Dominik Gront

Summary

Affiliation: Warsaw University
Country: Poland

Publications

  1. pmc Protein structure prediction by tempering spatial constraints
    Dominik Gront
    Department of Physics, Michigan Technological University, Houghton, MI 49931 1295, USA
    J Comput Aided Mol Des 19:603-8. 2005
  2. doi request reprint BioShell-Threading: versatile Monte Carlo package for protein 3D threading
    Pawel Gniewek
    Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02 093 Warsaw, Poland
    BMC Bioinformatics 15:22. 2014
  3. pmc BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles
    Dominik Gront
    University of Warsaw, Faculty of Chemistry, Pasteura 1, 02 093 Warsaw, Poland
    Nucleic Acids Res 40:W257-62. 2012
  4. pmc Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily
    Elena M Ibryashkina
    Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
    BMC Struct Biol 7:48. 2007
  5. pmc Generalized fragment picking in Rosetta: design, protocols and applications
    Dominik Gront
    Faculty of Chemistry, University of Warsaw, Warsaw, Poland
    PLoS ONE 6:e23294. 2011
  6. doi request reprint Fast and accurate methods for predicting short-range constraints in protein models
    Dominik Gront
    Faculty of Chemistry, University of Warsaw, Warsaw, Poland
    J Comput Aided Mol Des 22:783-8. 2008
  7. ncbi request reprint BioShell--a package of tools for structural biology computations
    Dominik Gront
    Faculty of Chemistry, Warsaw University Pasteura 1, 02 093 Warsaw, Poland
    Bioinformatics 22:621-2. 2006
  8. ncbi request reprint Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates
    Dominik Gront
    Faculty of Chemistry, Warsaw University, Pasteura 1 02 093, Warsaw, Poland
    J Comput Chem 28:1593-7. 2007
  9. doi request reprint Utility library for structural bioinformatics
    Dominik Gront
    CUniversity of Warsaw, Faculty of Chemistry, Pasteura 1 02 093 Warsaw, Poland
    Bioinformatics 24:584-5. 2008
  10. ncbi request reprint T-Pile--a package for thermodynamic calculations for biomolecules
    Dominik Gront
    Warsaw University, Faculty of Chemistry, Pasteura 1 02 093 Warsaw, Poland
    Bioinformatics 23:1840-2. 2007

Detail Information

Publications20

  1. pmc Protein structure prediction by tempering spatial constraints
    Dominik Gront
    Department of Physics, Michigan Technological University, Houghton, MI 49931 1295, USA
    J Comput Aided Mol Des 19:603-8. 2005
    ..In this work, we present a new parallel tempering variant that alleviates the energy barriers resulting from spatial constraints and therefore yields to an enhanced sampling in structure prediction simulations...
  2. doi request reprint BioShell-Threading: versatile Monte Carlo package for protein 3D threading
    Pawel Gniewek
    Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02 093 Warsaw, Poland
    BMC Bioinformatics 15:22. 2014
    ..Any error made on this stage may dramatically affects the quality of result. There is a need, therefore, to develop accurate and sensitive alignment protocols...
  3. pmc BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles
    Dominik Gront
    University of Warsaw, Faculty of Chemistry, Pasteura 1, 02 093 Warsaw, Poland
    Nucleic Acids Res 40:W257-62. 2012
    ..Careful evaluation shows that there is nearly 80% chance that the query sequence belongs to the same SCOP family as the top scoring template. The Bioshell Threader server is freely available at: http://www.bioshell.pl/threader/...
  4. pmc Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily
    Elena M Ibryashkina
    Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
    BMC Struct Biol 7:48. 2007
    ..The determination of a crystal structure of the GIY-YIG domain of homing endonuclease I-TevI provided a template for modeling of R.Eco29kI and prompted us to validate the model experimentally...
  5. pmc Generalized fragment picking in Rosetta: design, protocols and applications
    Dominik Gront
    Faculty of Chemistry, University of Warsaw, Warsaw, Poland
    PLoS ONE 6:e23294. 2011
    ..We demonstrate that the program provides at least as good building blocks for ab-initio structure prediction as the previous program, and provide examples of the wide range of applications that are now accessible...
  6. doi request reprint Fast and accurate methods for predicting short-range constraints in protein models
    Dominik Gront
    Faculty of Chemistry, University of Warsaw, Warsaw, Poland
    J Comput Aided Mol Des 22:783-8. 2008
    ..As a result a statistics of distances observed in the similar fragments is returned. The method can be used also as a scoring function or a short-range knowledge-based potential based on the computed statistics...
  7. ncbi request reprint BioShell--a package of tools for structural biology computations
    Dominik Gront
    Faculty of Chemistry, Warsaw University Pasteura 1, 02 093 Warsaw, Poland
    Bioinformatics 22:621-2. 2006
    ..BioShell design is based on UNIX shell flexibility and should be used as its extension. Using BioShell various molecular modeling procedures can be integrated in a single pipeline...
  8. ncbi request reprint Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates
    Dominik Gront
    Faculty of Chemistry, Warsaw University, Pasteura 1 02 093, Warsaw, Poland
    J Comput Chem 28:1593-7. 2007
    ..The BBQ package is available for downloading from our website at http://biocomp.chem.uw.edu.pl/services/BBQ/. This webpage also provides a user manual that describes BBQ functions in detail...
  9. doi request reprint Utility library for structural bioinformatics
    Dominik Gront
    CUniversity of Warsaw, Faculty of Chemistry, Pasteura 1 02 093 Warsaw, Poland
    Bioinformatics 24:584-5. 2008
    ..Availability The software is available for download free of charge from its website: http://bioshell.chem.uw.edu.pl. This website provides also numerous examples, code snippets and API documentation...
  10. ncbi request reprint T-Pile--a package for thermodynamic calculations for biomolecules
    Dominik Gront
    Warsaw University, Faculty of Chemistry, Pasteura 1 02 093 Warsaw, Poland
    Bioinformatics 23:1840-2. 2007
    ..The package can be used in studies of virtually any system governed by Boltzmann distribution...
  11. ncbi request reprint A new approach to prediction of short-range conformational propensities in proteins
    Dominik Gront
    Faculty of Chemistry, Warsaw University Pasteura 1, 02 093 Warsaw, Poland
    Bioinformatics 21:981-7. 2005
    ..The new potentials could be valuable components of threading algorithms, ab-initio protein structure prediction, comparative modeling and structure modeling based on fragmentary experimental data...
  12. ncbi request reprint HCPM--program for hierarchical clustering of protein models
    Dominik Gront
    Faculty of Chemistry, Warsaw University Pasteura 1, 02 093 Warsaw, Poland
    Bioinformatics 21:3179-80. 2005
    ..A hierarchical clustering algorithm is designed and tested, and a heuristic is provided for an optimal cluster selection. The method has been successfully tested during the CASP6 experiment...
  13. ncbi request reprint Comparative modeling without implicit sequence alignments
    Andrzej Kolinski
    University of Warsaw, Faculty of Chemistry, Pasteura 1 02 093 Warsaw, Poland
    Bioinformatics 23:2522-7. 2007
    ..The algorithm unifies de novo modeling, 3D threading and sequence-based methods. The main idea is general and could be easily combined with other efficient modeling tools as Rosetta, UNRES and others...
  14. ncbi request reprint Denatured proteins and early folding intermediates simulated in a reduced conformational space
    Sebastian Kmiecik
    Faculty of Chemistry, Warsaw University, Warszawa, Poland
    Acta Biochim Pol 53:131-44. 2006
    ..e. not only for the modeling of folded structures, as it was shown in previous studies. The results of the present studies also provide a new insight into the explanation of the Levinthal's paradox...
  15. doi request reprint Optimization of profile-to-profile alignment parameters for one-dimensional threading
    Pawel Gniewek
    Faculty of Chemistry, Warsaw University, Warsaw, Poland
    J Comput Biol 19:879-86. 2012
    ..Our benchmark set, which might be useful in other similar studies, as well as the fold-recognition software we developed may be downloaded (www.bioshell.pl/profile-alignments)...
  16. pmc Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field
    Sebastian Kmiecik
    University of Warsaw, Faculty of Chemistry, Pasteura 1, Warsaw, Poland
    BMC Struct Biol 7:43. 2007
    ..Development of high-accuracy computational methods that reliably generate near-experimental quality structural models is an important, unsolved problem in the protein structure modeling...
  17. ncbi request reprint A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition
    Andrzej Kolinski
    Faculty of Chemistry, Warsaw University, Pasteura 1, 02 093 Warsaw, Poland
    Biopolymers 69:399-405. 2003
    ....
  18. ncbi request reprint Clustering as a supporting tool for structural drug design
    Dominik Gront
    Warsaw University, Faculty of Chemistry, Pasteura 1, 02 093 Warsaw, Poland
    Acta Pol Pharm 63:436-8. 2006
  19. pmc Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics
    Jacek Wabik
    Faculty of Chemistry, University of Warsaw, L Pasteura 1, Warsaw 02 093, Poland
    Int J Mol Sci 14:9893-905. 2013
    ..The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems...
  20. doi request reprint From coarse-grained to atomic-level characterization of protein dynamics: transition state for the folding of B domain of protein A
    Sebastian Kmiecik
    Faculty of Chemistry, University of Warsaw, Pasteura 1, 02 093 Warsaw, Poland
    J Phys Chem B 116:7026-32. 2012
    ..This, together with the all-atom characterization of the obtained ensembles, in the form of contact maps, matches the experimental results well...