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

Druggable protein–protein interactions – from hot spots to hot segments

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

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

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

Comprehensive Experimental and Computational Analysis of Binding Energy Hot Spots at the NF-κB Essential Modulator/IKKβ Protein–Protein Interface

(2013) Mary S. Golden et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2013) Mikael Trellet et al.   PLoS One

Protein-Peptide Complex Prediction through Fragment Interaction Patterns

(2013) Erik Verschueren et al.   STRUCTURE

Motif switches: decision-making in cell regulation

(2012) Kim Van Roey et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein–Protein Interfaces

(2012) Brandon S. Zerbe et al.   Journal of Chemical Information and Modeling

PepSite: prediction of peptide-binding sites from protein surfaces

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

A Dynamic View of Domain-Motif Interactions

(2012) Eyal Akiva et al.   PLoS Computational Biology

FTSite: high accuracy detection of ligand binding sites on unbound protein structures

(2011) Chi-Ho Ngan et al.   BIOINFORMATICS

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

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

KFC2: A knowledge-based hot spot prediction method based on interface solvation, atomic density, and plasticity features

(2011) Xiaolei Zhu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Can self-inhibitory peptides be derived from the interfaces of globular protein-protein interactions?

(2010) Nir London et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Structural Basis of Peptide-Protein Binding Strategies

(2010) Nir London et al.   STRUCTURE

Fragment-based identification of druggable ‘hot spots’ of proteins using Fourier domain correlation techniques

(2009) Ryan Brenke et al.   BIOINFORMATICS

Generating Uniform Incremental Grids on SO(3) Using the Hopf Fibration

(2009) Anna Yershova et al.   INTERNATIONAL JOURNAL OF ROBOTICS RESEARCH

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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