iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics

Comparing the intrinsic dynamics of multiple protein structures using elastic network models

(2015) Edvin Fuglebakk et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

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

(2015) E. Eyal et al.   BIOINFORMATICS

Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions

(2015) Ivet Bahar et al.   BIOPHYSICAL JOURNAL

Adaptability of protein structures to enable functional interactions and evolutionary implications

(2015) Turkan Haliloglu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments

(2015) Giovanni Pinamonti et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Vincent Frappier et al.   NUCLEIC ACIDS RESEARCH

Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active-Site Residues

(2014) Chenxu Zhu et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Molecular Binding Sites Are Located Near the Interface of Intrinsic Dynamics Domains (IDDs)

(2014) Hongchun Li et al.   Journal of Chemical Information and Modeling

iMODS: internal coordinates normal mode analysis server

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

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

(2014) Peter W. Rose et al.   NUCLEIC ACIDS RESEARCH

Elastic network models capture the motions apparent within ensembles of RNA structures

(2014) M. T. Zimmermann et al.   RNA

Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank, which uses dihedral angles as independent variables

(2013) Hiroshi Wako et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Elastic Network Models of Nucleic Acids Flexibility

(2013) Piotr Setny et al.   Journal of Chemical Theory and Computation

Elastic Network Models Are Robust to Variations in Formalism

(2012) Nicholas Leioatts et al.   Journal of Chemical Theory and Computation

Combining Statistical Potentials with Dynamics-Based Entropies Improves Selection from Protein Decoys and Docking Poses

(2012) Michael T. Zimmermann et al.   JOURNAL OF PHYSICAL CHEMISTRY B

KOSMOS: a universal morph server for nucleic acids, proteins and their complexes

(2012) S. Seo et al.   NUCLEIC ACIDS RESEARCH

iMod: multipurpose normal mode analysis in internal coordinates

(2011) José Ramón Lopéz-Blanco et al.   BIOINFORMATICS

Models with Energy Penalty on Interresidue Rotation Address Insufficiencies of Conventional Elastic Network Models

(2011) Lee-Wei Yang   BIOPHYSICAL JOURNAL

Global Dynamics of Proteins: Bridging Between Structure and Function

(2010) Ivet Bahar et al.   Annual Review of Biophysics

On the functional significance of soft modes predicted by coarse-grained models for membrane proteins

(2010) Ivet Bahar   JOURNAL OF GENERAL PHYSIOLOGY

Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics

(2009) Lee-Wei Yang et al.   BIOINFORMATICS

All-Atom Contact Model for Understanding Protein Dynamics from Crystallographic B-Factors

(2009) Da-Wei Li et al.   BIOPHYSICAL JOURNAL

The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding

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

StoneHinge: Hinge prediction by network analysis of individual protein structures

(2009) Kevin S. Keating et al.   PROTEIN SCIENCE

A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations

(2009) Lin Liu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Proteins: Coexistence of Stability and Flexibility

(2008) Shlomi Reuveni et al.   PHYSICAL REVIEW LETTERS

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

Close Correspondence between the Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Elastic Network Modes

(2008) Lei Yang et al.   STRUCTURE