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10 UNRES server version 01.12.2017
13 <b><a href="http://unres.pl"> UNRES</a></b>
14 is a highly reduced protein model; only two interaction sites: united
15 side chain and united peptide group per residue are present. Owing to this
16 reduction, it offers ~1000-4000-fold speed up in molecular dynamics
17 simulations compared to all-atom approaches. With recently introduced
18 parallelization of energy and force evaluation, it enables us to perform <i>ab
19 initio</i> folding simulations of 200-residue proteins in hours and simulations
20 of large biologically inportant conformational changes in large proteins
21 (e.g., molecular chaperones) in days of wall-clock time.
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24 <img src="static/unres_model_new.png" width="320">
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29 The <b>UNRES</b> force field has been developed on a solid statistical-mechanical
30 basis, by expanding the potential of mean force of a system containing
31 polypeptide chain(s) in water into cluster-cumulant series and
32 parameterization of the terms of the series (factors) based on simple model
33 systems. Therefore, even though no knowledge-based information is used in
34 simulations (from homology modeling, loop and contact prediction, etc.), the
35 force field, in its present version can be used in <i>ab initio</i> folding
36 simulations and ab initio prediction of protein structures to predict the
37 folds of fragments with 50-200 residues in length.
43 A. Liwo, C. Czaplewski, S. Oldziej, A.V. Rojas, R. Kazmierkiewicz, M.
44 Makowski, R.K. Murarka, H.A. Scheraga. Simulation of protein structure and
45 dynamics with the coarse-grained UNRES force field. In: <i>Coarse-Graining of
46 Condensed Phase and Biomolecular Systems.</i>, ed. G. Voth, Taylor & Francis,
47 2008, Chapter 8, pp. 107-122
51 Y. He, Y. Xiao, A. Liwo, H.A. Scheraga. Exploring the parameter space of the
52 coarse-grained UNRES force field by random search: selecting a transferable
53 medium-resolution force field.
54 <i>J. Comput. Chem.</i> 2009, 30, 2127-2135.
58 A. Liwo, S. Ołdziej, C. Czaplewski, D. Kleinerman, P. Blood and H.A.
59 Scheraga. Implementation of molecular dynamics and its extensions with the
60 coarse-grained UNRES force field on massively parallel systems; towards
61 millisecond-scale simulations of protein structure, dynamics, and
62 thermodynamics. <i>J. Chem. Theory Comput.<i> 2010, 6, 890-909.
66 A. Liwo, M. Baranowski, C. Czaplewski, E. Gołaś, Y. He, D. Jagieła,
67 P. Krupa, M. Maciejczyk, M. Makowski, M.A. Mozolewska, A. Niadzvedtski,
68 S. Ołdziej, H.A. Scheraga, A.K. Sieradzan, R. Ślusarz, T. Wirecki, Y. Yin,
70 A unified coarse-grained model of biological macromolecules based on
71 mean-field multipole-multipole interactions
72 <i>J. Mol. Model.</i> 2014, 20, 1-15.
76 A.K. Sieradzan, P. Krupa, H.A. Scheraga, A. Liwo, C. Czaplewski.
77 Physics-based potentials for the coupling between backbone- and
78 side-chain-local conformational states in the United Residue (UNRES) force
79 field for protein simulations.
80 <i>J. Chem. Theory. Comput.</i> 2015, 11, 817-831.
84 P. Krupa, A. Hałabis, W. Żmudzińska, S. Ołdziej, H.A. Scheraga, A. Liwo.
85 Maximum Likelihood Calibration of the UNRES Force Field for Simulation of
86 Protein Structure and Dynamics.
87 <i>J. Chem. Inf. Model.</i> 2017, 57, 2364–2377.
91 A. Karczyńska, M.A. Mozolewska, P. Krupa, A. Giełdoń, A. Liwo, C.
92 Czaplewski.Prediction of protein structure with the coarse-grained UNRES
93 force field assisted by small X-ray scattering data and knowledge-based
95 <i>Proteins: Struct. Funct. Bioinf.</i> 2017, CASP12 special issue DOI: 10.1002/prot.25421
101 License terms of UNRES package implemented in the server
104 This software is provided free of charge to academic users, subject to
105 the condition that no part of it be sold or used otherwise for
106 commercial purposes, including, but not limited to its incorporation
107 into commercial software packages, without written consent from the
108 authors. For permission contact Prof. H. A. Scheraga, Cornell
111 This software package is provided on an "as is" basis. We in no way
112 warrant either this software or results it may produce.
114 Reports or publications using this software package must
115 contain an acknowledgment to the authors and the NIH Resource
116 in the form commonly used in academic research.
119 Third party software employed in the server
121 <li> <a href="https://github.com/arose/ngl"> NGL Viewer </a>
122 <li> <a href="http://pymol.org"> pymol </a>
123 <li> convpdb.pl from <a href="http://www.mmtsb.org/">MMTSB Tool Set</a>
124 <li> tleap, sander and ambpdb from <a href="http://ambermd.org">Amber Tools</a>
125 <li> <a href="http://cssb.biology.gatech.edu/PULCHRA"> pulchra </a>
126 <li> <a href="http://dunbrack.fccc.edu/scwrl4/"> Scwrl4</a>
127 <li> <a href="https://zhanglab.ccmb.med.umich.edu/TM-score/">tmscore</a>