Maya-K-PDB software for the three-dimensional modeling and visualization of the conformational dynamics of biomacromolecules
Matematičeskaâ biologiâ i bioinformatika, Tome 10 (2015) no. 1, pp. 260-282.

Voir la notice de l'article provenant de la source Math-Net.Ru

The concept of "active" molecular models was proposed. The Maya-K-PDB software for the creation of active molecular models in the 3D Maya environment was developed. The Maya-K-PDB provides various opportunities for dynamic visualization and modeling of conformational changes of biological macromolecules. Also many complicated processes on molecular level can be presented. The article describes the Maya-K-PDB user interface and illustrates basic examples of software implementation.
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S. V. Filippov; V. S. Sivozhelezov; V. L. Kim; V. V. Sychev; M. N. Ustinin. Maya-K-PDB  software for the three-dimensional modeling and visualization of the conformational dynamics of biomacromolecules. Matematičeskaâ biologiâ i bioinformatika, Tome 10 (2015) no. 1, pp. 260-282. http://geodesic.mathdoc.fr/item/MBB_2015_10_1_a17/

[1] Levinthal C., “Molecular Model-Building by Computer”, Scientific American, 214 (1966), 42–52 | DOI

[2] Chugunov A., Na zare molekulyarnoi grafiki, , Biomolekula (data obrascheniya: 11.06.2015) http://biomolecula.ru/print.php?id=50

[3] Polyanskii A., Molekulyarnaya dinamika biomolekul, , Biomolekula (data obrascheniya: 11.06.2015) http://biomolecula.ru/print.php?id=165

[4] Kholmurodov Kh. T., Altaiskii M. V., Puzynin I. V., Dardin T., Filatov F. P., “Metody molekulyarnoi dinamiki dlya modelirovaniya fizicheskikh i biologicheskikh protsessov”, Fizika elementarnykh chastits i atomnogo yadra, 34:2(5) (2003), 474–510

[5] Filippov S. V., Sobolev E. V., “Ispolzovanie tekhnologii professionalnoi kompyuternoi grafiki dlya vizualizatsii rezultatov nauchnykh issledovanii”, Kompyutery i superkompyutery v biologii, V 2-kh chastyakh, v. 2, eds. Lakhno V. D., Ustinin M. N., Institut kompyuternykh issledovanii, M.–Izhevsk, 2002, 476–497

[6] GROMACS, (data obrascheniya: 11.06.2015) http://www.gromacs.org

[7] Levitt M., “The birth of computational structural biology”, Nat. Struct. Biol., 8 (2001), 392–393 | DOI

[8] The RenderMan Interface. Version 3.2, , Pixar Inc., 2005 (data obrascheniya: 19.06.2015) http://renderman.pixar.com/products/rispec/rispec_pdf/RISpec3_2.pdf

[9] The RenderMan University. How To's, (data obrascheniya: 19.06.2015) http://renderman.pixar.com/view/how-to

[10] Blue Moon Rendering Tools, User Manual — release 2.6, Exluna Inc., Berkeley, 2000

[11] Blue Moon Rendering Tools, (data obrascheniya: 11.06.2015) http://web.archive.org/web/20020207051127/http://www.exluna.com/products/bmrt/download/index.html

[12] Pixie: an open source RenderMan, (data obrascheniya: 11.06.2015) http://www.renderpixie.com/

[13] Autodesk Maya: Comprehensive 3D animation software, (data obrascheniya: 11.06.2015) http://www.autodesk.com/products/autodesk-maya/overview

[14] Microsoft Visual Studio, (data obrascheniya: 11.06.2015) http://www.visualstudio.com/ru-ru/visual-studiohomepage-vs.aspx

[15] Worldwide Protein Data Bank, (data obrascheniya: 11.06.2015) http://www.wwpdb.org

[16] A Structural View of Biology, (data obrascheniya: 11.06.2015) http://www.rcsb.org/pdb/home/home.do

[17] Protein Data Bank Guide, (data obrascheniya: 11.06.2015) http://www.wwpdb.org/documentation/format33/v3.3.html

[18] Crabbe M. J. C., Appleyard J. R., Lay C. R., Desktop Molecular Modeller. Version 3.0, University Press, Oxford, 1995

[19] Autodesk Maya: MEL Overview, (data obrascheniya: 11.06.2015) http://knowledge.autodesk.com/support/maya/learn-explore/caas/CloudHelp/cloudhelp/2015/ENU/Maya/files/Background-MEL-Overview-htm.html?v=2015

[20] Gould A. D. D., Polnoe rukovodstvo po programmirovaniyu Maya. Podrobnoe opisanie yazyka MEL i interfeisa C++ ARG, KUDITs-OBRAZ, M., 2004, 528 pp.

[21] Humphrey W., Dalke A., Schulten K., “VMD — Visual Molecular Dynamics”, J. Molec. Graphics, 14:1 (1996), 33–38 | DOI

[22] Ivaikina A. G., Balabaev N. K., Shaitan K. V., “Opredelenie vliyaniya peptidnoi struktury na energetiku reaktsii okisleniya-vosstanovleniya belkov, soderzhaschikh Fe$_4$S$_4$ klastery, s pomoschyu kompyuternykh eksperimentov”, Biofizika, 46:4 (2001), 589–594

[23] Balabaev N. K., Lemak A. S., Shaitan K. V., “Molekulyarnaya dinamika i elektron-konformatsionnye vzaimodeistviya v ferredoksine”, Molekulyarnaya biologiya, 30:6 (1996), 1345–1356

[24] Filippov S. V., Metody i algoritmy vizualizatsii strukturnykh i dinamicheskikh dannykh, kharakterizuyuschikh makromolekulyarnye struktury, Dissertatsiya na soiskanie uchenoi stepeni k.f.-m.n., Puschino, 2014

[25] Pylypenko O., Rak A., Reents R., Niculae A., Sidorovitch V., Cioaca M. D., Bessolitsyna E., Thoma N. H., Wildmann H., Shlichting I., Goody R. S., Alexandrov K., “Structure of Rab escort protein-1 in complex with Rab geranylgeranyltransferase”, Molecular cell, 11:2 (2003), 483–494 | DOI

[26] Rak A., Pylypenko O., Niculae F., Pyatkov K., Goody R. S., Alexandrov K., “Structure of the Rab7:REP-1 complex: insighits into mechanism of Rab prenylation and choroidermia disease”, Cell, 117:6 (2004), 749–760 | DOI

[27] Fusion, (data obrascheniya: 11.06.2015) https://www.blackmagicdesign.com/products/fusion

[28] Novikov G. V., Sivozhelezov V. S., Shaitan K. V., “Issledovanie konformatsionnoi dinamiki ligand-aktiviruemykh membrannykh retseptorov metodom analiza glavnykh komponent”, Biokhimiya, 78 (2013), 522–532

[29] Novikov G. V., Sivozhelezov V. S., Shaitan K. V., “Vliyanie svyazyvaniya ortostericheskikh ligandov na konformatsionnuyu podvizhnost beta-2-adrenoretseptora”, Molekulyarnaya biologiya, 48 (2014), 463–479 | DOI

[30] Novikov G. V., Sivozhelezov V. S., Kolesnikov S. S., Shaitan K. V., “Investigation of the influence of external factors on the conformational dynamics of rhodopsin-like receptors by means of molecular dynamics simulation”, Journal of Receptors and Signal Transduction, 34 (2014), 104–118 | DOI

[31] Alekseev E. S., Bogdan T. V., “Vliyanie kholesterina na stabilizatsiyu sostoyaniya $\beta$2-adrenoretseptora s otkrytym ionnym zamkom: molekulyarno-dinamicheskoe modelirovanie”, Izvestiya RAN. Seriya khimicheskaya, 2013, no. 12, 2567–2573

[32] Alekseev E. S., Bogdan T. V., “Aktivatsiya $\beta$2-adrenoretseptora v rezultate mutatsii v saite svyazyvaniya kholesterina: molekulyarno-dinamicheskoe modelirovanie”, Izvestiya RAN. Seriya khimicheskaya, 2014, no. 5, 1095–1101

[33] Lakhno V. D., Fialko N. S., “Modelirovanie protsessov perenosa zaryada v DNK”, Dinamicheskie modeli protsessov v kletkakh i subkletochnykh strukturakh, eds. Riznichenko G. Yu., Rubin A. B., NITs «Regulyarnaya i khaoticheskaya dinamika», M.–Izhevsk, 2010, 11–67

[34] Nesterova E. N., Fedorov O. Yu., Poltev V. I., Chuprina V. P., “The study of possible A and B conformations of alternating DNA using a new program for conformational analysis of duplexes (CONAN)”, J. Biomol. Struct. Dyn., 1997, 459–474 | DOI

[35] Filippov S. V., Nesterova E. N., Chuprina V. P., Poltev V. I., “Modelirovanie izmenenii konformatsii i stabilnosti dvoinoi spirali DNK pri genotoksicheskoi modifikatsii osnovanii. I: Nizkoenergeticheskie konformatsii nativnogo dupleksa”, Molekulyarnaya biologiya, 31:5 (1997), 847–854