GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization

Predicting peptide binding sites on protein surfaces by clustering chemical interactions

(2014) Chengfei Yan et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces

(2014) Adrien Saladin et al.   NUCLEIC ACIDS RESEARCH

Protein Loop Modeling Using a New Hybrid Energy Function and Its Application to Modeling in Inaccurate Structural Environments

(2014) Hahnbeom Park et al.   PLoS One

Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how

(2013) Nir London et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

GalaxyRefine: protein structure refinement driven by side-chain repacking

(2013) Lim Heo et al.   NUCLEIC ACIDS RESEARCH

A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking

(2013) Mikael Trellet et al.   PLoS One

Detection of peptide-binding sites on protein surfaces: The first step toward the modeling and targeting of peptide-mediated interactions

(2013) Assaf Lavi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Docking, scoring, and affinity prediction in CAPRI

(2013) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

PepBind: A Comprehensive Database and Computational Tool for Analysis of Protein–peptide Interactions

(2013) Arindam Atanu Das et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions

(2012) Junsu Ko et al.   BMC BIOINFORMATICS

GalaxyWEB server for protein structure prediction and refinement

(2012) J. Ko et al.   NUCLEIC ACIDS RESEARCH

PepSite: prediction of peptide-binding sites from protein surfaces

(2012) L. G. Trabuco et al.   NUCLEIC ACIDS RESEARCH

PepCrawler: a fast RRT-based algorithm for high-resolution refinement and binding affinity estimation of peptide inhibitors

(2011) E. Donsky et al.   BIOINFORMATICS

How phosphorylation controls p53

(2011) Nicola J. Maclaine et al.   CELL CYCLE

Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions

(2011) Nir London et al.   NUCLEIC ACIDS RESEARCH

Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors

(2011) Barak Raveh et al.   PLoS One

Refinement of protein termini in template-based modeling using conformational space annealing

(2011) Hahnbeom Park et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Sub-angstrom modeling of complexes between flexible peptides and globular proteins

(2010) Barak Raveh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Structural Basis of Peptide-Protein Binding Strategies

(2010) Nir London et al.   STRUCTURE

Synthetic therapeutic peptides: science and market

(2009) Patrick Vlieghe et al.   DRUG DISCOVERY TODAY

Cell Signaling in Space and Time: Where Proteins Come Together and When They're Apart

(2009) J. D. Scott et al.   SCIENCE

Accurate Prediction of Peptide Binding Sites on Protein Surfaces

(2009) Evangelia Petsalaki et al.   PLoS Computational Biology

Peptide-mediated interactions in biological systems: new discoveries and applications

(2008) Evangelia Petsalaki et al.   CURRENT OPINION IN BIOTECHNOLOGY

Linear Motif Atlas for Phosphorylation-Dependent Signaling

(2008) M. L. Miller et al.   Science Signaling