iMod: multipurpose normal mode analysis in internal coordinates

A mixed molecular modeling-robotics approach to investigate lipase large molecular motions

(2011) Sophie Barbe et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Accounting for conformational changes during protein–protein docking

(2010) Martin Zacharias   CURRENT OPINION IN STRUCTURAL BIOLOGY

Approaching Elastic Network Models to Molecular Dynamics Flexibility

(2010) Laura Orellana et al.   Journal of Chemical Theory and Computation

Torsional Network Model: Normal Modes in Torsion Angle Space Better Correlate with Conformation Changes in Proteins

(2010) Raul Mendez et al.   PHYSICAL REVIEW LETTERS

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

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

Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations

(2010) Daniel Seeliger et al.   PLoS Computational Biology

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

(2009) Ivet Bahar et al.   CHEMICAL REVIEWS

RNA polymerase II flexibility during translocation from normal mode analysis

(2009) Michael Feig et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Recent advances in the study of nucleic acid flexibility by molecular dynamics

(2008) Modesto Orozco et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Can Morphing Methods Predict Intermediate Structures?

(2008) Dahlia R. Weiss et al.   JOURNAL OF MOLECULAR BIOLOGY

Normal mode analysis for proteins

(2008) Lars Skjaerven et al.   JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM

Building alternate protein structures using the elastic network model

(2008) Qingyi Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS