Elucidating the druggable interface of protein−protein interactions using fragment docking and coevolutionary analysis

Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes

(2016) R. R. Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules

(2016) Haim Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

Gd–Metallofullerenol Nanomaterial Suppresses Pancreatic Cancer Metastasis by Inhibiting the Interaction of Histone Deacetylase 1 and Metastasis-Associated Protein 1

(2015) Yuanming Pan et al.   ACS Nano

Predicting protein interface residues using easily accessible on-line resources

(2015) S. Maheshwari et al.   BRIEFINGS IN BIOINFORMATICS

Structure-based inhibition of protein–protein interactions

(2015) Andrew M. Watkins et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Computational prediction of protein interfaces: A review of data driven methods

(2015) Li C. Xue et al.   FEBS LETTERS

Prediction of protein-protein interaction sites from weakly homologous template structures using meta-threading and machine learning

(2015) Surabhi Maheshwari et al.   JOURNAL OF MOLECULAR RECOGNITION

The Fe-S cluster-containing NEET proteins mitoNEET and NAF-1 as chemotherapeutic targets in breast cancer

(2015) Fang Bai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CDK1 structures reveal conserved and unique features of the essential cell cycle CDK

(2015) Nicholas R. Brown et al.   Nature Communications

Dimeric interactions and complex formation using direct coevolutionary couplings

(2015) Ricardo N. dos Santos et al.   Scientific Reports

Protein-Protein Docking: From Interaction to Interactome

(2014) Ilya A. Vakser   BIOPHYSICAL JOURNAL

Dimerization of HIV-1 protease occurs through two steps relating to the mechanism of protease dimerization inhibition by darunavir

(2014) H. Hayashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrated strategy reveals the protein interface between cancer targets Bcl-2 and NAF-1

(2014) S. Tamir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information

(2014) Ryan R. Cheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Thomas A Hopf et al.   eLife

Targeting Protein-Protein Interaction by Small Molecules

(2013) Lingyan Jin et al.   Annual Review of Pharmacology and Toxicology

A dual role for Hdac1: oncosuppressor in tumorigenesis, oncogene in tumor maintenance

(2013) F. Santoro et al.   BLOOD

Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

Free energy landscape for the binding process of Huperzine A to acetylcholinesterase

(2013) Fang Bai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coevolutionary signals across protein lineages help capture multiple protein conformations

(2013) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeting protein–protein interactions as an anticancer strategy

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

Fragment-Based Approaches in Drug Discovery and Chemical Biology

(2012) Duncan E. Scott et al.   BIOCHEMISTRY

Predicting protein-protein interface residues using local surface structural similarity

(2012) Rafael A Jordan et al.   BMC BIOINFORMATICS

How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis

(2012) Mauno Vihinen   BMC GENOMICS

Computational Prediction of Protein Hot Spot Residues

(2012) John Kenneth Morrow et al.   CURRENT PHARMACEUTICAL DESIGN

Activation of the p53 pathway by small-molecule-induced MDM2 and MDMX dimerization

(2012) B. Graves et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomics-aided structure prediction

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

Structural biology and drug discovery for protein–protein interactions

(2012) Harry Jubb et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi diagrams

(2011) Joan Segura et al.   BMC BIOINFORMATICS

Sequencing technologies and genome sequencing

(2011) Chandra Shekhar Pareek et al.   JOURNAL OF APPLIED GENETICS

PredUs: a web server for predicting protein interfaces using structural neighbors

(2011) Q. C. Zhang et al.   NUCLEIC ACIDS RESEARCH

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural conservation of druggable hot spots in protein-protein interfaces

(2011) D. Kozakov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeting protein–protein interactions for therapeutic intervention: a challenge for the future

(2010) Giovanna Zinzalla et al.   Future Medicinal Chemistry

An Integrated View of Molecular Coevolution in Protein-Protein Interactions

(2010) S. C. Lovell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Progress and challenges in predicting protein-protein interaction sites

(2009) I. Ezkurdia et al.   BRIEFINGS IN BIOINFORMATICS

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

Inferred Biomolecular Interaction Server—a web server to analyze and predict protein interacting partners and binding sites

(2009) Benjamin A. Shoemaker et al.   NUCLEIC ACIDS RESEARCH

High-resolution protein complexes from integrating genomic information with molecular simulation

(2009) Alexander Schug et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human Protein Reference Database--2009 update

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

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

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