Normal Mode Analysis as a Routine Part of a Structural Investigation

Disease-Associated Mutations Alter the Dynamic Motion of the N-terminal Domain of the Human Cardiac Ryanodine Receptor

(2019) Jacob A. Bauer et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Normal mode analysis of Zika virus

(2018) Byung Ho Lee et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Conservation of intrinsic dynamics in proteins — what have computational models taught us?

(2018) Sandhya P Tiwari et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Not all pycnodysostosis-related mutants of human cathepsin K are inactive - crystal structure and biochemical studies of an active mutant I249T

(2018) Sumana Roy et al.   FEBS Journal

Structure of tRNA-Modifying Enzyme TiaS and Motions of Its Substrate Binding Zinc Ribbon

(2018) Jianshu Dong et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural analyses of theHaemophilus influenzaepeptidoglycan synthase activator LpoA suggest multiple conformations in solution

(2017) Karthik Sathiyamoorthy et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Dynamic characteristics of a flagellar motor protein analyzed using an elastic network model

(2017) Moon-ki Choi et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode

(2017) Kimberly A. Stanek et al.   Acta Crystallographica Section D-Structural Biology

Arabidopsis thaliana dehydroascorbate reductase 2: Conformational flexibility during catalysis

(2017) Nandita Bodra et al.   Scientific Reports

Crystal structure of phosphoglucomutase from Leishmania major at 3.5 Å resolution

(2016) Barnali Waugh et al.   BIOCHIMIE

New generation of elastic network models

(2016) José Ramón López-Blanco et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Crystal structure and dynamics of Spt16N-domain of FACT complex from Cicer arietinum

(2016) Venkat N. Are et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Deciphering conformational transitions of proteins by small angle X-ray scattering and normal mode analysis

(2016) Alejandro Panjkovich et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

On the relationship between low-frequency normal modes and the large-scale conformational changes of proteins

(2015) Swapnil Mahajan et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Fe Protein-Independent Substrate Reduction by Nitrogenase MoFe Protein Variants

(2015) Karamatullah Danyal et al.   BIOCHEMISTRY

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

(2015) E. Eyal et al.   BIOINFORMATICS

Structural plasticity of Cid1 provides a basis for its distributive RNA terminal uridylyl transferase activity

(2015) Luke A. Yates et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Hongchun Li et al.   NUCLEIC ACIDS RESEARCH

Toward decrypting the allosteric mechanism of the ryanodine receptor based on coarse-grained structural and dynamic modeling

(2015) Wenjun Zheng   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

X-ray, spectroscopic and normal-mode dynamics of calexcitin: structure–function studies of a neuronal calcium-signalling protein

(2015) P. T. Erskine et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Evol and ProDy for bridging protein sequence evolution and structural dynamics

(2014) A. Bakan et al.   BIOINFORMATICS

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

(2014) Sandhya P Tiwari et al.   BMC BIOINFORMATICS

iMODS: internal coordinates normal mode analysis server

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

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

Structure-guided analysis of catalytic specificity of the abundantly secreted chitosanase SACTE_5457 fromStreptomycessp. SirexAA-E

(2013) Taichi E. Takasuka et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structure of a Truncation Mutant of the Nuclear Export Factor CRM1 Provides Insights into the Auto-Inhibitory Role of Its C-Terminal Helix

(2013) Cyril Dian et al.   STRUCTURE

Rapid simulation of protein motion: merging flexibility, rigidity and normal mode analyses

(2012) J E Jimenez-Roldan et al.   PHYSICAL BIOLOGY

Crystal structure of the armadillo repeat domain of adenomatous polyposis coli which reveals its inherent flexibility

(2011) Zhenyi Zhang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

iMod: multipurpose normal mode analysis in internal coordinates

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

ProDy: Protein Dynamics Inferred from Theory and Experiments

(2011) A. Bakan et al.   BIOINFORMATICS

A few low-frequency normal modes predominantly contribute to conformational responses of hen egg white lysozyme in the tetragonal crystal to variations of molecular packing controlled by environmental humidity

(2011) Yuki Takayama et al.   BIOPHYSICAL CHEMISTRY

Accurate Flexible Fitting of High-Resolution Protein Structures into Cryo-Electron Microscopy Maps Using Coarse-Grained Pseudo-Energy Minimization

(2011) Wenjun Zheng   BIOPHYSICAL JOURNAL

Accurate Flexible Fitting of High-Resolution Protein Structures to Small-Angle X-Ray Scattering Data Using a Coarse-Grained Model with Implicit Hydration Shell

(2011) Wenjun Zheng et al.   BIOPHYSICAL JOURNAL

Mapping Conformational Transitions in Cyclic AMP Receptor Protein: Crystal Structure and Normal-Mode Analysis of Mycobacterium tuberculosis apo-cAMP Receptor Protein

(2010) Pramod Kumar et al.   BIOPHYSICAL JOURNAL

The normal modes of a protein: Native bovine pancreatic trypsin inhibitor

(2010) Michael Levitt et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Crystal structure of the zinc-, cobalt-, and iron-containing adenylate kinase from Desulfovibrio gigas: a novel metal-containing adenylate kinase from Gram-negative bacteria

(2010) A. Mukhopadhyay et al.   JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY

Normal mode analysis and applications in biological physics

(2010) Eric C Dykeman et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Predicting order of conformational changes during protein conformational transitions using an interpolated elastic network model

(2010) Mustafa Tekpinar 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

Crystal structure of a bacterial phosphoglucomutase, an enzyme involved in the virulence of multiple human pathogens

(2010) Ritcha Mehra-Chaudhary et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Generalized spring tensor models for protein fluctuation dynamics and conformation changes

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

Structural improvement of unliganded simian immunodeficiency virus gp120 core by normal-mode-based X-ray crystallographic refinement

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

Coupling between Normal Modes Drives Protein Conformational Dynamics: Illustrations Using Allosteric Transitions in Myosin II

(2009) Wenjun Zheng et al.   BIOPHYSICAL JOURNAL

Analysis of a new crystal form of procarboxypeptidase B: Further insights into the catalytic mechanism

(2009) Daniel Fernández et al.   BIOPOLYMERS

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

(2009) Ivet Bahar et al.   CHEMICAL REVIEWS

Conformational flexibility and molecular interactions of an archaeal homologue of the Shwachman-Bodian-Diamond syndrome protein

(2009) C Leong Ng et al.   BMC STRUCTURAL BIOLOGY

Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models

(2009) Timothy R. Lezon et al.   PLoS Computational Biology

A Unification of the Elastic Network Model and the Gaussian Network Model for Optimal Description of Protein Conformational Motions and Fluctuations

(2008) Wenjun Zheng   BIOPHYSICAL JOURNAL

Structure of Human J-type Co-chaperone HscB Reveals a Tetracysteine Metal-binding Domain

(2008) Eduard Bitto et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Effects of Protein Subunits Removal on the Computed Motions of Partial 30S Structures of the Ribosome

(2008) Aimin Yan et al.   Journal of Chemical Theory and Computation

Normal mode analysis for proteins

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

Collective dynamics of the ribosomal tunnel revealed by elastic network modeling

(2008) Ozge Kurkcuoglu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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