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. pmc 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. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Detail Information

Publications21

  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. pmc 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. 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...
  6. 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...
  7. 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...
  8. 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...
  9. 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...
  10. 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...
  11. 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...
  12. 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...
  13. 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...
  14. 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...
  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...
  21. doi request reprint Improving thermal stability of thermophilic l-threonine aldolase from Thermotoga maritima
    Lukasz Wieteska
    Department of Medical Biochemistry, Medical University of Lodz, ul Mazowiecka 6 8, 92 215 Lodz, Poland Laboratory of Theory of Biopolymers, University of Warsaw, Pasteura 1, 02 093 Warsaw, Poland Electronic address
    J Biotechnol 199:69-76. 2015
    ....