UNRES server version 29.06.2018
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.
UNRES-Dock extension of the UNRES server allows for
protein-protein and peptide-protein docking by coarse-grained
replica-exchange MD simulations.
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.
C. Czaplewski, A. Karczyńska, A.K. Sieradzan, A. Liwo.
UNRES server for physics-based coarse-grained simulations and prediction of
protein structure, dynamics and thermodynamics.
Nucleic Acids Res. 2018, 46, W304-W309.
P. Krupa, A.S. Karczyńska, M.A. Mozolewska, A. Liwo, C. Czaplewski.
UNRES-Dock - protein-protein and peptide-protein docking by coarse-grained
replica-exchange MD simulations.
Bioinformatics 2021, 37, 1613-1615.
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
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.
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
J. Chem. Theory Comput. 2010, 6, 890-909.
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,
A unified coarse-grained model of biological macromolecules based on
mean-field multipole-multipole interactions.
J. Mol. Model. 2014, 20, 1-15.
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.
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.
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
Proteins: Struct. Funct. Bioinf. 2018, 86, 228-239.
A. Liwo, A.K. Sieradzan, A.G. Lipska, C. Czaplewski, I.
Joung, W. Żmudzińska, A. Hałabis, S. Ołdziej.
A general method for the derivation of the functional forms of the effective
energy terms in coarse-grained energy functions of polymers. III.
Determination of scale-consistent backbone-local and correlation potentials
in the UNRES force field and force-field calibration and validation.
J. Chem. Phys. 2019, 150, 155104.
E.A. Lubecka, A.S. Karczyńska, A.G. Lipska, A.K.Sieradzan, K. Zięba, C. Sikorska,
U. Uciechowska, S.A. Samsonov, P. Krupa, M.A. Mozolewska, Ł. Golon, A. Giełdoń,
C. Czaplewski, R. Ślusarz, M. Ślusarz, S.N. Crivelli, A. Liwo.
Evaluation of the scale-consistent UNRES force field in template-free
prediction of protein structures in the CASP13 experiment.
J. Mol. Graph. Model. 2019, 92, 154-166.
License terms of UNRES package implemented in the server
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
For permission contact the authorities of Cornell Univesity and
University of Gdańsk
This software package is provided on an "as is" basis. We in no way
warrant either this software or results it may produce.
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