Reviews and Book Chapters


Suplatov, D., Kirilin, E., & Švedas, V. (2016). Bioinformatic Analysis of Protein Families to Select Function-Related Variable Positions. In Understanding Enzymes: Function, Design, Engineering, and Analysis (pp. 351-385) Ed. Allan Svendsen. Pan Stanford. DOI:10.1201/b19951-13


Суплатов Д.А., Воеводин Вл В., Попова Н.Н., Швядас В.К. (2016) Поиск новых путей регуляции функциональных свойств ферментов с использованием высокопроизводительных вычислений. В сборнике "Суперкомпьютерные технологии в науке, образовании и промышленности", 7-й выпуск, Под редакцией академика В.А. Садовничего, академика Г.И. Савина, чл.-корр. РАН Вл.В. Воеводина, Издательство Московского университета Москва, стр. 127-134.


Suplatov, D., & Švedas, V. (2015). Study of functional and allosteric sites in protein superfamilies. Acta Naturae, 7(4), 27, 34-45. PMID:26798490 PMC:PMC4717248


Suplatov D.A., Voevodin V.V., Švedas V.K. (2015) Robust enzyme design: Bioinformatic tools for improved protein stability. Biotechnol J., 10: 344–355. DOI:10.1002/biot.201400150 PMID:25524647


Suplatov D., Voevodin V., Švedas V. (2013) "Supercomputing technologies open new perspectives for bioinformatic analysis of large enzyme superfamilies and solving large-scale tasks of biocatalysis" in "Supercomputer technologies in science, education and industry, 4th edition", eds. Viktor Sadovnichiy, Gennady Savin and Vladimir Voevodin. Moscow State University Publishing: pp. 103-110





Research Papers


Suplatov D., Popova N., Zhumatiy S., Voevodin V., Švedas V. (2016). Parallel workflow manager for non-parallel bioinformatic applications to solve large-scale biological problems on a supercomputer. J. Bioinform. Comput. Biol., 14(02), 1641008. DOI:10.1142/S0219720016410080 PMID:27122320


Bezsudnova E., Stekhanova T., Suplatov D., Mardanov A., Ravin N., Popov V. (2016). Experimental and computational studies on the unusual substrate specificity of branched-chain amino acid aminotransferase from Thermoproteus uzoniensis. Arch. Biochem. Biophys., 607, 27-36. DOI:10.1016/j.abb.2016.08.009 PMID:27523731


Shcherbakova T.A., Panin N.V., Suplatov D.A., Shapovalova I.V., Švedas V.K. (2015) The βD484N mutant of penicillin acylase from Escherichia coli is more resistant to inactivation by substrates and can effectively perform peptide synthesis in aqueous medium J. Mol. Catal. B Enzym., 112: 66–68. DOI:10.1016/j.molcatb.2014.11.015


Suplatov D., Kirilin E., Arbatsky M., Takhaveev V., Švedas V. (2014). pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families. Nucl. Acids Res., 42(W1): W344-W349. DOI:10.1093/nar/gku448 PMID:24852248


Suplatov D., Panin N., Kirilin E., Shcherbakova T., Kudryavtsev P., Švedas V. (2014) Computational Design of a pH Stable Enzyme: Understanding Molecular Mechanism of Penicillin Acylase's Adaptation to Alkaline Conditions. PLoS ONE, 9(6): e100643. DOI:10.1371/journal.pone.0100643 PMID:24959852


Suplatov D., Shalaeva D., Kirilin E., Arzhanik V., Švedas V. (2014). Bioinformatic analysis of protein families for identification of variable amino acid residues responsible for functional diversity. J.Biomol.Struct.Dyn. 32(1): 75-87. DOI:10.1080/07391102.2012.750249 PMID:23384165


Suplatov D., Kirilin E., Takhaveev V., Švedas V. (2014). Zebra: web-server for bioinformatic analysis of diverse protein families, J.Biomol.Struct.Dyn., 32(11): 1752-1758. DOI:10.1080/07391102.2013.834514 PMID:24028489


Eldarov M., Lyashenko A., Sherbakova T., Suplatov D., Kopylov K., Švedas V. (2014) Probing the Substrate Specificity and Intersubunit Interactions of Brevundimonas Diminuta Glutaryl Acylase with Site-Directed Mutagenesis Am. J. Biochem. Biotechnol., 10(3): 169-179. DOI:10.3844/ajbbsp.2014.169.179


Suplatov D.A., Besenmatter W., Švedas V.K., Svendsen A. (2012). Bioinformatic analysis of alpha/beta-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities. Protein Eng.Des.Sel., 25(11): 689-697. DOI:10.1093/protein/gzs068 PMID:23043134


Suplatov D.A., Arzhanik V.K., Švedas V.K. (2011). Comparative Bioinformatic Analysis of Active Site Structures in Evolutionarily Remote Homologues of α,β-Hydrolase Superfamily Enzymes. Acta naturae, 3(1): 93-8. PMID:22649677


Khaliullin I., Suplatov D., Shalaeva D., Otsuka M., Asano Y., Švedas V. (2010). Bioinformatic analysis and molecular modeling reveal the role of Lys65 residue in the catalytic triad of D-aminopeptidase from Ochrobactrum anthropi. Acta Naturae, 2(2): 66-71. PMID:22649642





Patents


Suplatov D., Kudryavtsev P., Panin N., Sherbakova T., Švedas V.: The mutant of penicillin acylase from E.coli with enchanced properties. #RU 2564578 С2; October 10th, 2015.





Conferences: talks and lectures


Suplatov D., Popova N., Kopylov K., Shegay M., Voevodin V., Švedas V. (2017). Hybrid Computing Clusters to Study Protein Structure, Function and Regulation. International Conference Russian Supercomputing Days 2017, September 25-26, 2017, Russia (Moscow).


D.A. Suplatov, K.E. Kopylov, N.N. Popova, V.V. Voevodin, V.K. Švedas (2017). Structure-based sequence alignments of functionally diverse protein families as a tool in protein engineering. JOINT LIFE SCIENCES FORUM 2017: 12th International scientific conference on bioorganic chemistry devoted to the memory of professor Yuri Ovchinnikov and 8th Russian symposium “Proteins and peptides”, September 18–22, 2017, Russia (Moscow). Supplementary data.


Suplatov D., Schmalhausen E., Muronets V., Švedas V. (2017) Bioinformatic analysis of subfamily-specific positions reveals a previously unknown regulatory site in Glyceraldehyde 3-phosphate dehydrogenase family of proteins. International Moscow Conference on Computational Molecular Biology MCCMB-2017, July 27-30, 2017, Russia (Moscow)


Panin N., Shcherbakova T., Suplatov D., Švedas V. (2016) Design of stabilized penicillin acylase variants and their applications for synthesis. 22nd International Conference "INPEC-2016" (International Network of Protein Engineering Centers), November 6-10, 2016, Republic of Korea (Daejeon).


Suplatov D.A., Panin N.K., Kopylov K.E., Švedas V.K. (2016) Modulation Of Enzyme Functional Properties. V Biochemistry Congress, October 4-8, 2016, Russia (Sochi).


Suplatov D., Kopylov K., Mironov A.А., Švedas V. (2016) Statistical Analysis Of Linear Trends In Protein Motion To Study Induced Conformational Changes In Protein Structures. International Symposium «Systems Biology and Bioinformatics», June 30 - July 2, 2016, Russia (St. Petersburg).


Suplatov D., Panin N., Shcherbakova T., Khaliullin I., Švedas V. (2015) Bioinformatic analysis of diverse protein superfamilies to design improved enzymes. Moscow Conference on Computational Molecular Biology (MCCMB'15), July 16-19, 2015, Russia (Moscow).


Suplatov D., Zlobin A., Švedas V. (2015) Bioinformatic analysis of binding sites in protein superfamilies for design of selective inhibitors of enzymes from pathogens. Biocatalysis 2015, June 21-26, 2015, Russia (Istra).


Воеводин Вл В., Шегай М.В., Попова Н.Н., Суплатов Д.А., Швядас В.К. (2016) Использование параллельных вычислений для эффективного построения множественных выравниваний структур белков. Параллельные вычислительные технологии (ПаВТ) 2016, 28 марта - 1 апреля 2016, Россия (Архангельск).


Суплатов Д.А., Панин Н.В., Швядас В.К., Халиуллин И.Г. (2015) Рациональный дизайн ферментов с использованием методов биоинформатики и молекулярного моделирования. VIII Московский международный конгресс «Биотехнология: Состояние и перспективы развития», 17-20 марта 2015, Москва, Россия


Suplatov D., Švedas V. (2014) Bioinformatic analysis of diverse protein families: publicly available tools to study functional and regulatory sites in protein structures and design novel enzymes. INPEC-2014, September 10-14th, Russia (Sankt-Petersburg), pp. 22-23.
Supplementary materials: biokinet.belozersky.msu.ru/inpec2014


Švedas V., Khaliullin I., Panin N., Suplatov D. (2014) Design of novel biocatalysts with improved functional properties based on bioinformatic analysis of diverse enzyme families and molecular modeling. INPEC-2014, September 10-14th, Russia (Sankt-Petersburg), pp. 20-21.


Suplatov D., Panin N., Khaliullin I., Švedas V. (2014) Knowledge-based design of enzyme functional properties. XIII International Conference of Lithuanian Biochemical Society dedicated to the 50th anniversary of FEBS, Birstonas, Lithuania, June 17-20, 2014


Švedas V., Panin N., Shcherbakova T., Suplatov D. (2014) Computational design of stabilized penicillin acylase to improve its catalytic performance. ProtStab2014, May 7-9, Italy (Stresa), p.42


Suplatov D. and Švedas V. (2013) Understanding structure-function relationship in protein families: bioinformatics and molecular modeling provide new concept for enzyme engineering. FEBS Congress 2013 Mechanisms in Biology, July 6-11, Russia (Sankt-Petersburg), FEBS Journal, 280 (Suppl. 1), 589. DOI:10.1111/febs.12340


Suplatov D., Khaliullin I., Panin N., Švedas V. (2013) Bioinformatic analysis of sequence and structural data to study structure-function relationship in diverse protein superfamilies and develop novel enzyme engineering strategies. International conference Biocatalysis-2013, July 2-5, Russia (Moscow), p.25


Takhaveev V. and Suplatov D. (2013) Bioinformatic analysis of glutaryl acylases reveals key residues responsible for substrate discrimination. International Conference Lomonosov-2013, April 8-13, Russia (Moscow)


Suplatov D. and Švedas V. (2012) Bioinformatic selection of subfamily-specific positions as hotspots for rational enzyme engineering. In silico rational design and screening, May 8-9, Italy (Trieste), p.15


Takhaveev V. and Suplatov D. (2012) Comparative Analysis of Fungal Pyranose Dehydrogenases and Pyranose 2-Oxidases Reveals Aminoacid Residues Responsible for Regioselectivity of Monosaccharide Oxidation. International Conference Lomonosov-2012, April 9-13, Russia (Moscow)


Suplatov D., Shalaeva D., Arzhanik V., Kirilin E., Švedas V. (2011) Bioinformatic analysis of protein families for identification of variable amino acid residues responsible for functional specificity. 10th International Symposium on Biocatalysis and Biotransformations Biotrans-2011, October 2-6, Italy (Giardini Naxos), p.64


Pulyakhina I., Suplatov D., Švedas V. (2010) Structural analysis of substrate specificity to laurolactam in Laurolactam hydrolase from Rhodococcus sp. U224 using bioinformatics and computational chemistry. International Conference Lomonosov-2010, April 12-15, Russia (Moscow)


Suplatov D., Guranda D., Švedas V. (2008) Sequence, structural and kinetic analyses of penicillin acylase family. 2nd International Conference «Biocatalysis in Non-Conventional Media», June 12-15, Russia (Moscow), pp.33-34





Conferences: posters


Suplatov D., Kopylov K., Sharapova Y., Švedas V. (2017) Allosteric inhibitor Doramapimod can bind to human p38α MAP Kinase even when the activation loop is in the DFG-in state. International Moscow Conference on Computational Molecular Biology MCCMB-2017, July 27-30, 2017, Russia (Moscow)


Sharapova Y., Suplatov D., Švedas V. (2017) Molecular Modeling of Catalytic and Lectin Domains in Neuraminidase A from Streptococcus pneumoniae. International Moscow Conference on Computational Molecular Biology MCCMB-2017, July 27-30, 2017, Russia (Moscow)


Suplatov D., Kopylov K., Švedas V. (2016) GPU-accelerated analysis of linear trends in a protein motion. International Conference Russian Supercomputing Days 2016, September 26-27, 2016, Russia (Moscow).


Копылов К.Е., Суплатов Д.А., Швядас В.К. (2016) Изучение механизма распознавания субстратов с участием подвижных элементов структуры активных центров ферментов 3-гидроксибензоатгидроксилазы и 2-гидроксибифенил-3-монооксигеназы с использованием суперкомпьютера. Международная конференция "Суперкомпьютерные дни в России 2016", 26-27 сентября, 2016, Россия (Москва).


Lypetska K., Suplatov D. (2016) Identification of hotspots responsible for the reaction specificity in aspartate aminotransferase family of PLP-dependent enzymes. Gordon Research Conference on Biocatalysis (2016), July 10-15, 2016, USA (Biddeford).


Suplatov D., Popova N., Kopylov K., Shegai M., Voevodin V., Švedas V. (2015) High-performance computing in bioinformatic analysis of protein superfamilies to design enzymes with new properties. International Conference Russian Supercomputing Days 2015, September 28-29, 2015, Russia (Moscow).


Panin. N., Shcherbakova T., Suplatov D., Švedas V. (2014) Computationally designed βD484 variant of penicillin acylase from Escherichia coli is stabilized in alkaline medium and resistant to inactivation by substrates in highly concentrated reaction mixtures. INPEC-2014, September 10-14th, Russia (Sankt-Petersburg), pp. 44.


Khaliullin I., Suplatov D., Watanabe S., Komeda H., Asano Y., Švedas V. (2014) Bioinformatic analysis of D-aminopeptidase from Ochrobactrum anthropi for rational design of extended substrate specificity. INPEC-2014, September 10-14th, Russia (Sankt-Petersburg), pp. 44.


Suplatov D., Panin N., Kirilin E., Shcherbakova T., Kudravtsev P., Švedas V. (2013) Rational design of penicillin acylase based on bioinformatic analysis and molecular modeling to improve enzyme catalytic performance in alkaline medium. Enzyme Engineering XXII, September 22-26, Japan (Toyama)


Suplatov D., Kirilin E., Takhaveev V., Švedas V.K. (2013) Zebra: web-server for bioinformatic analysis of large protein superfamilies to identify variable amino acid residues responsible for functional diversity. International Moscow Conference on Computational Molecular Biology MCCMB-2013, July 25-28, Russia (Moscow)


Khaliullin I., Suplatov D., Tokunan K., Himi M., Asano Y., Švedas V. (2013) Bioinformatic analysis of penicillin-binding proteins identified amino acid residues responsible for substrate specificity of D-aminopeptidase from Ochrobactrum anthropi. FEBS Congress 2013 Mechanisms in Biology, July 6-11, Russia (Sankt-Petersburg), FEBS Journal, 280 (Suppl. 1), 592


Panin N., Suplatov D., Kirilin E., Shcherbakova T., Kudravtsev P., Švedas V. (2013) Bioinformatic analysis and molecular modeling reveal mutation bD484N to stabilize penicillin acylase and improve its catalytic performance in alkaline medium. FEBS Congress 2013 Mechanisms in Biology, July 6-11, Russia (Sankt-Petersburg), FEBS Journal, 280 (Suppl. 1), 614


Suplatov D., Kirilin E., Takhaveev V., Eldarov M., Švedas V. (2013) Bioinformatic analysis of glutaryl acylases to study molecular mechanisms of substrate recognition. International conference Biocatalysis-2013, July 2-5, Russia (Moscow), p.91


Khaliullin I., Suplatov D., Tokunan K., Himi M., Asano Y., Švedas V. (2013) Bioinformatic analysis of penicillin-binding proteins identified amino acid residues responsible for substrate specificity of D-aminopeptidase from Ochrobactrum anthropi. International Conference Biocatalysis-2013, July 2 5, Russia (Moscow), p.89


Panin N., Suplatov D., Kirilin E., Shcherbakova T., Kudravtsev P., Švedas V. (2013) Bioinformatic analysis and molecular modeling reveal mutation bD484N to stabilize penicillin acylase and improve its catalytic performance in alkaline medium. International Conference Biocatalysis-2013, July 2-5, Russia (Moscow), p.90


Klimchuk O., Suplatov D., Švedas V. (2013) Bioinformatic analysis of bacterial DNA-dependent RNA polymerase identifies new targets for selective inhibition. International Conference Lomonosov-2013, April 8-13, Russia (Moscow)


Suplatov D. and Švedas V. (2012) Bioinformatic analysis of subfamily-specific positions to study structure-function relationship in diverse enzyme families. EMBO Conference Catalytic Mechanisms by Biological Systems, October 7-10, The Netherlands (Groningen), p.94


Švedas V., Suplatov D., Besenmatter W., Shalaeva D., Svendsen A. (2011) Bioinformatic analysis of α/β-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities. 10th International Symposium on Biocatalysis and Biotransformations Biotrans-2011, October 2-6, Italy (Giardini Naxos), p.150


Khaliullin I., Tokunan K., Himi M., Suplatov D., Shalaeva D., Asano Y., Švedas V. (2011) Bioinformatic analysis and molecular modeling to predict mutations widening substrate specificity of D-aminopeptidase from Ochrobactrum anthropi. 10th International Symposium on Biocatalysis and Biotransformations Biotrans-2011, October 2-6, Italy (Giardini Naxos), p.149


Shalaeva D., Takhaveyev V., Suplatov D., Švedas V. (2011) Bioinformatic Analysis of Structural Factors of Selective Inhibition in Human Protein Kinase C Family. International Moscow Conference on Computational Molecular Biology MCCMB-2011, July 21-24, Russia (Moscow), pp.342-343


Arzhanik V., Kirilin E., Suplatov D., Švedas V. (2011) Multiple structural alignment of α/β-hydrolase-fold enzymes and bioinformatic analysis of catalytically important residue. International Moscow Conference on Computational Molecular Biology MCCMB-2011, July 21-24, Russia (Moscow), pp.53-54


Khaliullin I., Suplatov D., Švedas V., Asano Y., Otsuka M., Shalaeva D. (2010) The Role of Lys65 Residue in the Catalytic Triad of D-aminopeptidase from Ochrobactrum anthropi Revealed by Bioinformatic Analysis and Molecular Modeling. 5th International Congress on Biocatalysis Biocat2010, August 29 - September 2, Germany (Hamburg), p.196


Shalaeva D., Suplatov D., Khaliullin I., Švedas V. (2010) Bioinformatics insight into structural determinants of D-aminopeptidase from Ochrobactrum anthropi substrate specificity to amino acid derivatives. International Conference Lomonosov-2010, April 12-15, Russia (Moscow)


Suplatov D., Pouliakhina I., Arzhanik V., Švedas V. (2009) Modeling of structure and substrate recognition of penicillin acylase from Streptomyces mobaraensis using molecular docking to evaluate proper active site geometry. International Moscow Conference on Computational Molecular Biology MCCMB-2009, Russia (Moscow), July 20-23, pp.343-344


Suplatov D., Pouliakhina I., Arzhanik V., Guranda D., Švedas V. (2009) Bioinformatic analysis reveals crucial penicillin acylase inactivation step and outlines strategy for pH-stabilization. International Conference Biocatalysis-2009: Fundamentals & applications, June 19-24, Russia (Arkhangelsk), pp.70-71


Guranda D., Nemukhin A., Grigorenko B., Tishkov V., Suplatov D., et.al. (2009) Rational design of industrial enzymes based on molecular modeling methods. Final conference upon completion of tasks scheduled for 2009 as part of priority area «Living systems» of the Federal purpose-oriented program «Research and development in priority areas of scientific-technical complex of Russian Federation in 2007-2012» Russia (Moscow), pp.251-252


Suplatov D., Guranda D., Švedas V. (2008) Bioinformatic analysis of penicillin acylase family reveals key residues essential for enzyme stability. ESF-EMBO symposium «Protein Design and Evolution for Biocatalysis», October 25-30, Spain (San Feliu de Guixols), p.122


Suplatov D., Sidorova A., Guranda D., Yang Sh., Švedas V.K. (2005) Penicillin acylase from Bacillus megaterium displays high stability in alkaline media. International Conference Biocatalysis-2005: Fundamentals & applications, June 19-23, Russia (St.Petersburg, Valaam, Kighy), p.114


Suplatov D. (2005) pH-dependence of activity and stability of bacterial penicillin acylases. Proceedings of 200-years anniversary of Moscow Society of Naturalists, Russia (Moscow), pp.48-62