B. Žagrović

发表

FIBCD1 is an endocytic GAG receptor associated with a novel neurodevelopmental disorder

N. Perrimon, M. Burmeister, J. Penninger, 2022, EMBO molecular medicine.

Proteome-wide analysis reveals clues of complementary interactions between mRNAs and their cognate proteins as the physicochemical foundation of the genetic code

M. Hlevnjak, A. Polyansky, B. Žagrović, 2013, RNA biology.

VOLPES: an interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences

Lukas Bartonek, B. Žagrović, 2019, Nucleic Acids Res..

Widespread autogenous mRNA–protein interactions detected by CLIP-seq

Z. Lu, Weihao Zhao, Thomas H Kapral, 2022, Nucleic acids research.

Structural studies of cilia and flagella associated protein 410 (CFAP410) reveal its bimodular organization with an N-terminal LRR motif and a C-terminal tetrameric helical bundle

G. Dong, Kaiyao Huang, J. Sunter, 2022, bioRxiv.

How does averaging affect protein structure comparison on the ensemble level?

V. Pande, B. Zagrovic, B. Žagrović, 2004, Biophysical journal.

Unusual compactness of a polyproline type II structure.

V. Pande, E. Sorin, W. V. van Gunsteren, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study

Bojan Zagrovic, Vijay Pande, V. Pande, 2003, J. Comput. Chem..

Interaction preferences between protein side chains and key epigenetic modifications 5-methylcytosine, 5-hydroxymethycytosine and N6-methyladenine

Anita de Ruiter, A. Polyansky, Matea Hajnić, 2022, Scientific Reports.

Random-coil behavior and the dimensions of chemically unfolded proteins.

Robin S. Dothager, V. Pande, I. Ruczinski, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing.

Michael R. Shirts, M. Shirts, V. Pande, 2002, Journal of molecular biology.

Native-like mean structure in the unfolded ensemble of small proteins.

Michael R. Shirts, M. Shirts, V. Pande, 2002, Journal of molecular biology.

Microscopic Analysis of Protein Oxidative Damage: Effect of Carbonylation on Structure, Dynamics, and Aggregability of Villin Headpiece

D. Petrov, B. Žagrović, 2011, Journal of the American Chemical Society.

POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins

Z. Lu, B. Zagrovic, Yucheng T. Yang, 2021, Nucleic Acids Res..

Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors.

B. Zagrovic, Antonija Kuzmanic, B. Žagrović, 2010, Biophysical journal.

Direct interplay between stereochemistry and conformational preferences in aminoacylated oligoribonucleotides

J. Sutherland, A. Polyansky, B. Žagrović, 2019, Nucleic acids research.

The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators

A. Akalin, K. Djinović-Carugo, V. Franke, 2022, bioRxiv.

Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?

Drazen Petrov, Bojan Zagrovic, D. Petrov, 2014, PLoS Comput. Biol..

Life is translation

B. Žagrović, 2014, RNA biology.

The Structure and Regulation of Human Muscle α-Actinin

D. Svergun, M. Gautel, K. Djinović-Carugo, 2014, Cell.

Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications

Drazen Petrov, Bojan Zagrovic, Christian Margreitter, 2013, Nucleic Acids Res..

RNA polymerase II-binding aptamers in human ACRO1 satellites disrupt transcription in cis

Doris Chen, M. Żywicki, R. Schroeder, 2020, Transcription.

Mechanism of cargo-directed Atg8 conjugation during selective autophagy

C. Kraft, S. Martens, Anita de Ruiter, 2016, eLife.

Fuento: functional enrichment for bioinformatics

Bojan Zagrovic, David Weichselbaum, Anton A. Polyansky, 2017, Bioinform..

Order from disorder in the sarcomere: FATZ forms a fuzzy but tight complex and phase-separated condensates with α-actinin

R. Konrat, D. Svergun, M. Gautel, 2021, Science Advances.

A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications

Chris Oostenbrink, Drazen Petrov, Bojan Zagrovic, 2013, PLoS Comput. Biol..

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

B. Zagrovic, A. Polyansky, Matea Hajnić, 2016, Journal of the American Chemical Society.

Intrinsically Disordered Regions May Lower the Hydration Free Energy in Proteins: A Case Study of Nudix Hydrolase in the Bacterium Deinococcus radiodurans

Ivo F. Sbalzarini, Omar Awile, Bojan Zagrovic, 2010, PLoS Comput. Biol..

RNA‐protein interactions in an unstructured context

B. Zagrovic, Lukas Bartonek, A. Polyansky, 2018, FEBS letters.

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

Bojan Zagrovic, Lukas Bartonek, Lukas Bartonek, 2017, PLoS Comput. Biol..

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

A. Polyansky, B. Žagrović, Andreas Beier, 2014, Life.

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

B. Zagrovic, Matea Hajnić, J. I. Osorio, 2014, Nucleic acids research.

Of RNA-binding proteins and their targets: interaction determines expression

B. Žagrović, 2014, Genome Biology.

Evidence of direct complementary interactions between messenger RNAs and their cognate proteins

B. Zagrovic, A. Polyansky, B. Žagrović, 2013, Nucleic acids research.

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

Anita de Ruiter, B. Žagrović, Anton A Polyansky, 2017, Journal of chemical theory and computation.

Invariants of Frameshifted Variants

B. Zagrovic, Lukas Bartonek, D. Braun, 2019, bioRxiv.

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

B. Zagrovic, Anita de Ruiter, B. Žagrović, 2014, Nucleic acids research.

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

B. Zagrovic, F. Herzog, A. Köhler, 2016, Proceedings of the National Academy of Sciences.

Protein compactness and interaction valency define the architecture of a biomolecular condensate across scales

A. Köhler, R. Efremov, A. Polyansky, 2022, bioRxiv.

Beta-hairpin folding simulations in atomistic detail using an implicit solvent model.

Eric J. Sorin, V. Pande, E. Sorin, 2001, Journal of molecular biology.

Sequence signatures of direct complementarity between mRNAs and cognate proteins on multiple levels

M. Hlevnjak, A. Polyansky, B. Žagrović, 2012, Nucleic acids research.

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

A. Polyansky, Markus Fleck, B. Žagrović, 2018, Journal of chemical theory and computation.

Estimation of conformational entropy in protein-ligand interactions: a computational perspective.

B. Zagrovic, A. Polyansky, Ruben Zubac, 2012, Methods in molecular biology.

Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin

B. Zagrovic, Tomasz Włodarski, B. Žagrović, 2009, Proceedings of the National Academy of Sciences.

Conformational averaging in structural biology: issues, challenges and computational solutions.

B. Zagrovic, D. Kruschel, B. Žagrović, 2009, Molecular bioSystems.

Frameshifting preserves key physicochemical properties of proteins

Lukas Bartonek, D. Braun, B. Žagrović, 2020, Proceedings of the National Academy of Sciences.

Effect of deletion of the major brain G‐protein α subunit (αo) on coordination of G‐protein subunits and on adenylyl cyclase activity

E. Neer, M. Fishman, Ying-Lan Li, 1998 .

In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble.

Christian L. Müller, I. Sbalzarini, B. Zagrovic, 2009, The Journal of chemical physics.

Dynamics May Significantly Influence the Estimation of Interatomic Distances in Biomolecular X-ray Structures

Bojan Zagrovic, Navraj S. Pannu, Wilfred F. van Gunsteren, 2011, Journal of molecular biology.

Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing.

Michael R. Shirts, Eric J. Sorin, Stefan M. Larson, 2003, Biopolymers.

FIBCD1 is a Conserved Receptor for Chondroitin Sulphate Proteoglycans of the Brain Extracellular Matrix and a Candidate Gene for a Complex Neurodevelopmental Disorder

N. Perrimon, M. Burmeister, J. Penninger, 2021 .

Computational study of the mechanism and the relative free energies of binding of anticholesteremic inhibitors to squalene-hopene cyclase.

Wilfred F van Gunsteren, Bojan Zagrovic, Fabienne Schwab, 2008, Biochemistry.

Protein Electrostatic Properties Predefining the Level of Surface Hydrophobicity Change upon Phosphorylation

Bojan Zagrovic, Anton A. Polyansky, A. Polyansky, 2012, The journal of physical chemistry letters.

X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals

Bojan Zagrovic, Navraj S. Pannu, B. Zagrovic, 2014, Nature Communications.

On the Contribution of Linear Correlations to Quasi-harmonic Conformational Entropy in Proteins.

Antonija Kuzmanic, M. Hlevnjak, A. Polyansky, 2012, Journal of chemical theory and computation.

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

K. Mechtler, T. Kaufmann, K. Djinović-Carugo, 2017, Nucleic acids research.

Configurational Entropy Components and Their Contribution to Biomolecular Complex Formation

Markus Fleck, B. Žagrović, 2019, Journal of chemical theory and computation.

Dependence of protein crystal stability on residue charge states and ion content of crystal solvent.

Antonija Kuzmanic, B. Žagrović, 2014, Biophysical journal.

How Large is an α-Helix? Studies of the Radii of Gyration of Helical Peptides by Small-angle X-ray Scattering and Molecular Dynamics

V. Pande, G. Jayachandran, I. Millett, 2005 .

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

A. S. Kuznetsov, B. Zagrovic, O. Bocharova, 2019, Biochimica et biophysica acta. General subjects.

Structural correspondence between the α-helix and the random-flight chain resolves how unfolded proteins can have native-like properties

V. Pande, B. Žagrović, 2003, Nature Structural Biology.

The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations.

V. Pande, C. Snow, B. Zagrovic, 2002, Journal of the American Chemical Society.

Comparing atomistic simulation data with the NMR experiment: How much can NOEs actually tell us?

B. Zagrovic, W. V. van Gunsteren, B. Žagrović, 2006, Proteins.

Hydrophilicity Matching – A Potential Prerequisite for the Formation of Protein-Protein Complexes in the Cell

B. Zagrovic, Gordan Zitkovic, M. Hlevnjak, 2010, PloS one.

Hydrophilicity Matching – a Prerequisite for the Formation of Protein-Protein Complexes

B. Zagrovic, Gordan Zitkovic, M. Hlevnjak, 2010 .

Compositional complementarity between genomic RNA and coat proteins in positive-sense single-stranded RNA viruses

M. Hlevnjak, A. Polyansky, Florian Poetsch, 2022, Nucleic acids research.

Atomistic protein folding simulations on the hundreds of microsecond timescale using worldwide distributed computing

Vijay S. Pande, Michael R. Shirts, Jarrod Chapman, 2002 .

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

Bojan Zagrovic, Markus Fleck, Anton A Polyansky, 2016, Journal of chemical theory and computation.

Protein compactness and interaction valency define the architecture of a biomolecular condensate across scales

A. Köhler, R. Efremov, A. Polyansky, 2022, bioRxiv.

Mechanism and thermodynamics of binding of the polypyrimidine tract binding protein to RNA.

B. Zagrovic, W. V. van Gunsteren, Nathan Schmid, 2007, Biochemistry.

Analogue encoding of physicochemical properties of proteins in their cognate messenger RNAs

M. Hlevnjak, A. Polyansky, B. Žagrović, 2013, Nature Communications.

β-hairpin folding simulations in atomistic detail using an implicit solvent model1

Eric J. Sorin, V. Pande, E. Sorin, 2001 .

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

B. Zagrovic, X. Daura, D. Petrov, 2016, Biophysical journal.

Folding probabilities: a novel approach to folding transitions and the two-dimensional Ising-model.

Vijay S Pande, Bojan Zagrovic, Jessica Shapiro, 2004, The Journal of chemical physics.

Mechanism and thermodynamics of ligand binding to auxin amidohydrolase

S. Tomić, M. Simunovic, B. Žagrović, 2011, Journal of molecular recognition : JMR.

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

B. Zagrovic, Matea Hajnić, J. I. Osorio, 2015, Physical chemistry chemical physics : PCCP.

Erratum: Random-coil behavior and the dimensions of chemically unfolded proteins (Proceedings of The National Academy of Sciences of The United States of America (August 24, 2004) 101, 34 (12491-12496))

Vijay S. Pande, Ingo Ruczinski, Kevin W. Plaxco, 2005 .

Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin

Tomasz Włodarski, B. Žagrović, 2009, Proceedings of the National Academy of Sciences.

Driving forces behind phase separation of the carboxy-terminal domain of RNA polymerase II

P. Cramer, D. Flores-Solis, A. Polyansky, 2023, Nature communications.

Helical signature motif in the fibre diffraction patterns of random-walk chains

B. Žagrović, 2007 .

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

M. Hlevnjak, B. Žagrović, 2015, Nucleic acids research.