SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models

Role of the Biomolecular Energy Gap in Protein Design, Structure, and Evolution

(2012) Sarel J. Fleishman et al.   CELL

Protein-protein Docking and Hot-spot Prediction for Drug Discovery

(2012) Solene Grosdidier et al.   CURRENT PHARMACEUTICAL DESIGN

Next-generation protein engineering targets influenza

(2012) Shoshana J Wodak   NATURE BIOTECHNOLOGY

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing

(2012) Timothy A Whitehead et al.   NATURE BIOTECHNOLOGY

Computer-aided antibody design

(2012) D. Kuroda et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Kinetic Rate Constant Prediction Supports the Conformational Selection Mechanism of Protein Binding

(2012) Iain H. Moal et al.   PLoS Computational Biology

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

(2011) Iain H. Moal et al.   BIOINFORMATICS

A structure-based benchmark for protein-protein binding affinity

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

Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing

(2011) X. Wu et al.   SCIENCE

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

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

Deep mutational scanning: assessing protein function on a massive scale

(2011) Carlos L. Araya et al.   TRENDS IN BIOTECHNOLOGY

APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility

(2010) Jun-Feng Xia et al.   BMC BIOINFORMATICS

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

A Simple Definition of Structural Regions in Proteins and Its Use in Analyzing Interface Evolution

(2010) Emmanuel D. Levy   JOURNAL OF MOLECULAR BIOLOGY

Coevolution of PDZ domain–ligand interactions analyzed by high-throughput phage display and deep sequencing

(2010) Andreas Ernst et al.   Molecular BioSystems

Mutational robustness can facilitate adaptation

(2010) Jeremy A. Draghi et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

Deleterious effects of β-branched residues in the S1 specificity pocket of Streptomyces griseus proteinase B (SGPB): Crystal structures of the turkey ovomucoid third domain variants Ile18I, Val18I, Thr18I, and Ser18I in complex with SGPB

(2010) Katherine S. Bateman et al.   PROTEIN SCIENCE

Accounting for conformational entropy in predicting binding free energies of protein-protein interactions

(2010) Hetunandan Kamisetty et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2009) Nurcan Tuncbag et al.   BIOINFORMATICS

Computer-aided design of functional protein interactions

(2009) Daniel J Mandell et al.   Nature Chemical Biology

Identification of hot-spot residues in protein-protein interactions by computational docking

(2008) Solène Grosdidier et al.   BMC BIOINFORMATICS

Pathogenicity of the BRCA1 missense variant M1775K is determined by the disruption of the BRCT phosphopeptide-binding pocket: a multi-modal approach

(2008) Marc Tischkowitz et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Experimental and Computational Analyses of the Energetic Basis for Dual Recognition of Immunity Proteins by Colicin Endonucleases

(2008) Anthony H. Keeble et al.   JOURNAL OF MOLECULAR BIOLOGY

Computational Redesign of the SHV-1 β-Lactamase/β-Lactamase Inhibitor Protein Interface

(2008) Kimberly A. Reynolds et al.   JOURNAL OF MOLECULAR BIOLOGY

Predicting free energy changes using structural ensembles

(2008) Alexander Benedix et al.   NATURE METHODS

Electrostatic contributions drive the interaction betweenStaphylococcus aureusprotein Efb-C and its complement target C3d

(2008) Nurit Haspel et al.   PROTEIN SCIENCE

Selected-fit versus induced-fit protein binding: Kinetic differences and mutational analysis

(2008) Thomas R. Weikl et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The energetic cost of induced fit catalysis: Crystal structures of trypsinogen mutants with enhanced activity and inhibitor affinity

(2002) Annette Pasternak et al.   PROTEIN SCIENCE