Publications

Product Name Usage: The full name of the product is the “Selvita Protein Modeling Platform.” On first mention of the tool, use the product’s full name. Following that, it is appropriate to use “Selvita Platform” only. Some recent publications with the use of Selvita Platform technology: Sen TZ, Kloster M, Jernigan RL, Kolinski A, Bujnicki JM, Kloczkowski A. Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA. Biophys J. 2008, 94(7), 2482-91 Kmiecik S. & Kolinski A. Folding pathway of the b1 domain of protein G explored by multiscale modeling. Biophys. J. 2008, 94, 726-36   Latek D. & Kolinski A. Contact prediction in protein modeling. Scoring, folding and refinement of coarse-grained models. BMC Structural Biology, 2008, 8, 36 Kmiecik S., Jamroz M., Zwolinska A., Gniewek P., Kolinski A. Designing an Automatic Pipeline for Protein Structure Prediction. From Computational Biophysics to Systems Biology, 2008, ed. U. H. E. Hansmann, J. H. Meinke, S. Mohanty, W. Nadler, O. Zimmermann, 40, 105-108  D. Gront & A. Kolinski. Utility library for structural bioinformatics.Bioinformatics, 2008, 24(4):584-585 Kolinski, A. & Gront, D. Comparative modeling without implicit sequence alignments. Bioinformatics, 2007, 23, 2522-2527 Kmiecik S., Gront D. & Kolinski A. Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field. BMC Structural Biology, 2007, 7, 43 Kmiecik S. & Kolinski A. Characterization of protein folding pathways by reduced-space modeling,  Proc. Natl. Acad. Sci. USA, 2007, 104(30), 12330-12335 Latek D., Ekonomiuk D., Kolinski A., Protein structure prediction: combining de novo modeling with sparse experimental data J. Comput. Chem. 2007, 28(10), 1668 – 1676 Kurcinski M., Kolinski A. Hierarchical modeling of protein interactions. J. Mol. Modeling, 2007, 13, 691–698 Kurcinski M., Kolinski A. Steps towards flexible docking: Modeling of three-dimensional structures of the nuclear receptors bound with peptide ligands mimicking co-activators’ sequences. J. Steroid Biochem. and Mol. Biol., 2007, 103, 357-60 Ibryashkina E. M., Zakharova M.V., Bogdanova E.S., Den’mukhamedov M.M., Melnik B.S.,  Kolinski A., Gront D., Feder M., Solonin A.S., Bujnicki J.M. Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily. BMC Structural Biology  2007, 7, 48 Gront D., Kmiecik S., Kolinski A. Backbone Building from Quadrilaterals. A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates. J. Comput. Chemistry, 2007, 28(9), 1593-1597 D. Gront & A. Kolinski. BioShell - a package of tools for structural biology computations. Bioinformatics, 2006, 22(5):621-622 Kolinski, A. & Bujnicki, J. M. Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models. Proteins, 2005, 61, 84-90 Bolesta E, Kowalczyk A, Wierzbicki A, Rotkiewicz P, Bambach B, Tsao CY, Horwacik I, Kolinski A, Rokita H, Brecher M, Wang X, Ferrone S, Kozbor D. DNA vaccine expressing the mimotope of GD2 ganglioside induces protective GD2 cross-reactive antibody responses. Cancer Research, 2005, 65(8):3410-8 D. Gront & A. Kolinski. HCPM - program for hierarchical clustering of protein models.Bioinformatics, 2005, 21(14):3179-3180 Kolinski A,  Protein modeling and structure prediction with a reduced representation. Acta Biochimica Polonica, 2004, 51, 349-371 Boniecki M, Rotkiewicz P, Skolnick J, A. Kolinski A, Protein fragment reconstruction using various modeling techniques. J. Computer Aided Molecular Design, 2003, 17, 725-737 Kihara D., Zhang Y., Kolinski A. and Skolnick J., Ab initio protein structure prediction on a genomic scale: Application to the Mycoplasma Genitalium Genome. Proc. Natl. Acad. Sci., USA, 2002, 99, 5993-5998 Sicinski R. R., Kolinski A., Rotkiewicz P., Sicinska W., Prahl J. M., Smith C. M. and De Luca H. F. 2-Ethyl and 2-Ethylidene Analogs of 1, 25-Dihydroxy-19-norvitamin D3: Synthesis, Conformational Analysis, Biological Activities, and Docking to the Modeled rVDR Ligand Binding Domain. J. Med. Chem., 2002, 45, 3366-3380