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- <br>
- UNRES server version 28.11.2017
+<div class="container" style="width: 110%;">
+<div class="row">
+<div class="col-sm-6">
+ <h4>
+ UNRES server version 01.12.2017
+ </h4>
+ <p><p>
+<b><a href="http://unres.pl"> UNRES</a></b>
+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 <i>ab
+initio</i> 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.
+</div>
+<div class="col-sm-6">
+<img src="static/unres_model_new.png" width="320">
+</div>
+<div class="col-sm-12">
+<p>
+<p>
+The <b>UNRES</b> 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 <i>ab initio</i> folding
+simulations and ab initio prediction of protein structures to predict the
+folds of fragments with 50-200 residues in length.
+<p>
+Selected references:
+<ol>
+<li>
+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.<br>
+<i> Nucleic Acids Res.</i> 2018, 46. W304-W309.
+<a href="https://doi.org/10.1093/nar/gky328">doi:10.1093/nar/gky328</a>
+</li>
+<li>
+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. <br>In: <i>Coarse-Graining of
+Condensed Phase and Biomolecular Systems.</i>, ed. G. Voth, Taylor & Francis,
+2008, Chapter 8, pp. 107-122
+</li>
+<li>
+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. <br>
+<i>J. Comput. Chem.</i> 2009, 30, 2127-2135.
+</li>
+
+<li>
+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.<br> <i>J. Chem. Theory Comput.</i> 2010, 6, 890-909.
+</li>
+
+<li>
+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.<br>
+<i>J. Mol. Model.</i> 2014, 20, 1-15.
+</li>
+
+<li>
+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.<br>
+<i>J. Chem. Theory. Comput.</i> 2015, 11, 817-831.
+</li>
+
+<li>
+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.<br>
+<i>J. Chem. Inf. Model.</i> 2017, 57, 2364–2377.
+</li>
+
+<li>
+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.<br>
+<i>Proteins: Struct. Funct. Bioinf.</i> 2018, 86, 228-239.
+</li>
+
+<li>
+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.<br>
+<i>J. Chem. Phys.</i> 2019, 150, 155104.
+</li>
+
+<li>
+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.<br>
+<i>J. Mol. Graph. Model.</i> 2019, 92, 154-166.
+</li>
+
+</ol>
+
+<p>
+License terms of UNRES package implemented in the server
+<ul>
+<li>
+ 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.
+<li>
+ This software package is provided on an "as is" basis. We in no way
+ warrant either this software or results it may produce.
+<li>
+ 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.
+</ul>
+
+Third party software employed in the server
+<ul>
+<li> <a href="https://github.com/arose/ngl"> NGL Viewer </a>
+<li> <a href="http://pymol.org"> pymol </a>
+<li> convpdb.pl from <a href="http://www.mmtsb.org/">MMTSB Tool Set</a>
+<li> tleap, sander and ambpdb from <a href="http://ambermd.org">Amber Tools</a>
+<li> <a href="http://cssb.biology.gatech.edu/PULCHRA"> pulchra </a>
+<li> <a href="http://dunbrack.fccc.edu/scwrl4/"> Scwrl4</a>
+<li> <a href="https://zhanglab.ccmb.med.umich.edu/TM-score/">tmscore</a>
+<li> <a href="https://github.com/bjornwallner/DockQ">DockQ</a>
+</ul>
+</div>
+
+</div>
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projects / django_unres.git / blobdiff