<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. In: <i>Coarse-Graining of
+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.
+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
+mean-field multipole-multipole interactions.<br>
<i>J. Mol. Model.</i> 2014, 20, 1-15.
</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.
+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.
+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>
+</ul>
</div>
</div>
projects / django_unres.git / blobdiff