UNRES server version 29.06.2018

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.

UNRES-Dock extension of the UNRES server allows for protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations.

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. 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.
    Nucleic Acids Res. 2018, 46, W304-W309. doi:10.1093/nar/gky328
  2. P. Krupa, A.S. Karczyńska, M.A. Mozolewska, A. Liwo, C. Czaplewski. UNRES-Dock - protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations.
    Bioinformatics 2021, 37, 1613-1615. doi:10.1093/bioinformatics/btaa897
  3. 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
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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. 2018, 86, 228-239.
  10. 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.
    J. Chem. Phys. 2019, 150, 155104.
  11. 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.
    J. Mol. Graph. Model. 2019, 92, 154-166.

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 the authorities of Cornell Univesity and University of Gdańsk
  • 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