Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours

Performance of protein-structure predictions with the physics-based UNRES force field in CASP11

(2016) Paweł Krupa et al.   BIOINFORMATICS

Critical assessment of methods of protein structure prediction: Progress and new directions in round XI

(2016) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Blind protein structure prediction using accelerated free-energy simulations

(2016) A. Perez et al.   Science Advances

A Maximum-Likelihood Approach to Force-Field Calibration

(2015) Bartłomiej Zaborowski et al.   Journal of Chemical Information and Modeling

Folding Simulations for Proteins with Diverse Topologies Are Accessible in Days with a Physics-Based Force Field and Implicit Solvent

(2014) Hai Nguyen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Testing the validity of ensemble descriptions of intrinsically disordered proteins

(2014) M. R. Jensen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Benchmarking all-atom simulations using hydrogen exchange

(2014) John J. Skinner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient Parameter Estimation of Generalizable Coarse-Grained Protein Force Fields Using Contrastive Divergence: A Maximum Likelihood Approach

(2013) Csilla Várnai et al.   Journal of Chemical Theory and Computation

Simplified Protein Models: Predicting Folding Pathways and Structure Using Amino Acid Sequences

(2013) Aashish N. Adhikari et al.   PHYSICAL REVIEW LETTERS

De novo prediction of protein folding pathways and structure using the principle of sequential stabilization

(2012) A. N. Adhikari et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Fast-Folding Proteins Fold

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

Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model

(2010) Daniel Ting et al.   PLoS Computational Biology

Progress and challenges in the automated construction of Markov state models for full protein systems

(2009) Gregory R. Bowman et al.   JOURNAL OF CHEMICAL PHYSICS

Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides

(2009) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B