Modeling CAPRI targets 110-120 by template-based and free docking using contact potential and combined scoring function

Modeling complexes of modeled proteins

(2016) Ivan Anishchenko et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structural quality of unrefined models in protein docking

(2016) Ivan Anishchenko et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Simulated unbound structures for benchmarking of protein docking in the Dockground resource

(2015) Tatsiana Kirys et al.   BMC BIOINFORMATICS

New ways to boost molecular dynamics simulations

(2015) Elmar Krieger et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Template based protein structure modeling by global optimization in CASP11

(2015) Keehyoung Joo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structural templates for comparative protein docking

(2015) Ivan Anishchenko et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-Protein Docking: From Interaction to Interactome

(2014) Ilya A. Vakser   BIOPHYSICAL JOURNAL

Assessing the Applicability of Template-Based Protein Docking in the Twilight Zone

(2014) Jacopo Negroni et al.   STRUCTURE

Designing and evaluating the MULTICOM protein local and global model quality prediction methods in the CASP10 experiment

(2014) Renzhi Cao et al.   BMC STRUCTURAL BIOLOGY

Scoring functions for protein–protein interactions

(2013) Iain H Moal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structural templates for modeling homodimers

(2013) Petras J. Kundrotas et al.   PROTEIN SCIENCE

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

Protein Docking by the Interface Structure Similarity: How Much Structure Is Needed?

(2012) Rohita Sinha 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

DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking

(2011) Shiyong Liu et al.   BMC BIOINFORMATICS

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

Docking by structural similarity at protein-protein interfaces

(2010) Rohita Sinha et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking

(2008) Gwo-Yu Chuang et al.   BIOPHYSICAL JOURNAL

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

(2002) Hongyi Zhou et al.   PROTEIN SCIENCE