Protein–protein binding affinity prediction on a diverse set of structures

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

(2011) Sarel J. Fleishman et al.   JOURNAL OF MOLECULAR BIOLOGY

A structure-based benchmark for protein-protein binding affinity

(2011) Panagiotis L. Kastritis et al.   PROTEIN SCIENCE

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

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

(2011) S. J. Fleishman et al.   SCIENCE

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

(2010) S. Chaudhury et al.   BIOINFORMATICS

Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials

(2010) Yaping Feng et al.   BMC BIOINFORMATICS

Optimizing energy functions for protein-protein interface design

(2010) Oz Sharabi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computational Mapping of Anchoring Spots on Protein Surfaces

(2010) Avraham Ben-Shimon et al.   JOURNAL OF MOLECULAR BIOLOGY

Are Scoring Functions in Protein−Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark

(2010) Panagiotis L. Kastritis et al.   JOURNAL OF PROTEOME RESEARCH

HotPoint: hot spot prediction server for protein interfaces

(2010) N. Tuncbag et al.   NUCLEIC ACIDS RESEARCH

Protein interface conservation across structure space

(2010) Q. C. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Calculation of the free energy of association for protein complexes

(2010) Nancy Horton et al.   PROTEIN SCIENCE

Detection and refinement of encounter complexes for protein-protein docking: Taking account of macromolecular crowding

(2010) Xiaofan Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Predicting kinetic constants of protein-protein interactions based on structural properties

(2010) Hongjun Bai et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-protein docking benchmark version 4.0

(2010) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Polyubiquitin Binding and Disassembly By Deubiquitinating Enzymes

(2009) Francisca E. Reyes-Turcu et al.   CHEMICAL REVIEWS

CHARMM: The biomolecular simulation program

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

Fast predictions of thermodynamics and kinetics of protein–protein recognition from structures: from molecular design to systems biology

(2009) Daniele Dell’Orco   Molecular BioSystems

GWIDD: Genome-wide protein docking database

(2009) Petras J. Kundrotas et al.   NUCLEIC ACIDS RESEARCH

A feature-based approach to modeling protein–protein interaction hot spots

(2009) Kyu-il Cho et al.   NUCLEIC ACIDS RESEARCH

Quantitative prediction of protein-protein binding affinity with a potential of mean force considering volume correction

(2009) Yu Su et al.   PROTEIN SCIENCE

Analyzing Protein Interaction Networks Using Structural Information

(2008) Christina Kiel et al.   Annual Review of Biochemistry

ProtorP: a protein-protein interaction analysis server

(2008) C. Reynolds et al.   BIOINFORMATICS

Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces

(2008) Salim Bougouffa et al.   BMC BIOINFORMATICS

Structure-Based Design of a Potent and Selective Small Peptide Inhibitor of Mycobacterium tuberculosis 6-Hydroxymethyl-7, 8-Dihydropteroate Synthase: A Computer Modelling Approach

(2008) Gita Subba Rao et al.   Chemical Biology & Drug Design

Assessment of programs for ligand binding affinity prediction

(2008) Ryangguk Kim et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Targeting the Human Cancer Pathway Protein Interaction Network by Structural Genomics

(2008) Yuanpeng Janet Huang et al.   MOLECULAR & CELLULAR PROTEOMICS

Predicting free energy changes using structural ensembles

(2008) Alexander Benedix et al.   NATURE METHODS

Very fast prediction and rationalization of pKa values for protein-ligand complexes

(2008) Delphine C. Bas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS