Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models

Atomic torsional modal analysis for high-resolution proteins

(2015) Monique M. Tirion et al.   PHYSICAL REVIEW E

The performance of fine-grained and coarse-grained elastic network models and its dependence on various factors

(2015) Hyuntae Na et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Formation and structures of GroEL:GroES2 chaperonin footballs, the protein-folding functional form

(2014) X. Fei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conventional NMA as a better standard for evaluating elastic network models

(2014) Hyuntae Na et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Bridging between normal mode analysis and elastic network models

(2014) Hyuntae Na et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein

(2014) Jason Tenboer et al.   SCIENCE

Real-Time Observation of Multiple-Protein Complex Formation with Single-Molecule FRET

(2013) Woori Bae et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Multiple Unfolding Pathways of Leucine Binding Protein (LBP) Probed by Single-Molecule Force Spectroscopy (SMFS)

(2013) Hema Chandra Kotamarthi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A mass weighted chemical elastic network model elucidates closed form domain motions in proteins

(2013) Min Hyeok Kim et al.   PROTEIN SCIENCE

Generalized spring tensor models for protein fluctuation dynamics and conformation changes

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

Focused Functional Dynamics of Supramolecules by Use of a Mixed-Resolution Elastic Network Model

(2009) Ozge Kurkcuoglu et al.   BIOPHYSICAL JOURNAL

Defining Coarse-Grained Representations of Large Biomolecules and Biomolecular Complexes from Elastic Network Models

(2009) Zhiyong Zhang et al.   BIOPHYSICAL JOURNAL

Approximate normal mode analysis based on vibrational subsystem analysis with high accuracy and efficiency

(2009) Jeffrey Hafner et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL

(2009) Zheng Yang et al.   PLoS Computational Biology

Effects of Surface Water on Protein Dynamics Studied by a Novel Coarse-Grained Normal Mode Approach

(2008) Lei Zhou et al.   BIOPHYSICAL JOURNAL

Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit

(2008) H. Lee Woodcock et al.   JOURNAL OF CHEMICAL PHYSICS

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

(2008) W. G. Noid et al.   JOURNAL OF CHEMICAL PHYSICS

Allostery Wiring Diagrams in the Transitions that Drive the GroEL Reaction Cycle

(2008) Riina Tehver et al.   JOURNAL OF MOLECULAR BIOLOGY

Collective dynamics of the ribosomal tunnel revealed by elastic network modeling

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