Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method

Evolutionary-inspired probabilistic search for enhancing sampling of local minima in the protein energy surface

(2012) Brian S Olson et al.   Proteome Science

GUIDING PROBABILISTIC SEARCH OF THE PROTEIN CONFORMATIONAL SPACE WITH STRUCTURAL PROFILES

(2012) BRIAN OLSON et al.   Journal of Bioinformatics and Computational Biology

Randomized tree construction algorithm to explore energy landscapes

(2011) Léonard Jaillet et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

IN SEARCH OF THE PROTEIN NATIVE STATE WITH A PROBABILISTIC SAMPLING APPROACH

(2011) BRIAN OLSON et al.   Journal of Bioinformatics and Computational 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

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

Mimicking the folding pathway to improve homology-free protein structure prediction

(2009) J. DeBartolo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase

(2009) A. Korkut et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Restriction versus guidance in protein structure prediction

(2009) J. A. Hegler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiscale characterization of protein conformational ensembles

(2009) Amarda Shehu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improved prediction of protein side-chain conformations with SCWRL4

(2009) Georgii G. Krivov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

End-Point Targeted Molecular Dynamics: Large-Scale Conformational Changes in Potassium Channels

(2008) R.J. Mashl et al.   BIOPHYSICAL JOURNAL

Protein structure prediction using basin-hopping

(2008) Michael C. Prentiss et al.   JOURNAL OF CHEMICAL PHYSICS

Can Morphing Methods Predict Intermediate Structures?

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

Finding Transition Pathways Using the String Method with Swarms of Trajectories

(2008) Albert C. Pan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Guiding conformation space search with an all-atom energy potential

(2008) TJ Brunette et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Iterative cluster-NMA: A tool for generating conformational transitions in proteins

(2008) Adam D. Schuyler et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

BIOCHEMISTRY: How Do Proteins Interact?

(2008) D. D. Boehr et al.   SCIENCE

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

(2008) Marcus B. Kubitzki et al.   STRUCTURE

Ab Initio Folding of Proteins with All-Atom Discrete Molecular Dynamics

(2008) Feng Ding et al.   STRUCTURE