Exploration of conformational transition pathways from coarse-grained simulations

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

Discrete Molecular Dynamics Distinguishes Nativelike Binding Poses from Decoys in Difficult Targets

(2012) Elizabeth A. Proctor et al.   BIOPHYSICAL JOURNAL

Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations

(2012) Pedro Sfriso et al.   Journal of Chemical Theory and Computation

Efficient Relaxation of Protein–Protein Interfaces by Discrete Molecular Dynamics Simulations

(2012) Agusti Emperador et al.   Journal of Chemical Theory and Computation

Three-dimensional RNA structure refinement by hydroxyl radical probing

(2012) Feng Ding et al.   NATURE METHODS

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

(2012) Cristian Micheletti   Physics of Life Reviews

Kinetics of Conformational Sampling in Ubiquitin

(2011) David Ban et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

iMod: multipurpose normal mode analysis in internal coordinates

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

Weak Long-Range Correlated Motions in a Surface Patch of Ubiquitin Involved in Molecular Recognition

(2011) R. Bryn Fenwick et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

A Systematic Study of the Energetics Involved in Structural Changes upon Association and Connectivity in Protein Interaction Networks

(2011) Amelie Stein et al.   STRUCTURE

Discrete molecular dynamics

(2011) Elizabeth A. Proctor et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Multiple Routes to Characterize the Folding of a Small DNA Hairpin

(2010) Guillem Portella et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Global Dynamics of Proteins: Bridging Between Structure and Function

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

Targeting biomolecular flexibility with metadynamics

(2010) Vanessa Leone et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Approaching Elastic Network Models to Molecular Dynamics Flexibility

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

Computing ensembles of transitions from stable states: Dynamic importance sampling

(2010) Juan R. Perilla et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Elucidation of Amyloid β-Protein Oligomerization Mechanisms: Discrete Molecular Dynamics Study

(2010) B. Urbanc et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2010) Raul Mendez et al.   PHYSICAL REVIEW LETTERS

MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories

(2010) Tim Meyer et al.   STRUCTURE

Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open↔Closed Transitions

(2009) Oliver Beckstein et al.   JOURNAL OF MOLECULAR BIOLOGY

Native-like RNA Tertiary Structures Using a Sequence-Encoded Cleavage Agent and Refinement by Discrete Molecular Dynamics

(2009) Costin M. Gherghe et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials

(2009) Agustí Emperador 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

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

Exploring the Suitability of Coarse-Grained Techniques for the Representation of Protein Dynamics

(2008) Agustí Emperador et al.   BIOPHYSICAL JOURNAL

United-Atom Discrete Molecular Dynamics of Proteins Using Physics-Based Potentials

(2008) Agustí Emperador et al.   Journal of Chemical Theory and Computation

Can Morphing Methods Predict Intermediate Structures?

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

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

Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation

(2008) F. Ding et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms

(2008) F. Ding et al.   RNA

The Atomistic Mechanism of Conformational Transition in Adenylate Kinase: A TEE-REX Molecular Dynamics Study

(2008) Marcus B. Kubitzki et al.   STRUCTURE