Publications per year
Publications per year
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2024
An Atomistic View on the Mechanism of Diatom Peptide-Guided Biomimetic Silica Formation
Kozak, F., Brandis, D., Pötzl, C., Epasto, L. M., Reichinger, D., Obrist, D., Peterlik, H., Polyansky, A., Zagrovic, B., Daus, F., Geyer, A., Becker, C. F. W. & Kurzbach, D., 14 Aug 2024, In: Advanced science. 11, 30, 2401239.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
2023
Coding from Binding? Molecular Interactions at the Heart of Translation
Zagrovic, B., Adlhart, M. & Kapral, T. H., 9 May 2023, In: Annual Review of Biophysics. 52, p. 69-89 21 p.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
Driving forces behind phase separation of the carboxy-terminal domain of RNA polymerase II
Flores-Solis, D., Lushpinskaia, I. P., Polyansky, A. A., Changiarath, A., Boehning, M., Mirkovic, M., Walshe, J., Pietrek, L. M., Cramer, P., Stelzl, L. S., Zagrovic, B. & Zweckstetter, M., Dec 2023, In: Nature Communications. 14, 1, 5979.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
Protein compactness and interaction valency define the architecture of a biomolecular condensate across scales
Polyansky, A. A., Gallego, L. D., Efremov, R. G., Köhler, A. & Zagrovic, B., 20 Jul 2023, In: eLife. 12, e80038.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators
Appel, L. M., Franke, V., Benedum, J., Grishkovskaya, I., Strobl, X., Polyansky, A., Ammann, G., Platzer, S., Neudolt, A., Wunder, A., Walch, L., Kaiser, S., Zagrovic, B., Djinovic-Carugo, K., Akalin, A. & Slade, D., Dec 2023, In: Nature Communications. 14, 1, 166.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
2022
Compositional complementarity between genomic RNA and coat proteins in positive-sense single-stranded RNA viruses
Adlhart, M., Poetsch, F., Hlevnjak, M., Hoogmoed, M., Polyansky, A. A. & Zagrovic, B., 22 Apr 2022, In: Nucleic Acids Research. 50, 7, p. 4054-4067 14 p.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
FIBCD1 is an endocytic GAG receptor associated with a novel neurodevelopmental disorder
Fell, C. W., Hagelkruys, A., Cicvaric, A., Horrer, M., Liu, L., Li, J. S. S., Stadlmann, J., Polyansky, A. A., Mereiter, S., Tejada, M. A., Kokotović, T., Achuta, V. S., Scaramuzza, A., Twyman, K. A., Morrow, M. M., Juusola, J., Yan, H., Wang, J., Burmeister, M., Choudhury, B., & 9 others, 7 Sept 2022, In: EMBO Molecular Medicine. 14, 9, e15829.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
Interaction preferences between protein side chains and key epigenetic modifications 5-methylcytosine, 5-hydroxymethycytosine and N6-methyladenine
Hajnic, M., Gil, S. A., Polyansky, A. A., de Ruiter, A. & Zagrovic, B., 15 Nov 2022, In: Scientific Reports. 12, 1, 19583.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins
Zhao, W., Zhang, S., Zhu, Y., Xi, X., Bao, P., Ma, Z., Kapral, T., Chen, S., Zagrovic, B., Yang, Y. T. & Lu, Z. J., 7 Jan 2022, In: Nucleic Acids Research. 50, D1, p. D287-D294 8 p., gkab702.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
Widespread autogenous mRNA-protein interactions detected by CLIP-seq
Kapral, T. H., Farnhammer, F., Zhao, W., Lu, Z. J. & Zagrovic, B., 23 Sept 2022, In: Nucleic Acids Research. 50, 17, p. 9984-9999 16 p.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
2021
Order from disorder in the sarcomere: FATZ forms a fuzzy but tight complex and phase-separated condensates with α-actinin
Sponga, A., Arolas, J. L., Schwarz, T. C., Jeffries, C. M., Chamorro, A. R., Kostan, J., Ghisleni, A., Drepper, F., Polyansky, A., de Almeida Ribeiro, E., Pedron, M., Zawadzka-Kazimierczuk, A., Mlynek, G., Peterbauer, T., Doto, P., Schreiner, C., Hollerl, E., Mateos, B., Geist, L., Faulkner, G., & 7 others, 28 May 2021, In: Science Advances. 7, 22, 19 p., eabg7653.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
2020
Frameshifting preserves key physicochemical properties of proteins
Bartonek, L., Braun, D. & Zagrovic, B., 17 Mar 2020, In: Proceedings of the National Academy of Sciences of the United States of America (PNAS). 117, 11, p. 5907-5912 6 p.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
RNA polymerase II-binding aptamers in human ACRO1 satellites disrupt transcription in cis
Boots, J. L., von Pelchrzim, F., Weiss, A., Zimmermann, B., Friesacher, T., Radtke, M., Żywicki, M., Chen, D., Matylla-Kulińska, K., Zagrovic, B. & Schroeder, R., 2020, In: Transcription. 11, 5, p. 217-229 13 p.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
2019
Atomistic mechanism of the constitutive activation of PDGFRA via its transmembrane domain
Polyansky, A. A., Bocharov, E. V., Velghe, A. I., Kuznetsov, A. S., Bocharova, O. V., Urban, A. S., Arseniev, A. S., Zagrovic, B., Demoulin, J-B. & Efremov, R. G., Jan 2019, In: Biochimica et Biophysica Acta - General Subjects. 1863, 1, p. 82-95 14 p.Publications: Contribution to journal › Article › Peer Reviewed
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Configurational Entropy Components and Their Contribution to Biomolecular Complex Formation
Fleck, M. & Zagrovic, B., Jun 2019, In: Journal of Chemical Theory and Computation. 15, 6, p. 3844-3853 10 p.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
VOLPES: an interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences
Bartonek, L. & Zagrovic, B., 2 Jul 2019, In: Nucleic Acids Research. 47, W1, p. W632-W635 4 p.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
2017
A novel non-canonical PIP-box mediates PARG interaction with PCNA
Kaufmann, T., Polyansky, A., Grishkovskaya, I., Kostrhon, S., Kukolj, E., Olek, K. M., Herbert, S., Beltzung, E., Mechtler, K., Peterbauer, T., Gotzmann, J., Zhang, L., Hartl, M., Zagrovic, B., Elsayad, K., Djinovic-Carugo, K. & Slade, D., 19 Sept 2017, In: Nucleic Acids Research. 45, 16, p. 9741-9759 19 p.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
Dependence of Binding Free Energies between RNA Nucleobases and Protein Side Chains on Local Dielectric Properties
De Ruiter, A., Polyansky, A. A. & Zagrovic, B., 12 Sept 2017, In: Journal of Chemical Theory and Computation. 13, 9, p. 4504-4513 10 p.Publications: Contribution to journal › Article › Peer Reviewed
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Fuento: functional enrichment for bioinformatics
Weichselbaum, D., Zagrovic, B. & Polyansky, A. A., 15 Aug 2017, In: Bioinformatics. 33, 16, p. 2604-2606 3 p.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
mRNA/protein sequence complementarity and its determinants: The impact of affinity scales
Bartonek, L. & Zagrovic, B., 1 Jul 2017, In: PLoS Computational Biology. 13, 7, 16 p., e1005648.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
2016
A code within a code: How codons influence mRNA stability
Martinez, J. & Zagrovic, B., 4 Oct 2016, In: The EMBO Journal. 35, 19, p. 2064-2065 2 p.Publications: Contribution to journal › Article › Peer Reviewed
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Effect of Oxidative Damage on the Stability and Dimerization of Superoxide Dismutase 1
Petrov, D., Daura, X. & Zagrovic, B., 12 Apr 2016, In: Biophysical Journal. 110, 7, p. 1499-1509 11 p.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
Inosine Nucleobase Acts as Guanine in Interactions with Protein Side Chains
Hajnic, M., de Ruiter, A., Polyansky, A. A. & Zagrovic, B., 4 May 2016, In: Journal of the American Chemical Society. 138, 17, p. 5519-5522 4 p.Publications: Contribution to journal › Article › Peer Reviewed
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Mechanism of cargo-directed Atg8 conjugation during selective autophagy
Fracchiolla, D., Sawa-Makarska, J., Zens, B., de Ruiter, A., Zaffagnini, G., Brezovich, A., Romanov, J., Runggatscher, K., Kraft, C., Zagrovic, B. & Martens, S., 23 Nov 2016, In: eLife. 5, 30 p., 18544.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
PARENT: A Parallel Software Suite for the Calculation of Configurational Entropy in Biomolecular Systems
Fleck, M., Polyansky, A. A. & Zagrovic, B., 12 Apr 2016, In: Journal of Chemical Theory and Computation. 12, 4, p. 2055-2065 11 p.Publications: Contribution to journal › Article › Peer Reviewed
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Structural mechanism for the recognition and ubiquitination of a single nucleosome residue by Rad6-Bre1
Gallego, L. D., Steger, M. G., Polyansky, A., Schubert, T., Zagrovic, B., Zheng, N., Clausen, T., Herzog, F. & Koehler, A., 20 Sept 2016, In: Proceedings of the National Academy of Sciences of the United States of America (PNAS). 113, 38, p. 10553-10558 6 p.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
2015
Absolute binding-free energies between standard RNA/DNA nucleobases and amino-acid sidechain analogs in different environments
de Ruiter, A. & Zagrovic, B., Jan 2015, In: Nucleic Acids Research. 43, 2, p. 708-718 11 p.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
Interaction preferences between nucleobase mimetics and amino acids in aqueous solutions
Hajnic, M., Osorio, J. I. & Zagrovic, B., 20 Jul 2015, In: Physical Chemistry Chemical Physics. 17, 33, p. 21414-21422 9 p.Publications: Contribution to journal › Article › Peer Reviewed
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Malleable nature of mRNA-protein compositional complementarity and its functional significance
Hlevnjak, M. & Zagrovic, B., 31 Mar 2015, In: Nucleic Acids Research. 43, 6, p. 3012-3021 10 p.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
2014
Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?
Petrov, D. & Zagrovic, B., May 2014, In: PLoS Computational Biology. 10, 5, 11 p., e1003638.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
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., Iregui Osorio, J. & Zagrovic, B., Dec 2014, In: Nucleic Acids Research. 42, 21, p. 12984-12994 11 p.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
Dependence of Protein Crystal Stability on Residue Charge States and Ion Content of Crystal Solvent
Kuzmanic, A. & Zagrovic, B., 4 Feb 2014, In: Biophysical Journal. 106, 3, p. 677-686 10 p.Publications: Contribution to journal › Article › Peer Reviewed
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On the Contribution of Protein Spatial Organization to the Physicochemical Interconnection between Proteins and Their Cognate mRNAs
Beier, A., Zagrovic, B. & Polyansky, A. A., 21 Nov 2014, In: Life. 4, 4, p. 788-799 12 p.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
The structure and regulation of human muscle α-Actinin
Ribeiro, E. D. A., Pinotsis, N., Ghisleni, A., Salmazo, A., Konarev, P. V., Kostan, J., Sjoeblom, B., Schreiner, C., Polyansky, A. A., Gkougkoulia, E. A., Holt, M. R., Aachmann, F. L., Zagrovic, B., Bordignon, E., Pirker, K. F., Svergun, D. I., Gautel, M. & Djinovic-Carugo, K., 4 Dec 2014, In: Cell. 159, 6, p. 1447-1460 14 p.Publications: Contribution to journal › Article › Peer Reviewed
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X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals
Kuzmanic, A., Pannu, N. S. & Zagrovic, B., Feb 2014, In: Nature Communications. 5, p. 3220 1 p., 3220.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
2013
Analogue encoding of physicochemical properties of proteins in their cognate messenger RNAs
Polyansky, A. A., Hlevnjak, M. & Zagrovic, B., 20 Nov 2013, In: Nature Communications. 4, 11 p., 2784.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications
Petrov, D., Margreitter, C., Grandits, M., Oostenbrink, C. & Zagrovic, B., Jul 2013, In: PLoS Computational Biology. 9, 7, 9 p., 1003154.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
Evidence of direct complementary interactions between messenger RNAs and their cognate proteins
Polyanskiy, A. & Zagrovic, B., Oct 2013, In: Nucleic Acids Research. 41, 18, p. 8434-8443 10 p.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
Proteome-wide analysis reveals clues of complementary interactions between mRNAs and their cognate proteins as the physicochemical foundation of the genetic code
Polyanskiy, A., Hlevnjak, M. & Zagrovic, B., 1 Aug 2013, In: RNA Biology. 10, 8, p. 1248-1254 7 p.Publications: Contribution to journal › Article › Peer Reviewed
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Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications
Margreitter, C., Petrov, D. & Zagrovic, B., Jul 2013, In: Nucleic Acids Research. 41, W1, p. W422-W426 5 p.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
2012
Estimation of conformational entropy in protein-ligand interactions: a computational perspective
Polyansky, A. A., Zagrovic, B. & Zagrovic, B., 2012, In: Methods in Molecular Biology. 819, p. 327-353 27 p.Publications: Contribution to journal › Article › Peer Reviewed
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On the Contribution of Linear Correlations to Quasi-harmonic Conformational Entropy in Proteins
Polyanskiy, A., Kuzmanic, A., Hlevnjak, M. & Zagrovic, B., 2012, In: Journal of Chemical Theory and Computation. 8, 10, p. 3820-3829 10 p.Publications: Contribution to journal › Article › Peer Reviewed
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Protein electrostatic properties predefining the level of surface hydrophobicity change upon phosphorylation
Polyanskiy, A. & Zagrovic, B., 2012, In: The Journal of Physical Chemistry Letters. 3, 8, p. 973-976 4 p.Publications: Contribution to journal › Article › Peer Reviewed
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Sequence signature of direct complementarity between mRNAs and cognate proteins on multiple levels
Hlevnjak, M., Polyanskiy, A. & Zagrovic, B., 2012, In: Nucleic Acids Research. 40, 18, p. 8874-8882 9 p.Publications: Contribution to journal › Article › Peer Reviewed
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2011
Computational Analysis of Binding of the GBD Domain of WASP to Different Binding Partners
Janowska, M. K., Zubac, R. & Zagrovic, B., 2011, In: Croatica Chemica Acta. 84, 2, p. 211-220 10 p.Publications: Contribution to journal › Article › Peer Reviewed
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Dynamics May Significantly Influence the Estimation of Interatomic Distances in Biomolecular X-ray Structures
Kuzmanic, A., Kruschel, D., Van Gunsteren, W. F., Pannu, N. S. & Zagrovic, B., 2011, In: Journal of Molecular Biology. 411, 1, p. 286-297 12 p.Publications: Contribution to journal › Article › Peer Reviewed
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Mechanism and thermodynamics of ligand binding to auxin amidohydrolase
Simunovic, M., Zagrovic, B. & Tomic, S., 2011, In: Journal of Molecular Recognition. 24, 5, p. 854-861 8 p.Publications: Contribution to journal › Article › Peer Reviewed
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Microscopic Analysis of Protein Oxidative Damage: Effect of Carbonylation on Structure, Dynamics, and Aggregability of Villin Headpiece
Petrov, D. & Zagrovic, B., 2011, In: Journal of the American Chemical Society. 133, 18, p. 7016-7024 9 p.Publications: Contribution to journal › Article › Peer Reviewed
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2010
Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors.
Zagrovic, B., 2010, In: Biophysical Journal. 98, 5, p. 861-871 11 p.Publications: Contribution to journal › Article › Peer Reviewed
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Hydrophilicity Matching - A Potential Prerequisite for the Formation of Protein-Protein Complexes in the Cell
Hlevnjak, M., Zitkovic, G. & Zagrovic, B., 17 Jun 2010, In: PLoS ONE. 5, 6, 8 p., 11169.Publications: Contribution to journal › Article › Peer Reviewed