Coarse-grained force field: general folding theory

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino-Acid Side Chains in Water. V. Like-Charged Side Chains

(2011) Mariusz Makowski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino-Acid Side Chains in Water. VI. Oppositely Charged Side Chains

(2011) Mariusz Makowski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Relation between Free Energy Landscapes of Proteins and Dynamics

(2010) Gia G. Maisuradze et al.   Journal of Chemical Theory and Computation

Mechanism of Fiber Assembly: Treatment of Aβ Peptide Aggregation with a Coarse-Grained United-Residue Force Field

(2010) Ana Rojas et al.   JOURNAL OF MOLECULAR BIOLOGY

PDZ Binding to the BAR Domain of PICK1 is Elucidated by Coarse-grained Molecular Dynamics

(2010) Yi He et al.   JOURNAL OF MOLECULAR BIOLOGY

Investigation of Protein Folding by Coarse-Grained Molecular Dynamics with the UNRES Force Field

(2010) Gia G. Maisuradze et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Evidence, from Simulations, of a Single State with Residual Native Structure at the Thermal Denaturation Midpoint of a Small Globular Protein

(2010) Gia G. Maisuradze et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Minimalist models for proteins: a comparative analysis

(2010) Valentina Tozzini   QUARTERLY REVIEWS OF BIOPHYSICS

Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics

(2009) Ronald Hills et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

How Adequate are One- and Two-Dimensional Free Energy Landscapes for Protein Folding Dynamics?

(2009) Gia G. Maisuradze et al.   PHYSICAL REVIEW LETTERS

Implementations of Nosé–Hoover and Nosé–Poincaré thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain

(2008) Dana S. Kleinerman et al.   JOURNAL OF CHEMICAL PHYSICS

The MARTINI Coarse-Grained Force Field: Extension to Proteins

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

Principal Component Analysis for Protein Folding Dynamics

(2008) Gia G. Maisuradze et al.   JOURNAL OF MOLECULAR BIOLOGY

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force for the Interaction of Amino Acid Side Chains in Water. IV. Pairs of Different Hydrophobic Side Chains

(2008) Mariusz Makowski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Folding Pathway of the B1 Domain of Protein G Explored by Multiscale Modeling

(2007) Sebastian Kmiecik et al.   BIOPHYSICAL JOURNAL