WEBnm@ v2.0: Web server and services for comparing protein flexibility

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

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

Allosteric Regulation of the Hsp90 Dynamics and Stability by Client Recruiter Cochaperones: Protein Structure Network Modeling

(2014) Kristin Blacklock et al.   PLoS One

Structural and Biochemical Characterization of the Cop9 Signalosome CSN5/CSN6 Heterodimer

(2014) Melissa Birol et al.   PLoS One

Comparison of the Intrinsic Dynamics of Aminoacyl-tRNA Synthetases

(2014) Nicholas Warren et al.   PROTEIN JOURNAL

Experimentally Guided Structural Modeling and Dynamics Analysis of Hsp90–p53 Interactions: Allosteric Regulation of the Hsp90 Chaperone by a Client Protein

(2013) Kristin Blacklock et al.   Journal of Chemical Information and Modeling

Evaluation of Protein Elastic Network Models Based on an Analysis of Collective Motions

(2013) Edvin Fuglebakk et al.   Journal of Chemical Theory and Computation

Crystal Structures of the First Condensation Domain of CDA Synthetase Suggest Conformational Changes during the Synthetic Cycle of Nonribosomal Peptide Synthetases

(2013) Kristjan Bloudoff et al.   JOURNAL OF MOLECULAR BIOLOGY

The critical role of the loops of triosephosphate isomerase for its oligomerization, dynamics, and functionality

(2013) Ataur R. Katebi et al.   PROTEIN SCIENCE

The interplay of structure and dynamics: Insights from a survey of HIV-1 reverse transcriptase crystal structures

(2013) James M. Seckler et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Elastic network normal mode dynamics reveal the GPCR activation mechanism

(2013) Dikla Kolan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Modulation of Global Low-Frequency Motions Underlies Allosteric Regulation: Demonstration in CRP/FNR Family Transcription Factors

(2013) Thomas L. Rodgers et al.   PLOS BIOLOGY

Localized Lipid Packing of Transmembrane Domains Impedes Integrin Clustering

(2013) Mehrdad Mehrbod et al.   PLoS Computational Biology

Measuring and comparing structural fluctuation patterns in large protein datasets

(2012) Edvin Fuglebakk et al.   BIOINFORMATICS

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

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

NMSim Web Server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins

(2012) D. M. Kruger et al.   NUCLEIC ACIDS RESEARCH

Comparing proteins by their internal dynamics: Exploring structure–function relationships beyond static structural alignments

(2012) Cristian Micheletti   Physics of Life Reviews

Why are the low-energy protein normal modes evolutionarily conserved?

(2012) Julian Echave   PURE AND APPLIED CHEMISTRY

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

Dynamic coupling between the LID and NMP domain motions in the catalytic conversion of ATP and AMP to ADP by adenylate kinase

(2011) Biman Jana et al.   JOURNAL OF CHEMICAL PHYSICS

Changes in Dynamics upon Oligomerization Regulate Substrate Binding and Allostery in Amino Acid Kinase Family Members

(2011) Enrique Marcos et al.   PLoS Computational Biology

A Molecular Dynamics Investigation of Vinculin Activation

(2010) Javad Golji et al.   BIOPHYSICAL JOURNAL

On the Roles of Substrate Binding and Hinge Unfolding in Conformational Changes of Adenylate Kinase

(2010) Jason B. Brokaw et al.   BIOPHYSICAL JOURNAL

Evaluating Elastic Network Models of Crystalline Biological Molecules with Temperature Factors, Correlated Motions, and Diffuse X-Ray Scattering

(2010) Demian Riccardi et al.   BIOPHYSICAL JOURNAL

Many Local Motions Cooperate to Produce the Adenylate Kinase Conformational Transition

(2010) Michael D. Daily et al.   JOURNAL OF MOLECULAR BIOLOGY

Exploring the factors determining the dynamics of different protein folds

(2010) S. M. Hollup et al.   PROTEIN SCIENCE

Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses

(2010) Aqeel Ahmed et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Validating and improving elastic network models with molecular dynamics simulations

(2010) Tod D. Romo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit

(2010) Lars Skjaerven et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Conservation and Variation of Structural Flexibility in Protein Families

(2010) Adam W. Van Wynsberghe et al.   STRUCTURE

Deciphering the Deformation Modes Associated with Function Retention and Specialization in Members of the Ras Superfamily

(2010) Francesco Raimondi et al.   STRUCTURE

Targeted Optimization of a Protein Nanomachine for Operation in Biohybrid Devices

(2009) Mamta Amrute-Nayak et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Using dynamics-based comparisons to predict nucleic acid binding sites in proteins: an application to OB-fold domains

(2009) Andrea Zen et al.   BIOINFORMATICS

Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins

(2009) Ivet Bahar et al.   CHEMICAL REVIEWS

Accuracy analysis of multiple structure alignments

(2009) Christoph Berbalk et al.   PROTEIN SCIENCE

A perturbative view of protein structural variation

(2009) Julián Echave et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A network of dynamically conserved residues deciphers the motions of maltose transporter

(2009) Suryani Lukman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Comparison of molecular dynamics and superfamily spaces of protein domain deformation

(2009) Javier A Velazquez-Muriel et al.   BMC STRUCTURAL BIOLOGY

Molecular Mechanics of the α-Actinin Rod Domain: Bending, Torsional, and Extensional Behavior

(2009) Javad Golji et al.   PLoS Computational Biology

Small- and Large-Scale Conformational Changes of Adenylate Kinase: A Molecular Dynamics Study of the Subdomain Motion and Mechanics

(2008) Francesco Pontiggia et al.   BIOPHYSICAL JOURNAL

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

Correspondences between low-energy modes in enzymes: Dynamics-based alignment of enzymatic functional families

(2008) Andrea Zen et al.   PROTEIN SCIENCE

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