Towards the prediction of order parameters from molecular dynamics simulations in proteins

QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin

(2011) A. J. Savol et al.   BIOINFORMATICS

Determination of reaction coordinates via locally scaled diffusion map

(2011) Mary A. Rohrdanz et al.   JOURNAL OF CHEMICAL PHYSICS

Discovering Conformational Sub-States Relevant to Protein Function

(2011) Arvind Ramanathan et al.   PLoS One

Molecular Simulation Approaches to Membrane Proteins

(2011) Phillip J. Stansfeld et al.   STRUCTURE

Instantaneous Normal Modes as an Unforced Reaction Coordinate for Protein Conformational Transitions

(2010) Cheng Peng et al.   BIOPHYSICAL JOURNAL

Computing ensembles of transitions from stable states: Dynamic importance sampling

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

Hidden Complexity of Protein Free-Energy Landscapes Revealed by Principal Component Analysis by Parts

(2010) Abhinav Jain et al.   Journal of Physical Chemistry Letters

Protein folded states are kinetic hubs

(2010) G. R. Bowman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Basis of Alternating Access Membrane Transport by the Sodium-Hydantoin Transporter Mhp1

(2010) T. Shimamura et al.   SCIENCE

Extracting the Causality of Correlated Motions from Molecular Dynamics Simulations

(2009) Hiqmet Kamberaj et al.   BIOPHYSICAL JOURNAL

Comparison of Three Perturbation Molecular Dynamics Methods for Modeling Conformational Transitions

(2009) He Huang et al.   Journal of Chemical Theory and Computation

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Segmented Transition Pathway of the Signaling Protein Nitrogen Regulatory Protein C

(2009) Ming Lei et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

Cooperative nature of gating transitions in K+ channels as seen from dynamic importance sampling calculations

(2009) Elizabeth J. Denning et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Detection of Functional Modes in Protein Dynamics

(2009) Jochen S. Hub et al.   PLoS Computational Biology

Conformational Transition Pathways Explored by Monte Carlo Simulation Integrated with Collective Modes

(2008) Nigar Kantarci-Carsibasi et al.   BIOPHYSICAL JOURNAL

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

Normal mode analysis for proteins

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

Symbolic Transfer Entropy

(2008) Matthäus Staniek et al.   PHYSICAL REVIEW LETTERS