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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:

  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. 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. 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. 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. 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. 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. 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

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
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