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Items: 10

1.

On the importance of accounting for nuclear quantum effects in ab initio calibrated force fields in biological simulations.

Pereyaslavets L, Kurnikov I, Kamath G, Butin O, Illarionov A, Leontyev I, Olevanov M, Levitt M, Kornberg RD, Fain B.

Proc Natl Acad Sci U S A. 2018 Sep 4;115(36):8878-8882. doi: 10.1073/pnas.1806064115. Epub 2018 Aug 20. Erratum in: Proc Natl Acad Sci U S A. 2018 Sep 17;:.

2.

Prediction of cyclohexane-water distribution coefficient for SAMPL5 drug-like compounds with the QMPFF3 and ARROW polarizable force fields.

Kamath G, Kurnikov I, Fain B, Leontyev I, Illarionov A, Butin O, Olevanov M, Pereyaslavets L.

J Comput Aided Mol Des. 2016 Nov;30(11):977-988. doi: 10.1007/s10822-016-9958-4. Epub 2016 Sep 1.

PMID:
27585472
3.

FoldNucleus: web server for the prediction of RNA and protein folding nuclei from their 3D structures.

Pereyaslavets LB, Sokolovsky IV, Galzitskaya OV.

Bioinformatics. 2015 Oct 15;31(20):3374-6. doi: 10.1093/bioinformatics/btv369. Epub 2015 Jun 22.

PMID:
26104744
4.

What handedness and angles between helices has the studied three-helical protein domain?

Pereyaslavets LB, Glyakina AV, Dovidchenko NV, Sokolovskiy IV, Galzitskaya OV.

Bioinformatics. 2015 Mar 15;31(6):963-5. doi: 10.1093/bioinformatics/btu737. Epub 2014 Nov 10.

PMID:
25388147
5.

Right- and left-handed three-helix proteins. I. Experimental and simulation analysis of differences in folding and structure.

Glyakina AV, Pereyaslavets LB, Galzitskaya OV.

Proteins. 2013 Sep;81(9):1527-41. doi: 10.1002/prot.24301. Epub 2013 Jun 20.

PMID:
23588993
6.

On the universe of protein folds.

Kolodny R, Pereyaslavets L, Samson AO, Levitt M.

Annu Rev Biophys. 2013;42:559-82. doi: 10.1146/annurev-biophys-083012-130432. Epub 2013 Mar 20.

PMID:
23527781
7.

Development and testing of PFFSol1.1, a new polarizable atomic force field for calculation of molecular interactions in implicit water environment.

Pereyaslavets LB, Finkelstein AV.

J Phys Chem B. 2012 Apr 19;116(15):4646-54. doi: 10.1021/jp212474p. Epub 2012 Apr 9.

PMID:
22439906
8.

Prediction of folding nuclei in tRNA molecules.

Pereyaslavets LB, Baranov MV, Leonova EI, Galzitskaya OV.

Biochemistry (Mosc). 2011 Feb;76(2):236-44.

PMID:
21568857
9.

Assessment of performance of the general purpose polarizable force field QMPFF3 in condensed phase.

Donchev AG, Galkin NG, Illarionov AA, Khoruzhii OV, Olevanov MA, Ozrin VD, Pereyaslavets LB, Tarasov VI.

J Comput Chem. 2008 Jun;29(8):1242-9.

PMID:
18161686
10.

Quantum mechanical polarizable force field (QMPFF3): refinement and validation of the dispersion interaction for aromatic carbon.

Donchev AG, Galkin NG, Pereyaslavets LB, Tarasov VI.

J Chem Phys. 2006 Dec 28;125(24):244107.

PMID:
17199340

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