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

Coarse-Grained Protein Models and Their Applications

(2016) Sebastian Kmiecik et al.   CHEMICAL REVIEWS

A Maximum-Likelihood Approach to Force-Field Calibration

(2015) Bartłomiej Zaborowski 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

The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems

(2014) Fabio Sterpone et al.   CHEMICAL SOCIETY REVIEWS

Kinks, loops, and protein folding, with protein A as an example

(2014) Andrey Krokhotin et al.   JOURNAL OF CHEMICAL PHYSICS

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

Role of Backbone Dipole Interactions in the Formation of Secondary and Supersecondary Structures of Proteins

(2014) Sai J. Ganesan 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

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

Coarse graining: a tool for large-scale simulations or more?

(2013) Adam Liwo   PHYSICA SCRIPTA

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

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

Determination of Effective Potentials for the Stretching of Cα···Cα Virtual Bonds in Polypeptide Chains for Coarse-Grained Simulations of Proteins from ab Initio Energy Surfaces of N-Methylacetamide and N-Acetylpyrrolidine

(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

Discrete Nonlinear Schrödinger Equation and Polygonal Solitons with Applications to Collapsed Proteins

(2011) Nora Molkenthin et al.   PHYSICAL REVIEW LETTERS

A Nonradial Coarse-Grained Potential for Proteins Produces Naturally Stable Secondary Structure Elements

(2009) Davide Alemani 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 MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

Peptide Folding Using Multiscale Coarse-Grained Models

(2008) Ian F. Thorpe et al.   JOURNAL OF PHYSICAL CHEMISTRY B