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, S. Ołdziej, C. Czaplewski, D. Kleinerman, P. Blood and H.A.
Scheraga. Implementation of molecular dynamics and its extensions with the
coarse-grained UNRES force field on massively parallel systems; towards
millisecond-scale simulations of protein structure, dynamics, and
thermodynamics. J. Chem. Theory Comput. 2010, 6, 890-909.
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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.
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A. Karczyńska, M.A. Mozolewska, P. Krupa, A. Giełdoń, A. Liwo, C.
Czaplewski.Prediction of protein structure with the coarse-grained UNRES
force field assisted by small X-ray scattering data and knowledge-based
information.
Proteins: Struct. Funct. Bioinf. 2017, CASP12 special issue DOI: 10.1002/prot.25421
License terms of UNRES package implemented in the server
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This software is provided free of charge to academic users, subject to
the condition that no part of it be sold or used otherwise for
commercial purposes, including, but not limited to its incorporation
into commercial software packages, without written consent from the
authors. For permission contact Prof. H. A. Scheraga, Cornell
University.
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This software package is provided on an "as is" basis. We in no way
warrant either this software or results it may produce.
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Reports or publications using this software package must
contain an acknowledgment to the authors and the NIH Resource
in the form commonly used in academic research.
Third party software employed in the server