• Publication by year
    1. 2018
    2. 2017
    3. 2016
    4. 2015
    5. 2014
    6. 2013
    7. 2012
    8. 2011
    9. 2016
    10. 2015
    11. 2014
    12. 2013
    13. 2012
    14. 2011


    Dawid AE, Gront D, Kolinski A,
    ,, Coarse-Grained Modeling of the Interplay between Secondary Structure Propensities rotein Fold Assembly.''
    J Chem Theory Comput 2018; 14: 2277-2287.
    Sicinska W, Gront D, Sicinski K,
    ,, Mutation goals in the vitamin D receptor predicted by computational methods.''
    J Steroid Biochem Mol Biol 2018; 183: 210-220.
    Matowane RG, Wieteska L, Bamal HD, Kgosiemang IKR, Van Wyk M, Manume NA, Abdalla SMH, Mashele SS, Gront D, Syed K,
    ,, In silico analysis of cytochrome P450 monooxygenases in chronic granulomatous tious fungus Sporothrix schenckii: Special focus on CYP51.''
    Biochim Biophys Acta Proteins Proteom 2018; 1866: 166-177.


    Dawid AE, Gront D, Kolinski A,
    ,, SURPASS Low-Resolution Coarse-Grained Protein Modeling.''
    J Chem Theory Comput 2017; 13: 5766-5779.


    Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A,
    ,, Coarse-Grained Protein Models and Their Applications.''
    Chem Rev 2016; 116: 7898-936.


    Wieteska L, Ionov M, Szemraj J, Feller C, Kolinski A, Gront D,
    ,, Improving thermal stability of thermophilic L-threonine aldolase from Thermotoga ima.''
    J Biotechnol 2015; 199: 69-76.


    Gniewek P, Kolinski A, Kloczkowski A, Gront D,
    ,, BioShell-Threading: versatile Monte Carlo package for protein 3D threading.''
    BMC Bioinformatics 2014; 15: 22.


    Wabik J, Kmiecik S, Gront D, Kouza M, Kolinski A,
    ,, Combining coarse-grained protein models with replica-exchange all-atom molecular ics.''
    Int J Mol Sci 2013; 14: 9893-905.


    Gront D, Grabowski M, Zimmerman MD, Raynor J, Tkaczuk KL, Minor W,
    ,, Assessing the accuracy of template-based structure prediction metaservers by rison with structural genomics structures.''
    J Struct Funct Genomics 2012; 13: 213-25.
    Gniewek P, Kolinski A, Gront D,
    ,, Optimization of profile-to-profile alignment parameters for one-dimensional ding.''
    J Comput Biol 2012; 19: 879-86.
    Gront D, Blaszczyk M, Wojciechowski P, Kolinski A,
    ,, BioShell Threader: protein homology detection based on sequence profiles and dary structure profiles.''
    Nucleic Acids Res 2012; 40: W257-62.
    Kmiecik S, Gront D, Kouza M, Kolinski A,
    ,, From coarse-grained to atomic-level characterization of protein dynamics: ition state for the folding of B domain of protein A.''
    J Phys Chem B 2012; 116: 7026-32.


    Gront D, Kulp DW, Vernon RM, Strauss CE, Baker D,
    ,, Generalized fragment picking in Rosetta: design, protocols and applications.''
    PLoS One 2011; 6: e23294.


    Wang S, Kirillova O, Chruszcz M, Gront D, Zimmerman MD, Cymborowski MT, Shumilin IA, Skarina T, Gorodichtchenskaia E, Savchenko A, Edwards AM, Minor W,
    ,, The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 an unusual interdigitated dimer with a new type of alpha + beta fold.''
    Protein Sci 2009; 18: 2410-9.


    Gront D, Kolinski A,
    ,, Fast and accurate methods for predicting short-range constraints in protein s.''
    J Comput Aided Mol Des 2008; 22: 783-8.
    Gront D, Kolinski A,
    ,, Utility library for structural bioinformatics.''
    Bioinformatics 2008; 24: 584-5.


    Ibryashkina EM, Zakharova MV, Baskunov VB, Bogdanova ES, Nagornykh MO, Den'mukhamedov MM, Melnik BS, Kolinski A, Gront D, Feder M, Solonin AS, Bujnicki JM,
    ,, Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease family.''
    BMC Struct Biol 2007; 7: 48.
    Gront D, Kolinski A,
    ,, T-Pile--a package for thermodynamic calculations for biomolecules.''
    Bioinformatics 2007; 23: 1840-2.
    Kolinski A, Gront D,
    ,, Comparative modeling without implicit sequence alignments.''
    Bioinformatics 2007; 23: 2522-7.
    Gront D, Kmiecik S, Kolinski A,
    ,, Backbone building from quadrilaterals: a fast and accurate algorithm for protein one reconstruction from alpha carbon coordinates.''
    J Comput Chem 2007; 28: 1593-1597.
    Kmiecik S, Gront D, Kolinski A,
    ,, Towards the high-resolution protein structure prediction. Fast refinement of ed models with all-atom force field.''
    BMC Struct Biol 2007; 7: 43.


    Kmiecik S, Kurcinski M, Rutkowska A, Gront D, Kolinski A,
    ,, Denatured proteins and early folding intermediates simulated in a reduced rmational space.''
    Acta Biochim Pol 2006; 53: 131-44.
    Gront D, Kolinski A,
    ,, BioShell--a package of tools for structural biology computations.''
    Bioinformatics 2006; 22: 621-2.
    Gront D, Kurcinski M, Kolinski A,
    ,, Clustering as a supporting tool for structural drug design.''
    Acta Pol Pharm 2006; 63: 436-8.


    Gront D, Kolinski A,
    ,, A new approach to prediction of short-range conformational propensities in ins.''
    Bioinformatics 2005; 21: 981-7.
    Gront D, Hansmann UH, Kolinski A,
    ,, Exploring protein energy landscapes with hierarchical clustering.''
    Int J Quantum Chem 2005; 105: 826-830.
    Gront D, Kolinski A,
    ,, HCPM--program for hierarchical clustering of protein models.''
    Bioinformatics 2005; 21: 3179-80.
    Gront D, Kolinski A, Hansmann UH,
    ,, Protein structure prediction by tempering spatial constraints.''
    J Comput Aided Mol Des 2005; 19: 603-8.


    Kolinski A, Gront D, Pokarowski P, Skolnick J,
    ,, A simple lattice model that exhibits a protein-like cooperative all-or-none ng transition.''
    Biopolymers 2003; 69: 399-405.