UNRES server version 01.12.2017
UNRES
is a highly reduced protein model; only two interaction sites: united
side chain and united peptide group per residue are present. Owing to this
reduction, it offers ~1000-4000-fold speed up in molecular dynamics
simulations compared to all-atom approaches. With recently introduced
parallelization of energy and force evaluation, it enables us to perform ab
initio folding simulations of 200-residue proteins in hours and simulations
of large biologically inportant conformational changes in large proteins
(e.g., molecular chaperones) in days of wall-clock time.
The UNRES force field has been developed on a solid statistical-mechanical
basis, by expanding the potential of mean force of a system containing
polypeptide chain(s) in water into cluster-cumulant series and
parameterization of the terms of the series (factors) based on simple model
systems. Therefore, even though no knowledge-based information is used in
simulations (from homology modeling, loop and contact prediction, etc.), the
force field, in its present version can be used in ab initio folding
simulations and ab initio prediction of protein structures to predict the
folds of fragments with 50-200 residues in length.
Selected references:
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A. Liwo, C. Czaplewski, S. Oldziej, A.V. Rojas, R. Kazmierkiewicz, M.
Makowski, R.K. Murarka, H.A. Scheraga. Simulation of protein structure and
dynamics with the coarse-grained UNRES force field. In: Coarse-Graining of
Condensed Phase and Biomolecular Systems., ed. G. Voth, Taylor & Francis,
2008, Chapter 8, pp. 107-122
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Y. He, Y. Xiao, A. Liwo, H.A. Scheraga. Exploring the parameter space of the
coarse-grained UNRES force field by random search: selecting a transferable
medium-resolution force field.
J. Comput. Chem. 2009, 30, 2127-2135.
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A. Liwo, M. Baranowski, C. Czaplewski, E. Gołaś, Y. He, D. Jagieła,
P. Krupa, M. Maciejczyk, M. Makowski, M.A. Mozolewska, A. Niadzvedtski,
S. Ołdziej, H.A. Scheraga, A.K. Sieradzan, R. Ślusarz, T. Wirecki, Y. Yin,
B. Zaborowski.
A unified coarse-grained model of biological macromolecules based on
mean-field multipole-multipole interactions
J. Mol. Model. 2014, 20, 1-15.
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A.K. Sieradzan, P. Krupa, H.A. Scheraga, A. Liwo, C. Czaplewski.
Physics-based potentials for the coupling between backbone- and
side-chain-local conformational states in the United Residue (UNRES) force
field for protein simulations.
J. Chem. Theory. Comput. 2015, 11, 817-831.
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P. Krupa, A. Hałabis, W. Żmudzińska, S. Ołdziej, H.A. Scheraga, A. Liwo.
Maximum Likelihood Calibration of the UNRES Force Field for Simulation of
Protein Structure and Dynamics.
J. Chem. Inf. Model. 2017, 57, 2364–2377.