X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;ds=sidebyside;f=django_simple%2Ftodo%2Ftemplates%2Fabout.html;h=72262dff2d08cda5a0d9b886f96afdb75bc91574;hb=a5336a17e19ae271e1c139a9ba26422583aa116c;hp=deaf0a7dc93563bc321c483f1050442b1171ef8c;hpb=66d03f1186c3e250017870ebe160a66069536e4f;p=django_unres.git diff --git a/django_simple/todo/templates/about.html b/django_simple/todo/templates/about.html index deaf0a7..72262df 100644 --- a/django_simple/todo/templates/about.html +++ b/django_simple/todo/templates/about.html @@ -3,8 +3,130 @@ {% load i18n lazysignup_tags %} {% block content %} -
- UNRES server version 28.11.2017 +
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+ UNRES server version 01.12.2017 +

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+ 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. +

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+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: +

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  1. +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 +
    2. +
  2. +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. +
    3. + +
  3. +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. J. Chem. Theory Comput. 2010, 6, 890-909. +
    4. + +
  4. +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 +J. Mol. Model. 2014, 20, 1-15. +
    5. + +
  5. +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. +
    6. + +
  6. +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. +
    7. + +
  7. +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. +Proteins: Struct. Funct. Bioinf. 2017, CASP12 special issue DOI: 10.1002/prot.25421 +
    8. + +
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+License terms of UNRES package implemented in the server +

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  • + 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 + +
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