Publications

of the working group "Structures and Sequences"

• Ledneva R.K., Alekseevskii A.V., Vasil'ev S.A., Spirin S.A., Kariagina A.S. Structural aspects of interaction of homeodomains with DNA. Molecular Biology (Moscow) 2001, 35 (5):647–659 [SpringerLink]
• Vasil'ev S.A., Alekseevskii A.V., Spirin S.A., Tashlitskii V.N., Kariagina A.S. [Theoretical approaches for evaluation of DNA-protein interactions] (in Russian). Biofizika 2001, 46 (6):1010–1021 [PubMed]
• Anna S. KARYAGINA, Andrei V. ALEXEEVSKI, Andrei V. GOLOVIN, Sergei A. SPIRIN, Olga V. VOROB'EVA, Elena A. KUBAREVA. Computer modeling of complexes of (C5-cytosine)-DNA methyltransferase SsoII with target and regulatory DNAs. Biophysics (Moscow), vol. 48, Suppl. 1 (2004), p. 45 [draft version]
• Andrei ALEXEEVSKI, Sergei SPIRIN, Daniil ALEXEEVSKI, Oleg KLYCHNIKOV, Anna ERSHOVA, Mikhail TITOV, Anna KARYAGINA. CluD, a Program for Determination of Hydrophobic Clusters in 3D Structures of Protein and Protein-Nucleic Acids Complexes. Biophysics (Moscow), vol. 48, Suppl. 1 (2004), p. 146 [draft version]
• Mikhail Gribkov, Andrei Alexeevski, Darya Ivanova, Anna Karyagina, and Sergei Spirin. Life Core, program for classification of 3D structures of macromolecules. Biophysics (Moscow), vol. 48, Suppl. 1 (2004), p. 157 [draft version]
• Andrei V. Alexeevsky, Tatiana M. Dmitrieva, Galina S. Shatskaya, Dimitri Markouchevitch, Elena A. Tolskaya. Site-directed mutagenesis and 3D structure modeling reveal the functional role of C-terminal Trp460 of mengoviral RNA-dependent RNA polymerase. Biophysics (Moscow), vol. 48, Suppl. 1 (2004), p. 167 [draft version]
• Ershova A.S., Alexeevski A.V., Spirin S.A., Karyagina A.S. Common structural features of homeodomains and homeodomain-DNA complexes. In: Proceedings of the Fourth International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, 2004. Vol. 1, pp. 258–261
• Alexeevski A.V., Lukina E.N., Salnikov A.N., Spirin S.A. Database of long terminal repeats in human genome: structure and synchronization with main genome archives. In: Proceedings of the Fourth International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, 2004. Vol. 1, pp. 28–29
• Karyagina A., Ershova A., Spirin S., Alexeevski A. The role of water in homeodomain-DNA interaction. In: Bioinformatics of Genome Regulation and Structure II. (Eds. N.Kolchanov and R. Hofestaedt). NY: Springer Science+Business Media, Inc. 2005, P. 247–257.
• Karyagina A., Ershova A., Titov M., Olovnikov I., Aksianov E., Ryazanova A., Kubareva E., Spirin S. and Alexeevski A. Analysis of conserved hydrophobic cores in proteins and supramolecular complexes. J. Bioinformatics and Computational Biology 2006, 4 (2):357–372 [PubMed]
• Spirin S., Titov M., Karyagina A. and Alexeevski A. NPIDB, a Database of Nucleic Acids–Protein Interactions. Bioinformatics 2007, 23 (23):3247–3248 [PubMed].
• Aksianov E., Zanegina O., Grishin A., Spirin S., Karyagina A. and Alexeevski A. Conserved water molecules in X-ray structures highlight the role of water in intramolecular and intermolecular interactions. J. Bioinformatics and Computational Biology 2008, 6 (4):775–788 [PubMed]
• Grishin A.V., Alekseevskii A.V., Spirin S.A. and Karyagina A.S. Conserved structural features of ETS domain – DNA complexes. Molecular Biology (Moscow) 2009, 43 (4):612–619 [SpringerLink]
• Kariagina A.S., Alekseevskii A.V., Spirin S.A., Zigangirova N.A. and Gintsburg A.L. Effector proteins of Chlamidiae. Molecular Biology (Moscow) 2009, 43 (6):897–916 [SpringerLink]
• Grishin A., Fonfara I., Alexeevski A., Spirin S., Zanegina O., Karyagina A., Alexeyevsky D. and Wende W. Identification of conserved features of LAGLIDADG homing endonucleases. J. Bioinformatics and Computational Biology 2010, 8 (3):453–469 [PubMed]
• Burkov B., Nagaev B., Spirin S. and Alexeevski A. Malakite: an automatic tool for characterisation of structure of reliable blocks in multiple alignments of protein sequences. J. Bioinformatics and Computational Biology 2010, 8 (3):503–517 [PubMed]
• Mitrofanov S.I., Panchin A.Y., Spirin S.A., Alexeevski A.V. and Panchin Y.V. Exclusive sequences of different genomes. J. Bioinformatics and Computational Biology 2010, 8 (3):519–534 [PubMed]
• Krivozubov M.S. and Spirin S.A. Comparison of protein phylogeny reconstruction methods using natural protein sequences. Moscow University Biological Sciences Bulletin 2010, 65 (4):139–141 [SpringerLink]
• Panchin A., Mitrofanov S., Alexeevski A., Spirin S. and Panchin Y. New words in human mutagenesis. BMC Bioinformatics 2011, 12:268 [Full text]
• Aksianov E. and Alexeevski A. SheeP: A tool for description of β-sheets in protein 3D structures. J. Bioinformatics and Computational Biology 2012, 10 (2):1241003 [PubMed]
• Ershova A.S., Karyagina A.S., Vasiliev M.O., Lyashchuk A.M., Lunin V.G., Spirin S.A. and Alexeevski A.V. Solitary restriction endonucleases in prokaryotic genomes. Nucleic Acid Research 2012, 40 (20):10107–10115, doi: 10.1093/nar/gks853 [Full text]
• Kirsanov D.D., Zanegina O.N., Aksianov E.A., Spirin S.A., Karyagina A.S. and Alexeevski A.V. NPIDB: nucleic acid-protein interaction database. Nucleic Acid Research 2013, 41 (D1):D517–D523, doi: 10.1093/nar/gks1199 [Full text]
• Krivozubov M.S., Goebels F.A., Spirin S.A. Estimation of relative effectiveness of phylogenetic programs by machine learning. Journal of Bioinformatics and Computational Biology 2014, 12 (2). Article ID 1441004, doi: 10.1142/S0219720014410042
• Aksianov E. Motif Analyzer for protein 3D structures. Journal of Structural Biology 2014, 186 (1):62–67. [PubMed]
• Ershova A.S., Rusinov I.S., Spirin S.A., Karyagina A.S., Alexeevski A.V. Role of restriction-modification systems in prokaryotic evolution and ecology. Biochemistry (Moscow) 2015, 80 (10):1373–1386 [Springer Link]
• Popov Y.V., Galitsyna A.A., Alexeevski A.V., Karyagina A.S. and Spirin S.A. StructAlign, a program for alignment of structures of DNA-protein complexes. Biochemistry (Moscow) 2015, 80 (11):1465–1468 [Springer Link]
• Ershova A.S., Rusinov I.S., Spirin S.A., Karyagina A.S., Alexeevski A.V. Lifespan of restriction-modification systems critically affects avoidance of their recognition sites in host genomes. BMC Genomics 2015, 16:1084 [Full text]
• Zanegina O.N., Kirsanov D.D., Baulin E.F., Spirin S.A., Karyagina A.S. and Alexeevski A.V. An updated version of NPIDB includes new classifications of DNA-protein complexes and their families. Nucleic Acid Research 2016, 45 (D1):D144–D153, doi: 10.1093/nar/gkv1339 [Full text]