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Items: 42

1.

Consistent prediction of mutation effect on drug binding in HIV-1 protease using alchemical calculations.

Bastys T, Gapsys V, Doncheva NT, Kaiser R, de Groot BL, Kalinina OV.

J Chem Theory Comput. 2018 May 30. doi: 10.1021/acs.jctc.7b01109. [Epub ahead of print]

PMID:
29847122
2.

Spatial distribution of disease-associated variants in three-dimensional structures of protein complexes.

Gress A, Ramensky V, Kalinina OV.

Oncogenesis. 2017 Sep 25;6(9):e380. doi: 10.1038/oncsis.2017.79.

3.

Elucidating the energetic contributions to the binding free energy.

Ahmad M, Helms V, Kalinina OV, Lengauer T.

J Chem Phys. 2017 Jan 7;146(1):014105. doi: 10.1063/1.4973349.

PMID:
28063433
4.

Patterns of amino acid conservation in human and animal immunodeficiency viruses.

Voitenko OS, Dhroso A, Feldmann A, Korkin D, Kalinina OV.

Bioinformatics. 2016 Sep 1;32(17):i685-i692. doi: 10.1093/bioinformatics/btw441.

PMID:
27587690
5.

BALL-SNPgp-from genetic variants toward computational diagnostics.

Mueller SC, Backes C, Gress A, Baumgarten N, Kalinina OV, Moll A, Kohlbacher O, Meese E, Keller A.

Bioinformatics. 2016 Jun 15;32(12):1888-90. doi: 10.1093/bioinformatics/btw084. Epub 2016 Feb 15.

PMID:
27153685
6.

StructMAn: annotation of single-nucleotide polymorphisms in the structural context.

Gress A, Ramensky V, Büch J, Keller A, Kalinina OV.

Nucleic Acids Res. 2016 Jul 8;44(W1):W463-8. doi: 10.1093/nar/gkw364. Epub 2016 May 5.

7.

[VIRAL HEPATITIS C: EVOLUTION OF THE EPIDEMIOLOGIC PROCESS, EVOLUTION OF THE VIRUS].

Zhebrun AB, Kalinina OV.

Zh Mikrobiol Epidemiol Immunobiol. 2016 Jan-Feb;(1):102-12. Review. Russian.

PMID:
27029124
8.

The Role of Conformational Changes in Molecular Recognition.

Ahmad M, Helms V, Kalinina OV, Lengauer T.

J Phys Chem B. 2016 Mar 10;120(9):2138-44. doi: 10.1021/acs.jpcb.5b11593. Epub 2016 Mar 1.

PMID:
26901699
9.

[Phylodynamic of HCV Populations].

Kalinina OV, Zhebrun AB.

Vestn Ross Akad Med Nauk. 2015;(5):573-8. Review. Russian.

PMID:
26846083
10.

How Molecular Conformational Changes Affect Changes in Free Energy.

Ahmad M, Helms V, Lengauer T, Kalinina OV.

J Chem Theory Comput. 2015 Jul 14;11(7):2945-57. doi: 10.1021/acs.jctc.5b00235.

PMID:
26575732
11.

Enthalpy-Entropy Compensation upon Molecular Conformational Changes.

Ahmad M, Helms V, Lengauer T, Kalinina OV.

J Chem Theory Comput. 2015 Apr 14;11(4):1410-8. doi: 10.1021/ct501161t. Epub 2015 Mar 11.

PMID:
26574352
12.

Systematic discovery of linear binding motifs targeting an ancient protein interaction surface on MAP kinases.

Zeke A, Bastys T, Alexa A, Garai Á, Mészáros B, Kirsch K, Dosztányi Z, Kalinina OV, Reményi A.

Mol Syst Biol. 2015 Nov 3;11(11):837. doi: 10.15252/msb.20156269.

13.

Sequence and Structure Analysis of Distantly-Related Viruses Reveals Extensive Gene Transfer between Viruses and Hosts and among Viruses.

Caprari S, Metzler S, Lengauer T, Kalinina OV.

Viruses. 2015 Oct 19;7(10):5388-409. doi: 10.3390/v7102882.

14.

Large oligomeric complex structures can be computationally assembled by efficiently combining docked interfaces.

Dietzen M, Kalinina OV, Taškova K, Kneissl B, Hildebrandt AK, Jaenicke E, Decker H, Lengauer T, Hildebrandt A.

Proteins. 2015 Oct;83(10):1887-99. doi: 10.1002/prot.24873. Epub 2015 Aug 24.

15.

BALL-SNP: combining genetic and structural information to identify candidate non-synonymous single nucleotide polymorphisms.

Mueller SC, Backes C, Kalinina OV, Meder B, Stöckel D, Lenhof HP, Meese E, Keller A.

Genome Med. 2015 Jul 1;7(1):65. doi: 10.1186/s13073-015-0190-y. eCollection 2015.

16.

[Genome organization and life cycle of the hepatitis c virus].

Kalinina OV, Dmitriev AV.

Mol Gen Mikrobiol Virusol. 2015;33(2):9-13. Review. Russian.

PMID:
26182661
17.

Detection of atypical genes in virus families using a one-class SVM.

Metzler S, Kalinina OV.

BMC Genomics. 2014 Oct 20;15:913. doi: 10.1186/1471-2164-15-913.

18.

[Possibilities for the improvement of the quality of knowledge and their evaluation in the course of studying clinical medicine].

Tetenev FF, Bodrova TN, Ageeva TS, Karzilov AI, Kalinina OV.

Klin Med (Mosk). 2014;92(11):75-8. Russian.

PMID:
25796952
19.
20.

[Age peculiarities of the sebaceous glands in the temporal area of the scalp skin in men].

Kalinina OV, Belousova TA, Nozdrin VI.

Morfologiia. 2013;143(2):69-74. Russian.

PMID:
23898726
21.
22.

[Low-manifest infections in children and adolescents with consequences of perinatal damage of nervous system].

Vaĭnshenker IuI, Kalinina OV, Nuralova IV, Ivchenko IM, Meliucheva LA, Tsinzerling VA.

Zh Mikrobiol Epidemiol Immunobiol. 2012 Sep-Oct;(5):77-80. Russian.

PMID:
23163043
23.

[The development of secondary immunodeficiency in body when exposed to the effect of xenobiotics with immunosuppressive activity].

Kalinina OV, Zheleznova AD, Panfilova TV, Frolov BA.

Gig Sanit. 2012 May-Jun;(3):73-5. Russian.

PMID:
23088138
24.

Computational identification of novel amino-acid interactions in HIV Gag via correlated evolution.

Kalinina OV, Oberwinkler H, Glass B, Kräusslich HG, Russell RB, Briggs JA.

PLoS One. 2012;7(8):e42468. doi: 10.1371/journal.pone.0042468. Epub 2012 Aug 3.

25.

[Low-manifest infections with CNS damage in patients in prolonged unconscious state of non-inflammatory etiology].

Vaĭnshenker IuI, Ivchenko IM, Tsinzerling VA, Nuralova IV, Khlopunova OV, Berezina LA, Kuliashova LB, Viazovaia AA, Kalinina OV, Korotkov AD, Kataeva GV, Medvedev SV.

Zh Mikrobiol Epidemiol Immunobiol. 2011 Nov-Dec;(6):85-9. Russian.

PMID:
22308737
26.

ProtChemSI: a network of protein-chemical structural interactions.

Kalinina OV, Wichmann O, Apic G, Russell RB.

Nucleic Acids Res. 2012 Jan;40(Database issue):D549-53. doi: 10.1093/nar/gkr1049. Epub 2011 Nov 21.

27.

Combinations of protein-chemical complex structures reveal new targets for established drugs.

Kalinina OV, Wichmann O, Apic G, Russell RB.

PLoS Comput Biol. 2011 May;7(5):e1002043. doi: 10.1371/journal.pcbi.1002043. Epub 2011 May 5.

28.

[Clinical thinking: formation and development].

Tetenev FF, Bodrova TN, Kalinina OV.

Klin Med (Mosk). 2010;88(5):70-1. Russian. No abstract available.

PMID:
21089466
29.

An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies.

Mazin PV, Gelfand MS, Mironov AA, Rakhmaninova AB, Rubinov AR, Russell RB, Kalinina OV.

Algorithms Mol Biol. 2010 Jul 15;5:29. doi: 10.1186/1748-7188-5-29.

30.

Impact of genome reduction on bacterial metabolism and its regulation.

Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen WH, Wodke JA, Güell M, Martínez S, Bourgeois R, Kühner S, Raineri E, Letunic I, Kalinina OV, Rode M, Herrmann R, Gutiérrez-Gallego R, Russell RB, Gavin AC, Bork P, Serrano L.

Science. 2009 Nov 27;326(5957):1263-8. doi: 10.1126/science.1177263.

31.

Combining specificity determining and conserved residues improves functional site prediction.

Kalinina OV, Gelfand MS, Russell RB.

BMC Bioinformatics. 2009 Jun 9;10:174. doi: 10.1186/1471-2105-10-174.

32.

[Computational method for prediction of protein functional sites using specificity determinants].

Kalinina OV, Rassel RB, Rakhmaninova AB, Gel'fand MS.

Mol Biol (Mosk). 2007 Jan-Feb;41(1):151-62. Russian.

PMID:
17380902
33.

Harry Potter and the structural biologist's (Key)stone.

Devos D, Kalinina OV, Russell RB.

Genome Biol. 2006;7(12):333. No abstract available.

34.

[Anti-inflammatory effect of toothbrush use and oral hygiene].

Ulitovskiĭ SB, Kalinina OV.

Stomatologiia (Mosk). 2006;85(3):64-6. Russian. No abstract available.

PMID:
16858327
36.

Comparative genomics of regulation of heavy metal resistance in Eubacteria.

Permina EA, Kazakov AE, Kalinina OV, Gelfand MS.

BMC Microbiol. 2006 Jun 5;6:49.

37.

[Effects of different methods of physical therapy on the course of autonomic dysfunction syndrome].

Kalinina OV, Efimova EG.

Vopr Kurortol Fizioter Lech Fiz Kult. 2006 Jan-Feb;(1):19-21. Russian.

PMID:
16752738
38.

Common and specific amino acid residues in the prokaryotic polypeptide release factors RF1 and RF2: possible functional implications.

Oparina NJ, Kalinina OV, Gelfand MS, Kisselev LL.

Nucleic Acids Res. 2005 Sep 14;33(16):5226-34. Print 2005.

39.

SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins.

Kalinina OV, Novichkov PS, Mironov AA, Gelfand MS, Rakhmaninova AB.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W424-8.

40.
41.

The channel in transporters is formed by residues that are rare in transmembrane helices.

Kalinina OV, Makeev VJ, Sutormin RA, Gelfand MS, Rakhmaninova AB.

In Silico Biol. 2003;3(1-2):197-204.

PMID:
14524337
42.

[Infrared laser therapy in distal diabetic polyneuropathy].

Kalinina OV, Alekseeva NV, Burtsev EM.

Zh Nevrol Psikhiatr Im S S Korsakova. 1998;98(6):23-5. Russian.

PMID:
9677693

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