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Paul S. Nerenberg - Publications

Affiliations: 
2016- Physics & Astronomy and Biological Sciences Cal State LA, Los Angeles, CA, United States 
Area:
Molecular simulation
Website:
http://www.psnlab.org
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26 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
2021 Stoppelman JP, Ng TT, Nerenberg PS, Wang LP. Development and Validation of AMBER-FB15-Compatible Force Field Parameters for Phosphorylated Amino Acids. The Journal of Physical Chemistry. B. PMID 34668708 DOI: 10.1021/acs.jpcb.1c07547  0.323
2020 Huggins N, Ng T, Cruz N, Brewer SH, Phillips-Piro CM, Nerenberg PS. Using Molecular Dynamics Simulations to Understand IR Spectroscopy Results in Green Fluorescent Protein Biophysical Journal. 118: 143a-144a. DOI: 10.1016/J.Bpj.2019.11.907  0.304
2019 Zhou A, Schauperl M, Nerenberg PS. Benchmarking Electronic Structure Methods for Accurate Fixed-Charge Electrostatic Models. Journal of Chemical Information and Modeling. PMID 31805237 DOI: 10.1021/Acs.Jcim.9B00962  0.325
2019 Qiu Y, Nerenberg PS, Head-Gordon T, Wang LP. Systematic Optimization of Water Models Using Liquid/Vapor Surface Tension Data. The Journal of Physical Chemistry. B. PMID 31314516 DOI: 10.1021/Acs.Jpcb.9B05455  0.511
2018 Nerenberg PS, Head-Gordon T. New developments in force fields for biomolecular simulations. Current Opinion in Structural Biology. 49: 129-138. PMID 29477047 DOI: 10.1016/J.Sbi.2018.02.002  0.558
2015 Yedvabny E, Nerenberg PS, So C, Head-Gordon T. Disordered structural ensembles of vasopressin and oxytocin and their mutants. The Journal of Physical Chemistry. B. 119: 896-905. PMID 25231121 DOI: 10.1021/Jp505902M  0.577
2015 Yedvabny E, Nerenberg PS, So C, Head-Gordon T. Disordered structural ensembles of vasopressin and oxytocin and their mutants Journal of Physical Chemistry B. 119: 896-905. DOI: 10.1021/jp505902m  0.45
2014 Chapman DE, Steck JK, Nerenberg PS. Optimizing Protein-Protein van der Waals Interactions for the AMBER ff9x/ff12 Force Field. Journal of Chemical Theory and Computation. 10: 273-81. PMID 26579910 DOI: 10.1021/Ct400610X  0.722
2014 Chapman DE, Steck JK, Nerenberg PS. Optimizing protein-protein van der waals interactions for the AMBER ff9x/ff12 force field Journal of Chemical Theory and Computation. 10: 273-281. DOI: 10.1021/ct400610x  0.713
2014 Nerenberg PS, Yedvabny E, Ball KA, So C, Head-Gordon T. Computational Characterization of the Disordered Ensembles of Vasopressin and Oxytocin Biophysical Journal. 106: 481a-482a. DOI: 10.1016/J.Bpj.2013.11.2719  0.583
2014 Nerenberg PS, Steck JK, Wych DC. How Much Pre-Polarization is Ideal for Fixed-Charge MD Simulations? Biophysical Journal. 106. DOI: 10.1016/J.Bpj.2013.11.2278  0.319
2013 Liguori N, Nerenberg PS, Head-Gordon T. Embedding Aβ42 in heterogeneous membranes depends on cholesterol asymmetries Biophysical Journal. 105: 899-910. PMID 23972842 DOI: 10.1016/J.Bpj.2013.06.046  0.496
2012 Nerenberg PS, Jo B, So C, Tripathy A, Head-Gordon T. Optimizing solute-water van der Waals interactions to reproduce solvation free energies. The Journal of Physical Chemistry. B. 116: 4524-34. PMID 22443635 DOI: 10.1021/Jp2118373  0.578
2012 Nerenberg PS, Jo B, So C, Tripathy A, Head-Gordon T. Optimizing solute-water van der waals interactions to reproduce solvation free energies Journal of Physical Chemistry B. 116: 4524-4534. DOI: 10.1021/jp2118373  0.47
2011 Nerenberg PS, Head-Gordon T. Optimizing Protein-Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides. Journal of Chemical Theory and Computation. 7: 1220-1230. PMID 26606367 DOI: 10.1021/Ct2000183  0.64
2011 Ball KA, Phillips AH, Nerenberg PS, Fawzi NL, Wemmer DE, Head-Gordon T. Homogeneous and heterogeneous tertiary structure ensembles of amyloid-β peptides. Biochemistry. 50: 7612-28. PMID 21797254 DOI: 10.1021/Bi200732X  0.682
2011 Nerenberg PS, Head-Gordon T. Optimizing protein-solvent force fields to reproduce intrinsic conformational preferences of model peptides Journal of Chemical Theory and Computation. 7: 1220-1230. DOI: 10.1021/ct2000183  0.59
2011 Nerenberg PS, So C, Tripathy A, Head-Gordon T. Evaluation and Improvement of the Amber ff99SB Force Field with an Advanced Water Model Biophysical Journal. 100: 311a. DOI: 10.1016/J.Bpj.2010.12.1900  0.612
2010 Chen MM, Bartlett AI, Nerenberg PS, Friel CT, Hackenberger CP, Stultz CM, Radford SE, Imperiali B. Perturbing the folding energy landscape of the bacterial immunity protein Im7 by site-specific N-linked glycosylation. Proceedings of the National Academy of Sciences of the United States of America. 107: 22528-33. PMID 21148421 DOI: 10.1073/Pnas.1015356107  0.631
2010 Gurry T, Nerenberg PS, Stultz CM. The contribution of interchain salt bridges to triple-helical stability in collagen Biophysical Journal. 98: 2634-2643. PMID 20513408 DOI: 10.1016/J.Bpj.2010.01.065  0.626
2010 Salsas-Escat R, Nerenberg PS, Stultz CM. Cleavage site specificity and conformational selection in type i collagen degradation Biochemistry. 49: 4147-4158. PMID 20394413 DOI: 10.1021/Bi9021473  0.604
2009 Phillips CM, Nerenberg PS, Drennan CL, Stultz CM. Physical basis of metal-binding specificity in Escherichia coli NikR. Journal of the American Chemical Society. 131: 10220-8. PMID 19621966 DOI: 10.1021/Ja9026314  0.593
2009 Phillips CM, Nerenberg PS, Drennan CL, Stultz CM. Metal Preference At The Second Metal Binding Site Of E. coli NikR Biophysical Journal. 96: 58a. DOI: 10.1016/J.Bpj.2008.12.196  0.581
2008 Nerenberg PS, Stultz CM. Differential Unfolding of α1 and α2 Chains in Type I Collagen and Collagenolysis Journal of Molecular Biology. 382: 246-256. PMID 18644377 DOI: 10.1016/J.Jmb.2008.07.009  0.59
2008 Nerenberg PS, Salsas-Escat R, Stultz CM. Do collagenases unwind triple-helical collagen before peptide bond hydrolysis? Reinterpreting experimental observations with mathematical models Proteins: Structure, Function and Genetics. 70: 1154-1161. PMID 17932911 DOI: 10.1002/Prot.21687  0.637
2007 Nerenberg PS, Salsas-Escat R, Stultz CM. Collagen - A necessary accomplice in the metastatic process Cancer Genomics and Proteomics. 4: 319-328. PMID 17993716  0.53
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