☰

Bojan Zagrovic, Ph.D. - Publications

Affiliations: 
2004 Stanford University, Palo Alto, CA 
Area:
theoretical methods to understand the physical properties of biological molecules
Tree Info Similar researchers PubMed Report error

43 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Polyansky AA, Gallego LD, Efremov RG, Köhler A, Zagrovic B. Protein compactness and interaction valency define the architecture of a biomolecular condensate across scales. Elife. 12. PMID 37470705 DOI: 10.7554/eLife.80038  0.381
2022 Hajnic M, Gil SA, Polyansky AA, de Ruiter A, Zagrovic B. Interaction preferences between protein side chains and key epigenetic modifications 5-methylcytosine, 5-hydroxymethycytosine and N-methyladenine. Scientific Reports. 12: 19583. PMID 36380112 DOI: 10.1038/s41598-022-23585-z  0.315
2018 Fleck M, Polyansky AA, Zagrovic B. Self-Consistent Framework Connecting Experimental Proxies of Protein Dynamics with Configurational Entropy. Journal of Chemical Theory and Computation. PMID 29799751 DOI: 10.1021/acs.jctc.8b00100  0.308
2015 Hlevnjak M, Zagrovic B. Malleable nature of mRNA-protein compositional complementarity and its functional significance. Nucleic Acids Research. 43: 3012-21. PMID 25753660 DOI: 10.1093/Nar/Gkv166  0.349
2015 de Ruiter A, Zagrovic B. Absolute binding-free energies between standard RNA/DNA nucleobases and amino-acid sidechain analogs in different environments. Nucleic Acids Research. 43: 708-18. PMID 25550435 DOI: 10.1093/Nar/Gku1344  0.383
2014 Hajnic M, Osorio JI, Zagrovic B. Computational analysis of amino acids and their sidechain analogs in crowded solutions of RNA nucleobases with implications for the mRNA-protein complementarity hypothesis. Nucleic Acids Research. 42: 12984-94. PMID 25361976 DOI: 10.1093/Nar/Gku1035  0.426
2014 Petrov D, Zagrovic B. Are current atomistic force fields accurate enough to study proteins in crowded environments? Plos Computational Biology. 10: e1003638. PMID 24854339 DOI: 10.1371/Journal.Pcbi.1003638  0.533
2014 Kuzmanic A, Pannu NS, Zagrovic B. X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals. Nature Communications. 5: 3220. PMID 24504120 DOI: 10.1038/Ncomms4220  0.304
2013 Polyansky AA, Hlevnjak M, Zagrovic B. Analogue encoding of physicochemical properties of proteins in their cognate messenger RNAs. Nature Communications. 4: 2784. PMID 24253588 DOI: 10.1038/Ncomms3784  0.341
2013 Petrov D, Margreitter C, Grandits M, Oostenbrink C, Zagrovic B. A systematic framework for molecular dynamics simulations of protein post-translational modifications. Plos Computational Biology. 9: e1003154. PMID 23874192 DOI: 10.1371/Journal.Pcbi.1003154  0.47
2013 Polyansky AA, Zagrovic B. Evidence of direct complementary interactions between messenger RNAs and their cognate proteins. Nucleic Acids Research. 41: 8434-43. PMID 23868089 DOI: 10.1093/Nar/Gkt618  0.348
2013 Margreitter C, Petrov D, Zagrovic B. Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications. Nucleic Acids Research. 41: W422-6. PMID 23703210 DOI: 10.1093/Nar/Gkt416  0.519
2012 Polyansky AA, Kuzmanic A, Hlevnjak M, Zagrovic B. On the Contribution of Linear Correlations to Quasi-harmonic Conformational Entropy in Proteins. Journal of Chemical Theory and Computation. 8: 3820-9. PMID 26593023 DOI: 10.1021/ct300082q  0.374
2012 Kuzmanic A, Polyansky AA, Zubac R, Hlevnjak M, Kruschel D, van Gunsteren WF, Pannu NS, Zagrovic B. Implications of conformational heterogeneity in protein crystals: from interatomic distance measurements to entropy estimation Acta Crystallographica Section a Foundations of Crystallography. 68: s110-s110. DOI: 10.1107/S0108767312097875  0.359
2011 Simunovic M, Zagrovic B, Tomić S. Mechanism and thermodynamics of ligand binding to auxin amidohydrolase. Journal of Molecular Recognition : Jmr. 24: 854-61. PMID 21812060 DOI: 10.1002/Jmr.1128  0.345
2011 Kuzmanic A, Kruschel D, van Gunsteren WF, Pannu NS, Zagrovic B. Dynamics may significantly influence the estimation of interatomic distances in biomolecular X-ray structures. Journal of Molecular Biology. 411: 286-97. PMID 21645520 DOI: 10.1016/J.Jmb.2011.05.033  0.361
2011 Petrov D, Zagrovic B. Microscopic analysis of protein oxidative damage: effect of carbonylation on structure, dynamics, and aggregability of villin headpiece. Journal of the American Chemical Society. 133: 7016-24. PMID 21506564 DOI: 10.1021/Ja110577E  0.502
2010 Awile O, Krisko A, Sbalzarini IF, Zagrovic B. Intrinsically disordered regions may lower the hydration free energy in proteins: a case study of nudix hydrolase in the bacterium Deinococcus radiodurans. Plos Computational Biology. 6: e1000854. PMID 20657662 DOI: 10.1371/Journal.Pcbi.1000854  0.378
2010 Hlevnjak M, Zitkovic G, Zagrovic B. Hydrophilicity matching - a potential prerequisite for the formation of protein-protein complexes in the cell. Plos One. 5: e11169. PMID 20567518 DOI: 10.1371/Journal.Pone.0011169  0.356
2010 Kuzmanic A, Zagrovic B. Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors. Biophysical Journal. 98: 861-71. PMID 20197040 DOI: 10.1016/J.Bpj.2009.11.011  0.482
2009 Kruschel D, Zagrovic B. Conformational averaging in structural biology: issues, challenges and computational solutions. Molecular Biosystems. 5: 1606-16. PMID 20023721 DOI: 10.1039/B917186J  0.429
2009 Wlodarski T, Zagrovic B. Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin. Proceedings of the National Academy of Sciences of the United States of America. 106: 19346-51. PMID 19887638 DOI: 10.1073/Pnas.0906966106  0.389
2008 Zagrovic B, Gattin Z, Lau JK, Huber M, van Gunsteren WF. Structure and dynamics of two beta-peptides in solution from molecular dynamics simulations validated against experiment. European Biophysics Journal : Ebj. 37: 903-12. PMID 18368403 DOI: 10.1007/s00249-008-0307-y  0.321
2008 Schwab F, van Gunsteren WF, Zagrovic B. Computational study of the mechanism and the relative free energies of binding of anticholesteremic inhibitors to squalene-hopene cyclase. Biochemistry. 47: 2945-51. PMID 18247576 DOI: 10.1021/Bi702067H  0.417
2007 Zagrovic B, van Gunsteren WF. Computational Analysis of the Mechanism and Thermodynamics of Inhibition of Phosphodiesterase 5A by Synthetic Ligands. Journal of Chemical Theory and Computation. 3: 301-11. PMID 26627173 DOI: 10.1021/Ct600322D  0.361
2007 Schmid N, Zagrovic B, van Gunsteren WF. Mechanism and thermodynamics of binding of the polypyrimidine tract binding protein to RNA. Biochemistry. 46: 6500-12. PMID 17497933 DOI: 10.1021/Bi6026133  0.382
2007 Zagrovic B. Helical signature motif in the fibre diffraction patterns of random-walk chains Molecular Physics. 105: 1299-1306. DOI: 10.1080/00268970701395114  0.326
2007 Schmid N, Zagrovic B, Van Gunsteren WF. Folding-unfolding equilibrium of a methylidene-substituted β-peptide Helvetica Chimica Acta. 90: 1966-1979. DOI: 10.1002/Hlca.200790204  0.386
2006 Zagrovic B, Pande VS. Simulated unfolded-state ensemble and the experimental NMR structures of villin headpiece yield similar wide-angle solution X-ray scattering profiles. Journal of the American Chemical Society. 128: 11742-3. PMID 16953598 DOI: 10.1021/Ja0640694  0.555
2006 Zagrovic B, van Gunsteren WF. Comparing atomistic simulation data with the NMR experiment: how much can NOEs actually tell us? Proteins. 63: 210-8. PMID 16425239 DOI: 10.1002/Prot.20872  0.529
2005 Zagrovic B, Jayachandran G, Millett IS, Doniach S, Pande VS. How large is an alpha-helix? Studies of the radii of gyration of helical peptides by small-angle X-ray scattering and molecular dynamics. Journal of Molecular Biology. 353: 232-41. PMID 16171817 DOI: 10.1016/J.Jmb.2005.08.053  0.758
2005 Zagrovic B, Lipfert J, Sorin EJ, Millett IS, van Gunsteren WF, Doniach S, Pande VS. Unusual compactness of a polyproline type II structure. Proceedings of the National Academy of Sciences of the United States of America. 102: 11698-703. PMID 16085707 DOI: 10.1073/Pnas.0409693102  0.782
2004 Zagrovic B, Pande VS. How does averaging affect protein structure comparison on the ensemble level? Biophysical Journal. 87: 2240-6. PMID 15454426 DOI: 10.1529/Biophysj.104.042184  0.641
2004 Kohn JE, Millett IS, Jacob J, Zagrovic B, Dillon TM, Cingel N, Dothager RS, Seifert S, Thiyagarajan P, Sosnick TR, Hasan MZ, Pande VS, Ruczinski I, Doniach S, Plaxco KW. Random-coil behavior and the dimensions of chemically unfolded proteins. Proceedings of the National Academy of Sciences of the United States of America. 101: 12491-6. PMID 15314214 DOI: 10.1073/Pnas.0403643101  0.595
2004 Lenz P, Zagrovic B, Shapiro J, Pande VS. Folding probabilities: a novel approach to folding transitions and the two-dimensional Ising-model. The Journal of Chemical Physics. 120: 6769-78. PMID 15267572 DOI: 10.1063/1.1667470  0.623
2003 Zagrovic B, Pande VS. Structural correspondence between the alpha-helix and the random-flight chain resolves how unfolded proteins can have native-like properties. Nature Structural Biology. 10: 955-61. PMID 14555998 DOI: 10.1038/Nsb995  0.667
2003 Zagrovic B, Pande V. Solvent viscosity dependence of the folding rate of a small protein: distributed computing study. Journal of Computational Chemistry. 24: 1432-6. PMID 12868108 DOI: 10.1002/Jcc.10297  0.604
2003 Pande VS, Baker I, Chapman J, Elmer SP, Khaliq S, Larson SM, Rhee YM, Shirts MR, Snow CD, Sorin EJ, Zagrovic B. Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. Biopolymers. 68: 91-109. PMID 12579582 DOI: 10.1002/Bip.10219  0.65
2002 Snow CD, Zagrovic B, Pande VS. The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations. Journal of the American Chemical Society. 124: 14548-9. PMID 12465960 DOI: 10.1021/Ja028604L  0.77
2002 Zagrovic B, Snow CD, Shirts MR, Pande VS. Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. Journal of Molecular Biology. 323: 927-37. PMID 12417204 DOI: 10.1016/S0022-2836(02)00997-X  0.82
2002 Zagrovic B, Snow CD, Khaliq S, Shirts MR, Pande VS. Native-like mean structure in the unfolded ensemble of small proteins. Journal of Molecular Biology. 323: 153-64. PMID 12368107 DOI: 10.1016/S0022-2836(02)00888-4  0.804
2002 Zagrovic B, Snow CD, Shirts MR, Pande VS. Corrigendum to “Simulation of Folding of a Small Alpha-helical Protein in Atomistic Detail using Worldwide-distributed Computing” Journal of Molecular Biology. 324: 1051. DOI: 10.1016/S0022-2836(02)01244-5  0.774
2001 Zagrovic B, Sorin EJ, Pande V. Beta-hairpin folding simulations in atomistic detail using an implicit solvent model. Journal of Molecular Biology. 313: 151-69. PMID 11601853 DOI: 10.1006/Jmbi.2001.5033  0.769
Show low-probability matches.