A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation

Conformational Space Annealing explained: A general optimization algorithm, with diverse applications

(2018) InSuk Joung et al.   COMPUTER PHYSICS COMMUNICATIONS

Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics

(2017) Paweł Krupa et al.   Journal of Chemical Information and Modeling

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. II. Backbone-local potentials of coarse-grained O1→4-bonded polyglucose chains

(2017) Emilia A. Lubecka et al.   JOURNAL OF CHEMICAL PHYSICS

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains

(2017) Adam K. Sieradzan et al.   JOURNAL OF CHEMICAL PHYSICS

Dynamics of Disulfide-Bond Disruption and Formation in the Thermal Unfolding of Ribonuclease A

(2017) Paweł Krupa et al.   Journal of Chemical Theory and Computation

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

(2017) Agnieszka S. Karczyńska et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

(2016) Paweł Krupa et al.   BIOINFORMATICS

Improved in-cell structure determination of proteins at near-physiological concentration

(2016) Teppei Ikeya et al.   Scientific Reports

A Maximum-Likelihood Approach to Force-Field Calibration

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

Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach

(2015) Yi He et al.   JOURNAL OF CHEMICAL PHYSICS

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

Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force Field

(2014) Adam K. Sieradzan et al.   Journal of Chemical Theory and Computation

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

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

Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements

(2014) Rui Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Mean-Field Interactions between Nucleic-Acid-Base Dipoles can Drive the Formation of a Double Helix

(2013) Yi He et al.   PHYSICAL REVIEW LETTERS

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

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

Extension of UNRES Force Field to Treat Polypeptide Chains with d-Amino Acid Residues

(2012) Adam K. Sieradzan et al.   Journal of Chemical Theory and Computation

Coarse-grained force field: general folding theory

(2011) Adam Liwo et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. II. Resul

(2009) Urszula Kozłowska 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

The Trp-cage: optimizing the stability of a globular miniprotein

(2008) B. Barua et al.   PROTEIN ENGINEERING DESIGN & SELECTION