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Items: 19

1.

In Silico Identification of Novel Aromatic Compounds as Potential HIV-1 Entry Inhibitors Mimicking Cellular Receptor CD4.

Andrianov AM, Nikolaev GI, Kornoushenko YV, Xu W, Jiang S, Tuzikov AV.

Viruses. 2019 Aug 13;11(8). pii: E746. doi: 10.3390/v11080746.

2.

Gene ontology improves template selection in comparative protein docking.

Hadarovich A, Anishchenko I, Tuzikov AV, Kundrotas PJ, Vakser IA.

Proteins. 2019 Mar;87(3):245-253. doi: 10.1002/prot.25645. Epub 2018 Dec 27.

PMID:
30520123
3.

Potential HIV-1 fusion inhibitors mimicking gp41-specific broadly neutralizing antibody 10E8: In silico discovery and prediction of antiviral potency.

Andrianov AM, Kashyn IA, Tuzikov AV.

J Bioinform Comput Biol. 2018 Apr;16(2):1840007. doi: 10.1142/S0219720018400073. Epub 2018 Jan 15.

PMID:
29439644
4.

Genome-Wide Analysis of MDR and XDR Tuberculosis from Belarus: Machine-Learning Approach.

Sergeev RS, Kavaliou IS, Sataneuski UV, Gabrielian A, Rosenthal A, Tartakovsky M, Tuzikov AV.

IEEE/ACM Trans Comput Biol Bioinform. 2019 Jul-Aug;16(4):1398-1408. doi: 10.1109/TCBB.2017.2720669. Epub 2017 Jun 27.

PMID:
28678713
5.

Computational identification of novel entry inhibitor scaffolds mimicking primary receptor CD4 of HIV-1 gp120.

Andrianov AM, Kashyn IA, Tuzikov AV.

J Mol Model. 2017 Jan;23(1):18. doi: 10.1007/s00894-016-3189-4. Epub 2017 Jan 3.

PMID:
28050723
6.

Computational discovery of novel HIV-1 entry inhibitors based on potent and broad neutralizing antibody VRC01.

Andrianov AM, Kashyn IA, Tuzikov AV.

J Mol Graph Model. 2015 Sep;61:262-71. doi: 10.1016/j.jmgm.2015.08.003. Epub 2015 Aug 8.

PMID:
26298811
7.

Simulated unbound structures for benchmarking of protein docking in the DOCKGROUND resource.

Kirys T, Ruvinsky AM, Singla D, Tuzikov AV, Kundrotas PJ, Vakser IA.

BMC Bioinformatics. 2015 Jul 31;16:243. doi: 10.1186/s12859-015-0672-3.

8.

Protein models docking benchmark 2.

Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA.

Proteins. 2015 May;83(5):891-7. doi: 10.1002/prot.24784. Epub 2015 Mar 25.

9.

Structural templates for comparative protein docking.

Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA.

Proteins. 2015 Sep;83(9):1563-70. doi: 10.1002/prot.24736. Epub 2015 Jun 13.

10.

In silico design of novel broad anti-HIV-1 agents based on glycosphingolipid β-galactosylceramide, a high-affinity receptor for the envelope gp120 V3 loop.

Andrianov AM, Kornoushenko YV, Kashyn IA, Kisel MA, Tuzikov AV.

J Biomol Struct Dyn. 2015;33(5):1051-66. doi: 10.1080/07391102.2014.926832. Epub 2014 Jun 19.

PMID:
24942968
11.

Discovery of novel anti-HIV-1 agents based on a broadly neutralizing antibody against the envelope gp120 V3 loop: a computational study.

Andrianov AM, Kashyn IA, Tuzikov AV.

J Biomol Struct Dyn. 2014 Dec;32(12):1993-2004. doi: 10.1080/07391102.2013.848825. Epub 2013 Nov 20.

PMID:
24251545
12.

Protein models: the Grand Challenge of protein docking.

Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA.

Proteins. 2014 Feb;82(2):278-87. doi: 10.1002/prot.24385. Epub 2013 Oct 17.

13.

Ensemble-based characterization of unbound and bound states on protein energy landscape.

Ruvinsky AM, Kirys T, Tuzikov AV, Vakser IA.

Protein Sci. 2013 Jun;22(6):734-44. doi: 10.1002/pro.2256. Epub 2013 Apr 29.

14.

Correlation analysis of the side-chains conformational distribution in bound and unbound proteins.

Kirys T, Ruvinsky AM, Tuzikov AV, Vakser IA.

BMC Bioinformatics. 2012 Sep 17;13:236. doi: 10.1186/1471-2105-13-236.

15.

Structural analysis of the envelope gp120 V3 loop for some HIV-1 variants circulating in the countries of Eastern Europe.

Andrianov AM, Kornoushenko YV, Anishchenko IV, Eremin VF, Tuzikov AV.

J Biomol Struct Dyn. 2013;31(7):665-83. doi: 10.1080/07391102.2012.706455. Epub 2012 Aug 13.

PMID:
22888999
16.

Structure fluctuations and conformational changes in protein binding.

Ruvinsky AM, Kirys T, Tuzikov AV, Vakser IA.

J Bioinform Comput Biol. 2012 Apr;10(2):1241002. doi: 10.1142/S0219720012410028.

17.

Rotamer libraries and probabilities of transition between rotamers for the side chains in protein-protein binding.

Kirys T, Ruvinsky AM, Tuzikov AV, Vakser IA.

Proteins. 2012 Aug;80(8):2089-98. doi: 10.1002/prot.24103. Epub 2012 Jun 12.

18.

Discovery of novel promising targets for anti-AIDS drug developments by computer modeling: application to the HIV-1 gp120 V3 loop.

Andrianov AM, Anishchenko IV, Tuzikov AV.

J Chem Inf Model. 2011 Oct 24;51(10):2760-7. doi: 10.1021/ci200255t. Epub 2011 Sep 22.

PMID:
21888425
19.

Side-chain conformational changes upon Protein-Protein Association.

Ruvinsky AM, Kirys T, Tuzikov AV, Vakser IA.

J Mol Biol. 2011 Apr 29;408(2):356-65. doi: 10.1016/j.jmb.2011.02.030. Epub 2011 Feb 25.

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