PRISM: a web server and repository for prediction of protein–protein interactions and modeling their 3D complexes

Non-Redundant Unique Interface Structures as Templates for Modeling Protein Interactions

(2014) Engin Cukuroglu et al.   PLoS One

JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied toProteopedia

(2013) Robert M. Hanson et al.   ISRAEL JOURNAL OF CHEMISTRY

Mapping Monomeric Threading to Protein–Protein Structure Prediction

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

Exploiting Conformational Ensembles in Modeling Protein–Protein Interactions on the Proteome Scale

(2013) Guray Kuzu et al.   JOURNAL OF PROTEOME RESEARCH

Global and local structural similarity in protein-protein complexes: Implications for template-based docking

(2013) Petras J. Kundrotas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Interactome3D: adding structural details to protein networks

(2012) Roberto Mosca et al.   NATURE METHODS

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

HotRegion: a database of predicted hot spot clusters

(2011) E. Cukuroglu et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement

(2011) Nurcan Tuncbag et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2011) Srayanta Mukherjee et al.   STRUCTURE

Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy

(2009) Nurcan Tuncbag et al.   BIOINFORMATICS

An empirical framework for binary interactome mapping

(2008) Kavitha Venkatesan et al.   NATURE METHODS

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