Crossref journal-article
Public Library of Science (PLoS)
PLoS Computational Biology (340)
Bibliography

Petrov, D., & Zagrovic, B. (2014). Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments? PLoS Computational Biology, 10(5), e1003638.

Authors 2
  1. Drazen Petrov (first)
  2. Bojan Zagrovic (additional)
References 70 Referenced 133
  1. 10.1016/S0968-0004(01)01938-7 / Trends in Biochemical Sciences / Macromolecular crowding: Obvious but underappreciated by RJ Ellis (2001)
  2. 10.1038/425027a / Nature / Cell biology - Join the crowd by RJ Ellis (2003)
  3. 10.1146/annurev.biophys.37.032807.125817 / Annual Review of Biophysics / Macromolecular crowding and confinement: Biochemical, biophysical, and potential physiological consequences by HX Zhou (2008)
  4. 10.1016/j.sbi.2010.01.008 / Current Opinion in Structural Biology / Models of macromolecular crowding effects and the need for quantitative comparisons with experiment by AH Elcock (2010)
  5. 10.1038/nm1066 / Nature Medicine / Protein aggregation and neurodegenerative disease by CA Ross (2004)
  6. 10.1038/nchembio.131 / Nature Chemical Biology / Amyloid formation by globular proteins under native conditions by F Chiti (2009)
  7. 10.1529/biophysj.104.050351 / Biophysical Journal / Models for excluded volume interaction between an unfolded protein and rigid macromolecular cosolutes: Macromolecular crowding and protein stability revisited by AP Minton (2005)
  8. 10.1021/ja0706246 / Journal of the American Chemical Society / G protein-coupled receptors self-assemble in dynamics simulations of model bilayers by X Periole (2007)
  9. 10.1016/j.str.2008.01.014 / Structure / Coarse-grained MD simulations of membrane protein-bilayer self-assembly by KA Scott (2008)
  10. 10.1371/journal.pcbi.1000694 / PLoS Computational Biology / Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm by SR McGuffee (2010)
  11. 10.1002/anie.200502655 / Angewandte Chemie, International Edition in English / Biomolecular modeling: Goals, problems, perspectives by WF van Gunsteren (2006)
  12. 10.1021/ja802248m / Journal of the American Chemical Society / A role for confined water in chaperonin function by JL England (2008)
  13. 10.1021/jp209302e / The Journal of Physical Chemistry B / Variable interactions between protein crowders and biomolecular solutes are important in understanding cellular crowding by M Feig (2012)
  14. 10.1021/ja211115q / Journal of the American Chemical Society / Protein crowding affects hydration structure and dynamics by R Harada (2012)
  15. 10.1073/pnas.1201809109 / Proceedings of the National Academy of Sciences of the United States of America / Multimolecule test-tube simulations of protein unfolding and aggregation by ME McCully (2012)
  16. 10.1021/ct400371h / Journal of Chemical Theory and Computation / Molecular Dynamics Simulations of Highly Crowded Amino Acid Solutions: Comparisons of Eight Different Force Field Combinations with Experiment and with Each Other by CT Andrews (2013)
  17. 10.1073/pnas.0835307100 / Proceedings of the National Academy of Sciences of the United States of America / The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35 by J Gsponer (2003)
  18. 10.1073/pnas.0402634101 / Proceedings of the National Academy of Sciences of the United States of America / Kinetic control of dimer structure formation in amyloid fibrillogenesis by W Hwang (2004)
  19. 10.1073/pnas.0407273101 / Proceedings of the National Academy of Sciences of the United States of America / Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides by HD Nguyen (2004)
  20. 10.1073/pnas.0408653102 / Proceedings of the National Academy of Sciences of the United States of America / Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: Significant role of Asn ladder by HH Tsai (2005)
  21. 10.1016/j.cbpa.2006.08.018 / Current Opinion in Chemical Biology / Simulations as analytical tools to understand protein aggregation and predict amyloid conformation by B Ma (2006)
  22. 10.1002/jps.22705 / Journal of Pharmaceutical Sciences / Aggregation in protein-based biotherapeutics: Computational studies and tools to identify aggregation-prone regions by NJ Agrawal (2011)
  23. 10.1038/nsb0397-180 / Nature Structural Biology / NMR structure of the 35-residue villin headpiece subdomain by CJ McKnight (1997)
  24. 10.1073/pnas.0406130102 / Proceedings of the National Academy of Sciences of the United States of America / Probing site-specific conformational distributions in protein folding with solid-state NMR by RH Havlin (2005)
  25. 10.1073/pnas.1100587108 / Proceedings of the National Academy of Sciences of the United States of America / Dynamics of the folded and unfolded villin headpiece (HP35) measured with ultrafast 2D IR vibrational echo spectroscopy by JK Chung (2011)
  26. 10.1073/pnas.0505432102 / Proceedings of the National Academy of Sciences of the United States of America / Effect of modulating unfolded state structure on the folding kinetics of the villin headpiece subdomain by SH Brewer (2005)
  27. 10.1021/ja901860f / Journal of the American Chemical Society / Probing the folding transition state structure of the villin headpiece subdomain via side chain and backbone mutagenesis by MR Bunagan (2009)
  28. 10.1021/ja3126992 / Journal of the American Chemical Society / Reduced native state stability in crowded cellular environment due to protein-protein interactions by R Harada (2013)
  29. 10.1016/S0531-5565(01)00135-8 / Experimental Gerontology / Oxidative modification of proteins during aging by RL Levine (2001)
  30. 10.1373/clinchem.2005.061408 / Clinical chemistry / Biomarkers of oxidative damage in human disease by I Dalle-Donne (2006)
  31. 10.1146/annurev.biochem.75.101304.123901 / Annual review of biochemistry / Protein misfolding, functional amyloid, and human disease by F Chiti (2006)
  32. 10.1021/ja110577e / Journal of the American Chemical Society / Microscopic analysis of protein oxidative damage: Effect of carbonylation on structure, dynamics, and aggregability of villin headpiece by D Petrov (2011)
  33. 10.1038/nature01891 / Nature / Rationalization of the effects of mutations on peptide and protein aggregation rates by F Chiti (2003)
  34. 10.1002/jcc.1078 / Journal of Computational Chemistry / An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase by L Schuler (2001)
  35. 10.1007/s00249-011-0700-9 / European biophysics journal / Definition and testing of the GROMOS force-field versions 54A7 and 54B7 by N Schmid (2011)
  36. Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J (1981) Interaction models for water in relation to protein hydration; Pullman B, editor. Reidel, Dordrecht. 331–342 p. (10.1007/978-94-015-7658-1_21)
  37. 10.1063/1.470117 / Journal of Chemical Physics / A smooth particle mesh Ewald method by U Essmann (1995)
  38. 10.1063/1.469273 / Journal of Chemical Physics / A generalized reaction field method for molecular-dynamics simulations by IG Tironi (1995)
  39. 10.1021/ja00124a002 / Journal of the American Chemical Society / A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules by WD Cornell (1995)
  40. 10.1002/prot.22711 / Proteins-Structure Function and Bioinformatics / Improved side-chain torsion potentials for the Amber ff99SB protein force field by K Lindorff-Larsen (2010)
  41. 10.1021/ja057216r / Journal of the American Chemical Society / Balancing solvation and intramolecular interactions: Toward a consistent generalized born force field by JH Chen (2006)
  42. 10.1021/jp003919d / The Journal of Physical Chemistry B / Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides by GA Kaminski (2001)
  43. 10.1063/1.445869 / Journal of Chemical Physics / Comparison of simple potential functions for simulating liquid water by WL Jorgensen (1983)
  44. {'key': 'ref44', 'first-page': '129', 'article-title': 'Versuch einer mathematischen Theorie der Koagulationskinetik kolloidaler Lösungen', 'volume': '92', 'author': 'M Von Smoluchowski', 'year': '1917', 'journal-title': 'Zeitschrift fur Physikalische Chemie'} / Zeitschrift fur Physikalische Chemie / Versuch einer mathematischen Theorie der Koagulationskinetik kolloidaler Lösungen by M Von Smoluchowski (1917)
  45. 10.1016/j.sbi.2007.12.007 / Current Opinion in Structural Biology / Molecular simulation as an aid to experimentalists by WF van Gunsteren (2008)
  46. 10.1039/b917186j / Molecular Biosystems / Conformational averaging in structural biology: issues, challenges and computational solutions by D Kruschel (2009)
  47. 10.1016/S0006-3495(01)75700-1 / Biophysical Journal / Two-dimensional infrared correlation spectroscopy study of the aggregation of cytochrome c in the presence of dimyristoylphosphatidylglycerol by MJ Paquet (2001)
  48. 10.1016/S0006-3495(03)74623-2 / Biophysical Journal / Two-dimensional infrared correlation spectroscopy study of sequential events in the heat-induced unfolding and aggregation process of myoglobin by YB Yan (2003)
  49. 10.1039/b923515a / Physical Chemistry Chemical Physics / Insulin dimer dissociation and unfolding revealed by amide I two-dimensional infrared spectroscopy by Z Ganim (2010)
  50. {'key': 'ref50', 'first-page': '101', 'article-title': 'Spectroscopic techniques in the study of human tissues and their components. Part I: IR spectroscopy', 'volume': '14', 'author': 'S Olsztynska-Janus', 'year': '2012', 'journal-title': 'Acta of Bioengineering and Biomechanics'} / Acta of Bioengineering and Biomechanics / Spectroscopic techniques in the study of human tissues and their components. Part I: IR spectroscopy by S Olsztynska-Janus (2012)
  51. 10.1016/j.bbamem.2013.01.014 / Biochimica Et Biophysica Acta-Biomembranes / FTIR spectroscopic imaging of protein aggregation in living cells by LM Miller (2013)
  52. 10.1016/j.bbamem.2013.04.012 / Biochimica Et Biophysica Acta-Biomembranes / ATR-FTIR: A “rejuvenated” tool to investigate amyloid proteins by R Sarroukh (2013)
  53. 10.1016/j.jmb.2005.04.016 / Journal of Molecular Biology / Prediction of “aggregation-prone” and “aggregation-susceptible” regions in proteins associated with neurodegenerative diseases by AP Pawar (2005)
  54. 10.1038/nature03680 / Nature / Structure of the cross-beta spine of amyloid-like fibrils by R Nelson (2005)
  55. 10.2174/092986606775338407 / Protein and Peptide Letters / Theoretical approaches to protein aggregation by J Gsponer (2006)
  56. 10.1039/c1sm05726j / Soft Matter / Molecular and supramolecular studies on polyglycine and poly-L-proline by M Lorusso (2011)
  57. 10.1063/1.1587119 / Journal of Chemical Physics / Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins by MR Shirts (2003)
  58. 10.1002/jcc.20090 / Journal of Computational Chemistry / A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6 by C Oostenbrink (2004)
  59. 10.1021/jp2118373 / Journal of Physical Chemistry B / Optimizing Solute-Water van der Waals Interactions To Reproduce Solvation Free Energies by PS Nerenberg (2012)
  60. 10.1016/j.bpj.2011.03.051 / Biophysical Journal / How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization? by S Piana (2011)
  61. 10.1021/ja209931w / Journal of the American Chemical Society / Structure and dynamics of an unfolded protein examined by molecular dynamics simulation by K Lindorff-Larsen (2012)
  62. {'key': 'ref62', 'first-page': '4494', 'article-title': 'Are current molecular dynamics force fields too helical?', 'volume': '95', 'author': 'RB Best', 'year': '2008', 'journal-title': 'Biophysical Journal'} / Biophysical Journal / Are current molecular dynamics force fields too helical? by RB Best (2008)
  63. 10.1371/journal.pone.0032131 / Plos One / Systematic validation of protein force fields against experimental data by K Lindorff-Larsen (2012)
  64. 10.1371/journal.pcbi.1003154 / Plos Computational Biology / A systematic framework for molecular dynamics simulations of protein post-translational modifications by D Petrov (2013)
  65. 10.1093/nar/gkt416 / Nucleic Acids Research / Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications by C Margreitter (2013)
  66. 10.1021/ct700301q / Journal of Chemical Theory and Computation / GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation by B Hess (2008)
  67. 10.1063/1.448118 / Journal of Chemical Physics / Molecular-dynamics with coupling to an external bath by HJC Berendsen (1984)
  68. 10.1002/bip.360221211 / Biopolymers / Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features by W Kabsch (1983)
  69. Schrodinger LLC (2010) The PyMOL Molecular Graphics System, Version 1.3r1.
  70. Wickham H (2009) ggplot2: elegant graphics for data analysis. New York: Springer. (10.1007/978-0-387-98141-3)
Dates
Type When
Created 11 years, 3 months ago (May 22, 2014, 4:23 p.m.)
Deposited 5 years ago (Aug. 19, 2020, 4:46 p.m.)
Indexed 3 months, 2 weeks ago (May 20, 2025, 1:29 p.m.)
Issued 11 years, 3 months ago (May 22, 2014)
Published 11 years, 3 months ago (May 22, 2014)
Published Online 11 years, 3 months ago (May 22, 2014)
Funders 0

None

@article{Petrov_2014, title={Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?}, volume={10}, ISSN={1553-7358}, url={http://dx.doi.org/10.1371/journal.pcbi.1003638}, DOI={10.1371/journal.pcbi.1003638}, number={5}, journal={PLoS Computational Biology}, publisher={Public Library of Science (PLoS)}, author={Petrov, Drazen and Zagrovic, Bojan}, editor={Dunbrack, Roland L.}, year={2014}, month=may, pages={e1003638} }