Bojan Zagrovic: search on Z-Library

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1

Configurational entropy components and their contribution to biomolecular complex formation

Fleck, Markus, Zagrovic, Bojan

Journal:

Journal of Chemical Theory and Computation

Year:

2019

File:

PDF, 6.55 MB

2019

2

Interaction preferences between nucleobase mimetics and amino acids in aqueous solutions

Hajnic, Matea, Osorio, Juan I., Zagrovic, Bojan

Journal:

Physical Chemistry Chemical Physics

Year:

2015

Language:

english

File:

PDF, 2.36 MB

english, 2015

3

Understanding without Reading: Analogue Encoding of Physicochemical Properties of Proteins in their Cognate Messenger RNA

Polyansky, Anton A., Hlevnjak, Mario, Zagrovic, Bojan

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 39 KB

english, 2015

4

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

Petrov, Drazen, Zagrovic, Bojan, Dunbrack, Roland L.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.23 MB

english, 2014

5

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

Antonija Kuzmanic, Daniela Kruschel, Wilfred F. van Gunsteren, Navraj S. Pannu, Bojan Zagrovic

Journal:

Journal of Molecular Biology

Year:

2011

Language:

english

File:

PDF, 1.03 MB

english, 2011

6

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

Zagrovic, Bojan

Journal:

Molecular Physics

Year:

2007

Language:

english

File:

PDF, 1.71 MB

english, 2007

7

Childhood of a phoenix: modern biology in Eastern and South-Eastern Europe

Zagrovic, Bojan, Dikic, Ivan

Journal:

Nature Reviews Molecular Cell Biology

Year:

2008

Language:

english

File:

PDF, 607 KB

english, 2008

8

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

Bojan Zagrovic, Eric J Sorin, Vijay Pande

Journal:

Journal of Molecular Biology

Year:

2001

Language:

english

File:

PDF, 1.03 MB

english, 2001

9

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

Bojan Zagrovic, Guha Jayachandran, Ian S. Millett, Sebastian Doniach, Vijay S. Pande

Journal:

Journal of Molecular Biology

Year:

2005

Language:

english

File:

PDF, 485 KB

english, 2005

10

Dependence of Protein Crystal Stability on Residue Charge States and Ion Content of Crystal Solvent

Kuzmanic, Antonija, Zagrovic, Bojan

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 1.85 MB

english, 2014

11

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

Bojan Zagrovic, Vijay Pande

Journal:

Journal of Computational Chemistry

Year:

2003

Language:

english

File:

PDF, 163 KB

english, 2003

12

Direct interplay between stereochemistry and conformational preferences in aminoacylated oligoribonucleotides

Polyansky, Anton A, Kreuter, Mathias, Sutherland, John D, Zagrovic, Bojan

Journal:

Nucleic Acids Research

Year:

2019

Language:

english

File:

PDF, 2.92 MB

english, 2019

13

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

Vijay S. Pande, Ian Baker, Jarrod Chapman, Sidney P. Elmer, Siraj Khaliq, Stefan M. Larson, Young Min Rhee, Michael R. Shirts, Christopher D. Snow, Eric J. Sorin, Bojan Zagrovic

Journal:

Year:

2003

Language:

english

File:

PDF, 744 KB

english, 2003

14

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

Polyansky, Anton A., Bocharov, Eduard V., Velghe, Amélie I., Kuznetsov, Andrey S., Bocharova, Olga V., Urban, Anatoly S., Arseniev, Alexander S., Zagrovic, Bojan, Demoulin, Jean-Baptiste, Efremov, Rom

Journal:

Biochimica et Biophysica Acta (BBA) - General Subjects

Year:

2019

Language:

english

File:

PDF, 1.89 MB

english, 2019

15

Simulation of Folding of a Small Alpha-helical Protein in Atomistic Detail using Worldwide-distributed Computing

Bojan Zagrovic, Christopher D. Snow, Michael R. Shirts, Vijay S. Pande

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 1.06 MB

english, 2002

16

Mechanism and Thermodynamics of Binding of the Polypyrimidine Tract Binding Protein to RNA †

Schmid, Nathan, Zagrovic, Bojan, van Gunsteren, Wilfred F.

Journal:

Year:

2007

Language:

english

File:

PDF, 1.63 MB

english, 2007

17

Computational Study of the Mechanism and the Relative Free Energies of Binding of Anticholesteremic Inhibitors to Squalene-Hopene Cyclase †

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

Journal:

Year:

2008

Language:

english

File:

PDF, 699 KB

english, 2008

18

A code within a code: how codons influence mRNA stability

Martinez, Javier, Zagrovic, Bojan

Journal:

The EMBO Journal

Year:

2016

Language:

english

File:

PDF, 200 KB

english, 2016

19

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

Polyansky, Anton A., Zagrovic, Bojan

Journal:

The Journal of Physical Chemistry Letters

Year:

2012

Language:

english

File:

PDF, 1.64 MB

english, 2012

20

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

Polyansky, Anton A., Hlevnjak, Mario, Zagrovic, Bojan

Journal:

Nature Communications

Year:

2013

Language:

english

File:

PDF, 3.29 MB

english, 2013

21

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

Ulrike Mende, Bojan Zagrovic, Allison Cohen, Ying Li, Dario Valenzuela, Mark C. Fishman, Eva J. Neer

Journal:

Journal of Neuroscience Research

Year:

1998

Language:

english

File:

PDF, 203 KB

english, 1998

22

Mechanism and thermodynamics of ligand binding to auxin amidohydrolase

Mijo Simunovic, Bojan Zagrovic, Sanja Tomić

Journal:

Journal of Molecular Recognition

Year:

2011

Language:

english

File:

PDF, 788 KB

english, 2011

23

Computational Analysis of the Mechanism and Thermodynamics of Inhibition of Phosphodiesterase 5A by Synthetic Ligands

Zagrovic, Bojan, van Gunsteren, Wilfred F.

Journal:

Journal of Chemical Theory and Computation

Year:

2007

Language:

english

File:

PDF, 573 KB

english, 2007

24

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

Awile, Omar, Krisko, Anita, Sbalzarini, Ivo F., Zagrovic, Bojan, Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.38 MB

english, 2010

25

Folding–Unfolding Equilibrium of a Methylidene-Substituted β-Peptide

Nathan Schmid, Bojan Zagrovic, Wilfred F. van Gunsteren

Journal:

Helvetica Chimica Acta

Year:

2007

Language:

english

File:

PDF, 1.01 MB

english, 2007

26

Determination of Ensemble-Average Pairwise Root Mean-Square Deviation from Experimental B-Factors

Kuzmanic, Antonija, Zagrovic, Bojan

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 674 KB

english, 2010

27

The Mediterranean Institute for Life Sciences—An attempt at scientific excellence in Croatia

Journal:

Year:

2008

Language:

english

File:

PDF, 130 KB

english, 2008

28

Life is translation

Zagrovic, Bojan

Journal:

Year:

2014

Language:

english

File:

PDF, 149 KB

english, 2014

29

Simulated Unfolded-State Ensemble and the Experimental NMR Structures of Villin Headpiece Yield Similar Wide-Angle Solution X-ray Scattering Profiles

Zagrovic, Bojan, Pande, Vijay S.

Journal:

Journal of the American Chemical Society

Year:

2006

Language:

english

File:

PDF, 83 KB

english, 2006

30

Corrigendum to “Simulation of Folding of a Small Alpha-helical Protein in Atomistic Detail using Worldwide-distributed Computing”: J. Mol. Biol. (2002) 323 927–937

Bojan Zagrovic, Christopher D. Snow, Michael R. Shirts, Vijay S. Pande

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 34 KB

english, 2002

31

How Does Averaging Affect Protein Structure Comparison on the Ensemble Level?

Zagrovic, Bojan, Pande, Vijay S.

Journal:

Biophysical Journal

Year:

2004

Language:

english

File:

PDF, 175 KB

english, 2004

32

RNA-Protein Interactions in an Unstructured Context

Zagrovic, Bojan, Bartonek, Lukas, Polyansky, Anton A

Journal:

Year:

2018

Language:

english

File:

PDF, 1.59 MB

english, 2018

33

Structure and dynamics of two β-peptides in solution from molecular dynamics simulations validated against experiment

Bojan Zagrovic, Zrinka Gattin, Justin Kai-Chi Lau, Matthias Huber, Wilfred F. van Gunsteren

Journal:

European Biophysics Journal

Year:

2008

Language:

english

File:

PDF, 497 KB

english, 2008

34

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

Zagrovic, Bojan, Pande, Vijay S

Journal:

Natural Structural Biology

Year:

2003

Language:

english

File:

PDF, 940 KB

english, 2003

35

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

Polyansky, Anton A, Hlevnjak, Mario, Zagrovic, Bojan

Journal:

Year:

2013

Language:

english

File:

PDF, 1.63 MB

english, 2013

36

Computational Analysis of Binding of the GBD Domain of WASP to Different Binding Partners

K. Janowska, Maria, Zubac, Ruben, Zagrovic, Bojan

Journal:

Croatica Chemica Acta

Year:

2011

Language:

english

File:

PDF, 8.80 MB

english, 2011

37

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

Beier, Andreas, Zagrovic, Bojan, Polyansky, Anton

Journal:

Year:

2014

Language:

english

File:

PDF, 1.03 MB

english, 2014

38

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

Gallego, Laura D., Ghodgaonkar Steger, Medini, Polyansky, Anton A., Schubert, Tobias, Zagrovic, Bojan, Zheng, Ning, Clausen, Tim, Herzog, Franz, Köhler, Alwin

Journal:

Proceedings of the National Academy of Sciences

Year:

2016

Language:

english

File:

PDF, 1.54 MB

english, 2016

39

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

Petrov, Drazen, Margreitter, Christian, Grandits, Melanie, Oostenbrink, Chris, Zagrovic, Bojan, Wei, Guanghong

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 656 KB

english, 2013

40

Inosine Nucleobase Acts as Guanine in Interactions with Protein Side Chains

Hajnic, Matea, Ruiter, Anita de, Polyansky, Anton A., Zagrovic, Bojan

Journal:

Journal of the American Chemical Society

Year:

2016

Language:

english

File:

PDF, 1.10 MB

english, 2016

41

The Trp Cage: Folding Kinetics and Unfolded State Topology via Molecular Dynamics Simulations

Snow, Christopher D., Zagrovic, Bojan, Pande, Vijay S.

Journal:

Journal of the American Chemical Society

Year:

2002

Language:

english

File:

PDF, 146 KB

english, 2002

42

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

Petrov, Drazen, Zagrovic, Bojan

Journal:

Journal of the American Chemical Society

Year:

2014

Language:

english

File:

PDF, 495 KB

english, 2014

43

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

Fleck, Markus, Polyansky, Anton A., Zagrovic, Bojan

Journal:

Journal of Chemical Theory and Computation

Year:

2018

Language:

english

File:

PDF, 1.20 MB

english, 2018

44

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

Boots, Jennifer L., von Pelchrzim, Frederike, Weiss, Adam, Zimmermann, Bob, Friesacher, Theres, Radtke, Maximilian, Å»ywicki, Marek, Chen, Doris, Matylla-KuliÅska, Katarzyna, Zagrovic, Bojan, Schroed

Journal:

Year:

2020

File:

PDF, 2.04 MB

2020

45

Frameshifting preserves key physicochemical properties of proteins

Bartonek, Lukas, Braun, Daniel, Zagrovic, Bojan

Journal:

Proceedings of the National Academy of Sciences

Year:

2020

File:

PDF, 1.44 MB

2020

46

Native-like Mean Structure in the Unfolded Ensemble of Small Proteins

Bojan Zagrovic, Christopher D Snow, Siraj Khaliq, Michael R Shirts, Vijay S Pande

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 1.61 MB

english, 2002

47

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

Petrov, Drazen, Zagrovic, Bojan

Journal:

Journal of the American Chemical Society

Year:

2011

Language:

english

File:

PDF, 4.16 MB

english, 2011

48

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

Bartonek, Lukas, Zagrovic, Bojan

Journal:

Nucleic Acids Research

Year:

2019

Language:

english

File:

PDF, 739 KB

english, 2019

49

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

Lenz, Peter, Zagrovic, Bojan, Shapiro, Jessica, Pande, Vijay S.

Journal:

The Journal of Chemical Physics

Year:

2004

Language:

english

File:

PDF, 879 KB

english, 2004

50

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

Polyansky, Anton A., Kuzmanic, Antonija, Hlevnjak, Mario, Zagrovic, Bojan

Journal:

Journal of Chemical Theory and Computation

Year:

2012

Language:

english

File:

PDF, 1.52 MB

english, 2012

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