ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability

The anisotropic network model web server at 2015 (ANM 2.0)

(2015) E. Eyal et al.   BIOINFORMATICS

iMODS: internal coordinates normal mode analysis server

(2014) José Ramón López-Blanco et al.   NUCLEIC ACIDS RESEARCH

Vibrational entropy differences between mesophile and thermophile proteins and their use in protein engineering

(2014) Vincent Frappier et al.   PROTEIN SCIENCE

A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations

(2014) Vincent Frappier et al.   PLoS Computational Biology

A Distal Mutation Perturbs Dynamic Amino Acid Networks in Dihydrofolate Reductase

(2013) David D. Boehr et al.   BIOCHEMISTRY

SwarmDock: a server for flexible protein–protein docking

(2013) Mieczyslaw Torchala et al.   BIOINFORMATICS

Ligand-induced conformational change of a protein reproduced by a linear combination of displacement vectors obtained from normal mode analysis

(2011) Hiroshi Wako et al.   BIOPHYSICAL CHEMISTRY

PSCDB: a database for protein structural change upon ligand binding

(2011) T. Amemiya et al.   NUCLEIC ACIDS RESEARCH

Can Enzyme Engineering Benefit from the Modulation of Protein Motions? Lessons Learned from NMR Relaxation Dispersion Experiments

(2011) Nicolas Doucet   PROTEIN AND PEPTIDE LETTERS

How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis

(2010) Olivier Sperandio et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

AUTO-MUTE: web-based tools for predicting stability changes in proteins due to single amino acid replacements

(2010) M. Masso et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Generalized spring tensor models for protein fluctuation dynamics and conformation changes

(2010) Tu-Liang Lin et al.   BMC STRUCTURAL BIOLOGY

Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0

(2009) Yves Dehouck et al.   BIOINFORMATICS

Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes

(2009) Manuel Rueda et al.   Journal of Chemical Information and Modeling

A force field for virtual atom molecular mechanics of proteins

(2009) A. Korkut et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction

(2008) Colin A. Smith et al.   JOURNAL OF MOLECULAR BIOLOGY

Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking

(2008) S. E. Dobbins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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