+
+ 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:
+
+-
+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. OÅdziej, 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.
+
+
+-
+A. Liwo, M. Baranowski, C. Czaplewski, E. GoÅaÅ, Y. He, D. JagieÅa,
+P. Krupa, M. Maciejczyk, M. Makowski, M.A. Mozolewska, A. Niadzvedtski,
+S. OÅdziej, H.A. Scheraga, A.K. Sieradzan, R. Ålusarz, 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.
+
+
+-
+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. HaÅabis, W. Å»mudziÅska, S. OÅdziej, 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, 2364â2377.
+
+
+-
+A. KarczyÅska, M.A. Mozolewska, P. Krupa, A. GieÅdoÅ, 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
+
+-
+ 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.
+
-
+ 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
+
+