Гайнулин Мурат Рушанович

Кафедра прикладной математики
Доцент
Кандидат медицинских наук
muratg@fmed.uc.pt

• Введение в биоинформатику
• Биоинформатика

Избранные публикации:

• Prakhov N.D., Chernorudskiy A.L., Gainullin M.R. (2010) VSDocker: a tool for parallel high-throughput virtual screening using AutoDock on Windows-based computer clusters. Bioinformatics, Vol. 26 (10), P. 1374-1375. PMID: 20378556.
• Chernorudskiy A.L., Garcia A., Eremin E.V., Shorina A.S., Kondratieva E.V., Gainullin M.R. (2007) UbiProt: a database of ubiquitylated proteins. BMC Bioinformatics 8 (1): 126. PMID: 17442109.
• Khvatova E.M., Garsia A., Gainullin M.R. (2007) [Properties of NAD-dependent brain enzymes under the conditions of hypoxia and ischemia] Vestn Ross Akad Med Nauk N2: 13 – 6. (in Russian). PMID: 17396558
• Chernorudskiy A.L., Shorina A.S., Garcia A., Gainullin M.R. (2006) Prediction of direct effects of protein ubiquitylation using computational analysis. Biophysics, Vol. 51, Suppl. 1, 39-43.
• Chernorudskiy A.L., Shorina A.S., Garcia A., Gainullin M.R. (2006) Direct influence of ubiquitylation on a target protein activity: “loss-of-function” mechanism revealed by computational analysis. Proceedings of the Fifth International Conference on Bioinformatics of Genome Regulation and Structure. Edited by N. Kolchanov and R. Hofestadt (Novosibirsk, Russia, July 16–22, 2006), Vol. 1, p. 252 – 255. ISBN: 978-5-7692-0846-1
• Gainullin M.R., Garcia A. (2005) Role of ubiquitin system in the pathogenesis of malignancies. Nizhegorodsky Medical Journal N1: 128 – 134 (in Russian)
• Gainullin M.R., Shorina A.S. (2003) Bioinformatical analysis of the spatial organization of ubiquitylation target proteins. Nizhegorodsky Medical Journal N1: 66 – 73 (in Russian)
• Jennissen H.P., Khvatova E.M., Gainullin M.R. (2000) Ubiquitin – factor of protein degradation and functional regulation in the cell. The role in pathology. Nizhegorodsky Medical Journal N1: 104 – 109 (in Russian)
• Khvatova E.M., Yerlykina E.I., Gaynullin M.R., Michaleva I.I. (1997) Brain metabolic adaptation to hypoxia stress. In: Neurochemistry: cellular, molecular and clinical aspects (Teelken A., Korf J., eds.), New York, London, Washington D.C., Boston: Plenum Press, p. 757-760. ISBN: 0-306-45705-9
• Khvatova, E.M., Gainullin, M.R., Mikhaleva, I.I. (1995) The effect of delta sleep-inducing peptide on catalytic properties of brain mitochondrial malate dehydrogenase. Biull. Eksp. Biol. Med. 119 (2): 141 – 143 (in Russian). PMID: 7670034
• Prakhov N.D., Chernorudskiy A.L., Gainullin M.R. (2010) VSDocker tool: using Autodock 4 on Windows-based computer clusters for virtual screening. The 7th International Conference on Bioinformatics of Genome Regulation and Structure/System Biology, Novosibirsk, Russia, June 20-27, 2010. P. 236.
• Zhabereva A.S., Chaplygina E.V., Gainullin M.R. (2010) Classification of the HECT domain ubiquitin ligases based on phylogenetic and structure-function analisys. Fifth International Conference “SUMO, Ubiquitin, and UBL Proteins: Implications for Human Diseases”; Houston, Texas, February 10-13, 2010, P. 105
• Gainullin M.R., Chernorudskiy A., Zgoda V., Astashev M., Kondratieva E., Garcia A. (2009) Combining computational and proteomic approaches to inventory ubiquitylated proteins. 5th Congress of the Portuguese Proteomics Network – ProCura / 1st International Congress on Analytical Proteomics - ICAP, Caparica, Portugal, September 30th - October 3rd, 2009, P. 113.
• Chernorudskiy A.L., Kondratieva E.V., Zhabereva A.S., Zgoda V.G., Gainullin M.R. (2009) Probing the mechanism of autoubiquitylation of UBC13 (UBE2N) protein using Mass Spectrometry. International Conference on Biomolecular Science in honor of the 75th anniversary of the birth of Professor Yuri Ovchinnikov. September 28 - October 2, 2009. Moscow - Pushchino, Russia. Abstracts: Vol. 1, P. 401-402.
• Chernorudskiy A.L., Astashev M.E., Gainullin M.R. (2008) Ubident: a new tool for MS-based identification of ubiquitylation sites. The Sixth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS’2008), Novosibirsk, Russia, June 22-28, 2008, P. 50.
• Gainullin M.R., Chernorudskiy A.L., Kovalyov V.A., Eremin E.V., Astashev M.E., Garcia A. (2008) New computational resources for the studies of the ubiquitin system. Ibid, P. 79.
• Kovalyov V.A., Gainullin M.R., Eremin E.V., Garcia A. (2008) Ubiquitomix database: a new resource on ubiquitin system. Ibid, P. 125.
• Zhabereva A.S., Chaplygina E.V., Okunev O.E., Gainullin M.R. (2008) Classification and functional characterization of the HECT-domain ubiquitin-protein ligases. Ibid, P. 266.
• Gainullin M.R., Chernorudskiy A.L., Eremin E.V., Astashev M.E., Zhabereva A.S., Garcia A. (2008) A systems biology strategy for the studies of the ubiquitin system. 4th International Conference “Genomics, Proteomics, Bioinformatics and Nanobiotechnologies for Medicine” (GPBNM-2008), Moscow - Nizhny Novgorod - Moscow, June 1-7, 2008, P. 59.
• Chernorudskiy A., Shorina-Zhabereva A., Garcia A., Gainullin M. (2007) Direct effects of protein ubiquitylation revealed by computational analysis. EMBO Conference “Ubiquitin and Ubiquitin-like modifiers in cellular regulation”, Riva Del Garda, Italy, September 22-26, 2007, P. 45
• Chernorudskiy A., Garcia A., Eremin E., Shorina-Zhabereva A., Kondratieva E., Gainullin M. (2008) UbiProt database and analysis of protein ubiquitylation for application in pharmacological research. Fourth International Symposium on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources, Moscow, Russia, September 1-5, 2007, P. 88
• Gainullin M.R., Garcia A. (2007) Ubiquitin System as a Matter of Systems Biology. Proceedings of the 3-rd Moscow Conference on Computational Molecular Biology, Moscow, Russia, July 27-31 2007, P. 96-97
• Chernorudskiy A.L., Garcia A., Eremin E.V., Shorina A.S., Kondratieva E.V., Gainullin M.R. (2007) UbiProt: a database of ubiquitylated proteins as a tool for computational analysis of ubiquitylation. A joint meeting of the Genetics Society and the British Societies for the Cell and Developmental Biology, Edinburgh, UK, 29th March - 1st April 2007, P. 102-103
• Gainullin M. (2005) Introduction of bioinformatical approach in the study of protein ubiquitylation. Abstracts: The 2005 BGRS International Summer School "Evolution, Systems Biology and High Performance Computing Bioinformatics" (Novosibirsk, Russia, September 11-16, 2005).
• Chernorudskiy A. L., Gainullin M. R., Garcia A. (2005) Spatial limitations caused by ubiquitylation: analysis of 3D model of yeast peroxisomal citrate synthase–ubiquitin complex (Abstracts, 30th FEBS Congress - 9th IUBMB Conference, July 2-7, 2005, Budapest, Hungary, A3-013P) FEBS Journal 272, S1, p. 106.
• Chernorudsky A., Garcia A., Eremin E., Gainullin M. (2005) UbiProt: a tool for the study of protein ubiquitylation. Ubiquitin and Signaling (Tony Hunter, Claudio Joazeiro and Mark Hochstrasser, eds.). Abstracts: Keystone Symposium on Ubiquitin and Signaling (Taos Convention Center, Taos, New Mexico, USA, February 22 - 27, 2005), p. 46.
• Gainullin M.R., Jennissen H.P. (2000) Purification and identification of ubiquitin-protein conjugate from rabbit reticulocytes (Abstracts, Annual Fall Meeting of the GBM, October 10-13, 2000, Munich, Germany) Biol. Chem. 381, Suppl., S249.
• Alexander L. Chernorudskiy and Murat R. Gainullin, Ubiquitin System: Direct Effects Join the Signaling, Sci. Signal. 6 (280), pe22. (IF =7.6)