Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins

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

(2016) Paweł Krupa et al.   BIOINFORMATICS

Coarse-Grained Protein Models and Their Applications

(2016) Sebastian Kmiecik et al.   CHEMICAL REVIEWS

Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field

(2016) Magdalena A. Mozolewska et al.   Journal of Chemical Information and Modeling

Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest

(2015) Juyong Lee et al.   BMC BIOINFORMATICS

Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field

(2015) Paweł Krupa et al.   Journal of Chemical Information and Modeling

Physics-Based Potentials for the Coupling between Backbone- and Side-Chain-Local Conformational States in the United Residue (UNRES) Force Field for Protein Simulations

(2015) Adam K. Sieradzan et al.   Journal of Chemical Theory and Computation

Template based protein structure modeling by global optimization in CASP11

(2015) Keehyoung Joo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11

(2015) Wenxuan Zhang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions

(2014) Adam Liwo et al.   JOURNAL OF MOLECULAR MODELING

WeFold: A coopetition for protein structure prediction

(2014) George A. Khoury et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Segment assembly, structure alignment and iterative simulation in protein structure prediction

(2013) Yang Zhang et al.   BMC BIOLOGY

Improvement of the Treatment of Loop Structures in the UNRES Force Field by Inclusion of Coupling between Backbone- and Side-Chain-Local Conformational States

(2013) Paweł Krupa et al.   Journal of Chemical Theory and Computation

Adaptive Biasing Combined with Hamiltonian Replica Exchange to Improve Umbrella Sampling Free Energy Simulations

(2013) Fabian Zeller et al.   Journal of Chemical Theory and Computation

Application of replica exchange umbrella sampling to protein structure refinement of nontemplate models

(2013) Mark A. Olson et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29-42) peptides

(2013) Satoru G. Itoh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Lessons from application of the UNRES force field to predictions of structures of CASP10 targets

(2013) Y. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein structure modeling for CASP10 by multiple layers of global optimization

(2013) Keehyoung Joo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Critical assessment of methods of protein structure prediction (CASP) - round x

(2013) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Replica-Permutation Method with the Suwa–Todo Algorithm beyond the Replica-Exchange Method

(2012) Satoru G. Itoh et al.   Journal of Chemical Theory and Computation

Implementation of Molecular Dynamics and Its Extensions with the Coarse-Grained UNRES Force Field on Massively Parallel Systems: Toward Millisecond-Scale Simulations of Protein Structure, Dynamics, and Thermodynamics

(2010) Adam Liwo et al.   Journal of Chemical Theory and Computation

Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins

(2009) Cezary Czaplewski et al.   Journal of Chemical Theory and Computation

Exploring the parameter space of the coarse-grained UNRES force field by random search: Selecting a transferable medium-resolution force field

(2009) Yi He et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

An Improved Functional Form for the Temperature Scaling Factors of the Components of the Mesoscopic UNRES Force Field for Simulations of Protein Structure and Dynamics

(2009) Hujun Shen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

QMEAN server for protein model quality estimation

(2009) Pascal Benkert et al.   NUCLEIC ACIDS RESEARCH

Progress and challenges in protein structure prediction

(2008) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

Optimized Explicit-Solvent Replica Exchange Molecular Dynamics from Scratch

(2008) Walter Nadler et al.   JOURNAL OF PHYSICAL CHEMISTRY B

QMEAN: A comprehensive scoring function for model quality assessment

(2007) Pascal Benkert et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS