

(2012) Andrea Califano et al.   NATURE GENETICS

Interactome3D: adding structural details to protein networks

(2012) Roberto Mosca et al.   NATURE METHODS

Reverse engineering and analysis of large genome-scale gene networks

(2012) Maneesha Aluru et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Qiangfeng Cliff Zhang 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

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores

(2012) Martin H. Schaefer et al.   PLoS One

Prediction of Chemical-Protein Interactions Network with Weighted Network-Based Inference Method

(2012) Feixiong Cheng 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

IDDI: integrated domain-domain interaction and protein interaction analysis system

(2012) Yul Kim et al.   Proteome Science

Computational structural analysis of protein interactions and networks

(2012) Yogesh Hooda et al.   PROTEOMICS

Heterogeneous data integration by tree-augmented naïve Bayes for protein-protein interactions prediction

(2012) Xiaotong Lin et al.   PROTEOMICS

Human diseases through the lens of network biology

(2012) Laura I. Furlong   TRENDS IN GENETICS

Kaposi’s sarcoma: a computational approach through protein–protein interaction and gene regulatory networks analysis

(2012) Aubhishek Zaman et al.   VIRUS GENES

Predicting the Fission Yeast Protein Interaction Network

(2012) Vera Pancaldi et al.   G3-Genes Genomes Genetics

Chapter 4: Protein Interactions and Disease

(2012) Mileidy W. Gonzalez et al.   PLoS Computational Biology

Chapter 5: Network Biology Approach to Complex Diseases

(2012) Dong-Yeon Cho et al.   PLoS Computational Biology

Proteome-wide prediction of protein-protein interactions from high-throughput data

(2012) Zhi-Ping Liu et al.   Protein & Cell

Toward a three-dimensional view of protein networks between species

(2012) Eric A. Franzosa et al.   Frontiers in Microbiology

Gene Ontology-driven inference of protein–protein interactions using inducers

(2011) Stefan R. Maetschke et al.   BIOINFORMATICS

Gaussian interaction profile kernels for predicting drug–target interaction

(2011) Twan van Laarhoven et al.   BIOINFORMATICS

Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database

(2011) George R Bickerton et al.   BMC BIOINFORMATICS

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Structure-based systems biology for analyzing off-target binding

(2011) Lei Xie et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Recent advances in protein–protein interaction prediction: experimental and computational methods

(2011) Matthew Jessulat et al.   Expert Opinion on Drug Discovery

De novo discovery of mutated driver pathways in cancer

(2011) F. Vandin et al.   GENOME RESEARCH

Supervised learning and prediction of physical interactions between human and HIV proteins

(2011) Matthew D. Dyer et al.   INFECTION GENETICS AND EVOLUTION

Human Proteome-scale Structural Modeling of E2–E3 Interactions Exploiting Interface Motifs

(2011) Gozde Kar et al.   JOURNAL OF PROTEOME RESEARCH

From in silico target prediction to multi-target drug design: Current databases, methods and applications

(2011) Alexios Koutsoukas et al.   Journal of Proteomics

Large-scaleDe NovoPrediction of Physical Protein-Protein Association

(2011) Antigoni Elefsinioti et al.   MOLECULAR & CELLULAR PROTEOMICS

Towards the prediction of protein interaction partners using physical docking

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

Structural and functional protein network analyses predict novel signaling functions for rhodopsin

(2011) C. Kiel et al.   Molecular Systems Biology

Analysis of multiple compound-protein interactions reveals novel bioactive molecules

(2011) H. Yabuuchi et al.   Molecular Systems 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

Rare De Novo Variants Associated with Autism Implicate a Large Functional Network of Genes Involved in Formation and Function of Synapses

(2011) Sarah R. Gilman et al.   NEURON

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

Transferring network topological knowledge for predicting protein-protein interactions

(2011) Qian Xu et al.   PROTEOMICS

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

(2011) Srayanta Mukherjee et al.   STRUCTURE

CAERUS: Predicting CAncER oUtcomeS Using Relationship between Protein Structural Information, Protein Networks, Gene Expression Data, and Mutation Data

(2011) Kelvin Xi Zhang et al.   PLoS Computational Biology

Identifying Causal Genes and Dysregulated Pathways in Complex Diseases

(2011) Yoo-Ah Kim et al.   PLoS Computational Biology

Genome-Wide Association Studies and Beyond

(2010) John S. Witte   Annual Review of Public Health

geWorkbench: an open source platform for integrative genomics

(2010) Aris Floratos et al.   BIOINFORMATICS

Large-scale prediction of protein-protein interactions from structures

(2010) Martial Hue 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

An Integrated Approach to Uncover Drivers of Cancer

(2010) Uri David Akavia et al.   CELL

Machine learning in drug discovery and development

(2010) Nikil Wale   DRUG DEVELOPMENT RESEARCH

Computational Tools for the Interactive Exploration of Proteomic and Structural Data

(2010) John H. Morris et al.   MOLECULAR & CELLULAR PROTEOMICS

Proof of Concept: Network and Systems Biology Approaches Aid in the Discovery of Potent Anticancer Drug Combinations

(2010) A. S. Azmi et al.   MOLECULAR CANCER THERAPEUTICS

A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers

(2010) Celine Lefebvre et al.   Molecular Systems Biology

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

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

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

ModBase, a database of annotated comparative protein structure models, and associated resources

(2010) U. Pieper et al.   NUCLEIC ACIDS RESEARCH

The protein common interface database (ProtCID)--a comprehensive database of interactions of homologous proteins in multiple crystal forms

(2010) Q. Xu et al.   NUCLEIC ACIDS RESEARCH

Large-Scale Discovery and Characterization of Protein Regulatory Motifs in Eukaryotes

(2010) Daniel S. Lieber et al.   PLoS One

DEGAS: De Novo Discovery of Dysregulated Pathways in Human Diseases

(2010) Igor Ulitsky et al.   PLoS One

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

Accumulation of driver and passenger mutations during tumor progression

(2010) I. Bozic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unveiling the role of network and systems biology in drug discovery

(2010) Albert Pujol et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens

(2010) Janet M Doolittle et al.   Virology Journal

Literature curation of protein interactions: measuring agreement across major public databases

(2010) A. L. Turinsky et al.   Database-The Journal of Biological Databases and Curation

Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks

(2010) Sumeet Agarwal et al.   PLoS Computational Biology

Protein–Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks

(2010) Javier De Las Rivas et al.   PLoS Computational Biology

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

(2009) Xue-wen Chen et al.   BIOINFORMATICS

Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression

(2009) Stefanie De Bodt et al.   BMC GENOMICS

Machine Learning in Virtual Screening

(2009) James Melville et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Is protein classification necessary? Toward alternative approaches to function annotation

(2009) Donald Petrey et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Novel web-based tools combining chemistry informatics, biology and social networks for drug discovery

(2009) Moses Hohman et al.   DRUG DISCOVERY TODAY

Towards inferring time dimensionality in protein–protein interaction networks by integrating structures: the p53 example

(2009) Nurcan Tuncbag et al.   Molecular BioSystems

Predicting protein–protein interactions in the context of protein evolution

(2009) Anna C. F. Lewis et al.   Molecular BioSystems

Molecular networks as sensors and drivers of common human diseases

(2009) Eric E. Schadt   NATURE

Genome-wide identification of post-translational modulators of transcription factor activity in human B cells

(2009) Kai Wang et al.   NATURE BIOTECHNOLOGY

GWIDD: Genome-wide protein docking database

(2009) Petras J. Kundrotas et al.   NUCLEIC ACIDS RESEARCH

Protinfo PPC: A web server for atomic level prediction of protein complexes

(2009) Weerayuth Kittichotirat et al.   NUCLEIC ACIDS RESEARCH

Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments

(2009) Roberto Mosca et al.   PLoS Computational Biology

Human Cancer Protein-Protein Interaction Network: A Structural Perspective

(2009) Gozde Kar et al.   PLoS Computational Biology

Enhancing the prediction of protein pairings between interacting families using orthology information

(2008) Jose MG Izarzugaza et al.   BMC BIOINFORMATICS

Predicting biological networks from genomic data

(2008) Eoghan D. Harrington et al.   FEBS LETTERS

Network medicine

(2008) Tony Pawson et al.   FEBS LETTERS

Protein networks in disease

(2008) T. Ideker et al.   GENOME RESEARCH

A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas

(2008) Kartik M Mani et al.   Molecular Systems Biology

Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method

(2008) Lukas Burger et al.   Molecular Systems Biology

Regulatory networks define phenotypic classes of human stem cell lines

(2008) Franz-Josef Müller et al.   NATURE

Targeting and tinkering with interaction networks

(2008) Robert B Russell et al.   Nature Chemical Biology

Network pharmacology: the next paradigm in drug discovery

(2008) Andrew L Hopkins   Nature Chemical Biology

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

(2008) Jun Zhu et al.   NATURE GENETICS

An experimentally derived confidence score for binary protein-protein interactions

(2008) Pascal Braun et al.   NATURE METHODS

PIPs: human protein-protein interaction prediction database

(2008) M. D. McDowall et al.   NUCLEIC ACIDS RESEARCH

High-confidence prediction of global interactomes based on genome-wide coevolutionary networks

(2008) D. Juan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA