Nitano - novel inter/intramolecular colocation calculator

• Autorzy: Kuśka J. , Leluk J. , Lesyng B.
• Języki publikacji: EN

Abstrakty

EN

Nitano is a stand-alone Windows application. The main purpose of this software is to calculate the intra- or intermolecular residue colocations. A PDB file is used as input file. The application is to detect and analyse the intramolecular contacts as well as the contacts between residues from two separate chains/molecules (see Fig. 2). Nitano can be used for study the proteins and nucleic acids. The output files contain names, numbers and distances between the atoms that reveal collocation. The application gives two types of maps that show the structure on a two-dimensional image. Nitano allows to perform basic statistical analysis of obtained results. This application is a useful tool supporting the work of drug designers in creating more specific ligands. The application is freely available for educational and academic purposes at: http://www.bioware.republika.pl. Nitano is a user friendly application and does not require any advanced course to be applied for any kind of analysis.

Słowa kluczowe

EN

residue colocation; contact map; intermolecular/intramolecular interaction

• Wydawca: Uniwersytet Jagielloński - Collegium Medicum ; Index Copernicus Sp. z o.o.
• Czasopismo: Bio-Algorithms and Med-Systems
• Rocznik: 2010
• Tom: Vol. 6, no. 12
• Strony: 91--97
• Opis fizyczny: Bibliogr. 12 poz., rys., tab., wykr.

Twórcy

autor

Kuśka J.

• Faculty of Biology, Warsaw University, Poland
• CoE BioExploratorium, Warsaw University, Poland

autor

Leluk J.

• Faculty of Biological Sciences, University of Zielona Góra, Poland
• CoE BioExploratorium, Warsaw University, Poland

autor

Lesyng B.

• Faculty of Physics, University of Warsaw, Poland
• CoE BioExploratorium, Warsaw University, Poland

Bibliografia

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• 4. Kass I., Horovitz A.: Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations Proteins: Struct. Funct. & Genet. 48: 611-617, 2002.
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• 9. Pieper U.,  Eswar N., Davis F.P., Braberg H., Madhusudhan M.S., Rossi A., Marti-Renom M., Karchin R,, Webb B.M., Eramian D., Shen M.Y., Kelly L., Melo F.,  Sali A.,:  MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Research 34, D291-D295, 2006.
• 10. Sonnhammer E. L. L., Wooton J. C.: Dynamic contact maps of protein structure, Journal of Molecular Graphics and Modelling 16: 1-5, 1998.
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• 12. Vullo A., Walsh I., Pollastri G,: A two-stage approach for improved prediction of residue contact maps, BMC Bioinformatics 7:180, 2006.