Modeling the structure, dynamics, and transformations of proteins with the UNRES force field
The physics-based united-residue (UNRES) model of proteins (www. unres. pl) has been
designed to carry out large-scale simulations of protein folding. The force field has been …
designed to carry out large-scale simulations of protein folding. The force field has been …
Maximum likelihood calibration of the UNRES force field for simulation of protein structure and dynamics
P Krupa, A Hałabis, W Zmudzinska… - Journal of chemical …, 2017 - ACS Publications
By using the maximum likelihood method for force-field calibration recently developed in our
laboratory, which is aimed at achieving the agreement between the simulated …
laboratory, which is aimed at achieving the agreement between the simulated …
The multiscale coarse-graining method. X. Improved algorithms for constructing coarse-grained potentials for molecular systems
A Das, L Lu, HC Andersen, GA Voth - The Journal of Chemical Physics, 2012 - pubs.aip.org
The multiscale coarse-graining (MS-CG) method uses simulation data for an atomistic model
of a system to construct a coarse-grained (CG) potential for a coarse-grained model of the …
of a system to construct a coarse-grained (CG) potential for a coarse-grained model of the …
The multiscale coarse-graining method. III. A test of pairwise additivity of the coarse-grained potential and of new basis functions for the variational calculation
A Das, HC Andersen - The Journal of chemical physics, 2009 - pubs.aip.org
The multiscale coarse-graining (MS-CG) method, proposed by Izvekov and Voth [J. Phys.
Chem. B 109, 2469 (2005); Izvekov and Voth J. Chem. Phys. 123, 134105 (2005)], is a …
Chem. B 109, 2469 (2005); Izvekov and Voth J. Chem. Phys. 123, 134105 (2005)], is a …
Simulation of protein structure and dynamics with the coarse-grained UNRES force field
Simulations of protein structure were originally based on a hard-sphere potential coupled
with the requirement to avoid steric interactions [Ramachandran, Ramakrishnan, and …
with the requirement to avoid steric interactions [Ramachandran, Ramakrishnan, and …
Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements
R Zhou, GG Maisuradze, D Suñol… - Proceedings of the …, 2014 - National Acad Sciences
To demonstrate the utility of the coarse-grained united-residue (UNRES) force field to
compare experimental and computed kinetic data for folding proteins, we have performed …
compare experimental and computed kinetic data for folding proteins, we have performed …
Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers
In this chapter the scale-consistent approach to the derivation of coarse-grained force fields
developed in our laboratory is presented, in which the effective energy function originates …
developed in our laboratory is presented, in which the effective energy function originates …
Exploring the parameter space of the coarse‐grained UNRES force field by random search: Selecting a transferable medium‐resolution force field
We explored the energy‐parameter space of our coarse‐grained UNRES force field for large‐
scale ab initio simulations of protein folding, to obtain good initial approximations for …
scale ab initio simulations of protein folding, to obtain good initial approximations for …
Kinetic studies of folding of the B-domain of staphylococcal protein A with molecular dynamics and a united-residue (UNRES) model of polypeptide chains
M Khalili, A Liwo, HA Scheraga - Journal of molecular biology, 2006 - Elsevier
Langevin dynamics is used with our physics-based united-residue (UNRES) force field to
study the folding pathways of the B-domain of staphylococcal protein A (1BDD (α; 46 …
study the folding pathways of the B-domain of staphylococcal protein A (1BDD (α; 46 …
A novel high resolution CαCα distance dependent force field based on a high quality decoy set
R Rajgaria, SR McAllister… - … : Structure, Function, and …, 2006 - Wiley Online Library
This work presents a novel Cα Cα distance dependent force field which is successful in
selecting native structures from an ensemble of high resolution near‐native conformers. An …
selecting native structures from an ensemble of high resolution near‐native conformers. An …