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Items: 1 to 20 of 61


Atomistic mechanism of the constitutive activation of PDGFRA via its transmembrane domain.

Polyansky AA, Bocharov EV, Velghe AI, Kuznetsov AS, Bocharova OV, Urban AS, Arseniev AS, Zagrovic B, Demoulin JB, Efremov RG.

Biochim Biophys Acta Gen Subj. 2019 Jan;1863(1):82-95. doi: 10.1016/j.bbagen.2018.09.011. Epub 2018 Sep 22.


RNA-protein interactions in an unstructured context.

Zagrovic B, Bartonek L, Polyansky AA.

FEBS Lett. 2018 Sep;592(17):2901-2916. doi: 10.1002/1873-3468.13116. Epub 2018 Jun 21. Review.


Self-Consistent Framework Connecting Experimental Proxies of Protein Dynamics with Configurational Entropy.

Fleck M, Polyansky AA, Zagrovic B.

J Chem Theory Comput. 2018 Jul 10;14(7):3796-3810. doi: 10.1021/acs.jctc.8b00100. Epub 2018 Jun 8.


A novel non-canonical PIP-box mediates PARG interaction with PCNA.

Kaufmann T, Grishkovskaya I, Polyansky AA, Kostrhon S, Kukolj E, Olek KM, Herbert S, Beltzung E, Mechtler K, Peterbauer T, Gotzmann J, Zhang L, Hartl M, Zagrovic B, Elsayad K, Djinovic-Carugo K, Slade D.

Nucleic Acids Res. 2017 Sep 19;45(16):9741-9759. doi: 10.1093/nar/gkx604.


Dependence of Binding Free Energies between RNA Nucleobases and Protein Side Chains on Local Dielectric Properties.

de Ruiter A, Polyansky AA, Zagrovic B.

J Chem Theory Comput. 2017 Sep 12;13(9):4504-4513. doi: 10.1021/acs.jctc.6b01202. Epub 2017 Aug 16.


mRNA/protein sequence complementarity and its determinants: The impact of affinity scales.

Bartonek L, Zagrovic B.

PLoS Comput Biol. 2017 Jul 27;13(7):e1005648. doi: 10.1371/journal.pcbi.1005648. eCollection 2017 Jul.


Fuento: functional enrichment for bioinformatics.

Weichselbaum D, Zagrovic B, Polyansky AA.

Bioinformatics. 2017 Aug 15;33(16):2604-2606. doi: 10.1093/bioinformatics/btx179.


Mechanism of cargo-directed Atg8 conjugation during selective autophagy.

Fracchiolla D, Sawa-Makarska J, Zens B, Ruiter A, Zaffagnini G, Brezovich A, Romanov J, Runggatscher K, Kraft C, Zagrovic B, Martens S.

Elife. 2016 Nov 23;5. pii: e18544. doi: 10.7554/eLife.18544.


Structural mechanism for the recognition and ubiquitination of a single nucleosome residue by Rad6-Bre1.

Gallego LD, Ghodgaonkar Steger M, Polyansky AA, Schubert T, Zagrovic B, Zheng N, Clausen T, Herzog F, Köhler A.

Proc Natl Acad Sci U S A. 2016 Sep 20;113(38):10553-8. doi: 10.1073/pnas.1606863113. Epub 2016 Sep 6.


A code within a code: how codons influence mRNA stability.

Martinez J, Zagrovic B.

EMBO J. 2016 Oct 4;35(19):2064-2065. Epub 2016 Aug 25. No abstract available.


Inosine Nucleobase Acts as Guanine in Interactions with Protein Side Chains.

Hajnic M, Ruiter Ad, Polyansky AA, Zagrovic B.

J Am Chem Soc. 2016 May 4;138(17):5519-22. doi: 10.1021/jacs.6b02417. Epub 2016 Apr 22.


Effect of Oxidative Damage on the Stability and Dimerization of Superoxide Dismutase 1.

Petrov D, Daura X, Zagrovic B.

Biophys J. 2016 Apr 12;110(7):1499-1509. doi: 10.1016/j.bpj.2016.02.037.


PARENT: A Parallel Software Suite for the Calculation of Configurational Entropy in Biomolecular Systems.

Fleck M, Polyansky AA, Zagrovic B.

J Chem Theory Comput. 2016 Apr 12;12(4):2055-65. doi: 10.1021/acs.jctc.5b01217. Epub 2016 Mar 18.


Interaction preferences between nucleobase mimetics and amino acids in aqueous solutions.

Hajnic M, Osorio JI, Zagrovic B.

Phys Chem Chem Phys. 2015 Sep 7;17(33):21414-22. doi: 10.1039/c5cp01486g. Epub 2015 Jul 29.


Malleable nature of mRNA-protein compositional complementarity and its functional significance.

Hlevnjak M, Zagrovic B.

Nucleic Acids Res. 2015 Mar 31;43(6):3012-21. doi: 10.1093/nar/gkv166. Epub 2015 Mar 8.


Absolute binding-free energies between standard RNA/DNA nucleobases and amino-acid sidechain analogs in different environments.

de Ruiter A, Zagrovic B.

Nucleic Acids Res. 2015 Jan;43(2):708-18. doi: 10.1093/nar/gku1344. Epub 2014 Dec 30.


The structure and regulation of human muscle α-actinin.

Ribeiro Ede A Jr, Pinotsis N, Ghisleni A, Salmazo A, Konarev PV, Kostan J, Sjöblom B, Schreiner C, Polyansky AA, Gkougkoulia EA, Holt MR, Aachmann FL, Zagrović B, Bordignon E, Pirker KF, Svergun DI, Gautel M, Djinović-Carugo K.

Cell. 2014 Dec 4;159(6):1447-60. doi: 10.1016/j.cell.2014.10.056. Epub 2014 Nov 26.


On the Contribution of Protein Spatial Organization to the Physicochemical Interconnection between Proteins and Their Cognate mRNAs.

Beier A, Zagrovic B, Polyansky AA.

Life (Basel). 2014 Nov 21;4(4):788-99. doi: 10.3390/life4040788.


Computational analysis of amino acids and their sidechain analogs in crowded solutions of RNA nucleobases with implications for the mRNA-protein complementarity hypothesis.

Hajnic M, Osorio JI, Zagrovic B.

Nucleic Acids Res. 2014 Dec 1;42(21):12984-94. doi: 10.1093/nar/gku1035. Epub 2014 Oct 31.


Are current atomistic force fields accurate enough to study proteins in crowded environments?

Petrov D, Zagrovic B.

PLoS Comput Biol. 2014 May 22;10(5):e1003638. doi: 10.1371/journal.pcbi.1003638. eCollection 2014 May.

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