#Undergraduate student author from Nerenberg Lab.
%MS student author from Nerenberg Lab.
*Both authors contributed equally to this work.

  1. Risheh A, Rebel A, Nerenberg PS, and Forouzesh N. Calculation of Protein-Ligand Binding Entropies Using a Rule-Based Molecular Fingerprint. Biophysical Journal 2024; in press. [DOI]

  2. Lee BU, Papoutsis BM, Wong NY, Piacentini J, Kearney C, Huggins NA#, Cruz N#, Ng TT#, Hao KH, Kramer JS, Fenlon EE, Nerenberg PS, Phillips-Piro CM, and Brewer SH. Unraveling Complex Local Protein Environments with 4-Cyano-L-phenylalanine. Journal of Physical Chemistry B 2022; 126:8957-8969. [DOI]

  3. Stoppelman JP, Ng TT#, Nerenberg PS, and Wang L-P. Development and Validation of AMBER-FB15-compatible Force Field Parameters for Phosphorylated Amino Acids. Journal of Physical Chemistry B 2021; 125:11927-11942. [DOI] [GitHub: force field parameters]

  4. Leal JA*, Estrada-Tober ZM*, Wade F%, Mendiola AJP, Meza A, Mendoza M, Nerenberg PS, and Zurita-Lopez CI. Phosphoserine Inhibits Neighboring Arginine Methylation in the RKS Motif of Histone H3. Archives of Biochemistry and Biophysics 2021; 698: 108716. [DOI]

  5. McDonald AR, Nash JA, Nerenberg PS, Ball KA, Sode O, Foley JJ, Windus TL, and Crawford TD. Building Capacity for Undergraduate Education and Training in Computational Molecular Science: A Collaboration between the MERCURY Consortium and the Molecular Sciences Software Institute. International Journal of Quantum Chemistry 2020; 120:e26359. [DOI]

  6. Menezes GB, Nerenberg PS, Li N, and Allen EL. Results of an Intro to Mechanics Course Designed to Support Student Success in Physics I and Foundational Engineering Courses. ASEE Virtual Conference 2020. [link]

  7. Schauperl M, Nerenberg PS, Jang H, Wang L-P, Bayly CI, Mobley DL, and Gilson MK. Non-bonded Force Field Model with Advanced Restrained Electrostatic Potential Charges (RESP2). Nature Communications Chemistry 2020; 3:44. [DOI]

  8. Zhou A#, Schauperl M, and Nerenberg PS. Benchmarking Electronic Structure Methods for Accurate Fixed-Charge Electrostatic Models. Journal of Chemical Information and Modeling 2020; 60:249-258. [DOI]

  9. Qiu Y, Nerenberg PS, Head-Gordon T, and Wang L-P. Systematic Optimization of Water Models Using Liquid/Vapor Surface Tension Data. Journal of Physical Chemistry B 2019; 123:7061-7073. [DOI]

  10. Nerenberg PS and Head-Gordon T. New developments in force fields for biomolecular simulations. Current Opinion in Structural Biology 2018; 49:129-139. [DOI]

  11. Li N, Menezes GB, Allen EL, and Nerenberg PS. First-Year Experience (FYrE@ECST): Intro to Physics Course (WIP). ASEE CoNECD Conference 2018. [link]

  12. Yedvabny E, Nerenberg PS, So C#, and Head-Gordon T. Disordered Structural Ensembles of Vasopressin and Oxytocin and Their Mutants. Journal of Physical Chemistry B 2015; 119:896-905. [DOI]

  13. Chapman DE#*, Steck JK#*, and Nerenberg PS. Optimizing Protein-Protein van der Waals Interactions for the AMBER ff9x/ff12 Force Field. Journal of Chemical Theory and Computation 2014; 10:273-281. [DOI]

  14. Liguori N, Nerenberg PS, and Head-Gordon T. Embedding Aβ42 in Heterogenous Membranes Depends on Cholesterol Asymmetries. Biophysical Journal 2013; 105:899-910. [DOI]

  15. Nerenberg PS, Jo B#, So C#, Tripathy A#, and Head-Gordon T. Optimizing solute-water van der Waals interactions to reproduce solvation free energies. Journal of Physical Chemistry B 2012; 116:4524-4534. [DOI]

  16. Ball KA, Phillips AH, Nerenberg PS, Fawzi NL, Wemmer DE, and Head-Gordon T. Homogeneous and Heterogeneous Tertiary Structure Ensembles of Amyloid-β Peptides. Biochemistry 2011; 50:7612-7628. [DOI]

  17. Nerenberg PS and Head-Gordon T. Optimizing Protein-Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides. Journal of Chemical Theory and Computation 2011; 7:1220-1230. [DOI]

  18. Chen MM, Bartlett AI, Nerenberg PS, Friel CT, Hackenberger CPR, Stultz CM, Radford SE, and 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 2010; 107:22528-22533. [DOI]

  19. Salsas-Escat R*, Nerenberg PS*, and Stultz CM. Cleavage site specificity and conformational selection in type I collagen degradation. Biochemistry 2010; 49:4147-4158. [DOI]

  20. Gurry T, Nerenberg PS, and Stultz CM. The contribution of interchain salt bridges to triple helical stability in collagen. Biophysical Journal 2010; 98:2634-2643. [DOI]

  21. Phillips CM, Nerenberg PS, Drennan CL, and Stultz CM. The Physical Basis of Metal Binding Specificity in E. coli NikR. Journal of the American Chemical Society 2009; 131:10220-10228. [DOI]

  22. Nerenberg PS and Stultz CM. Differential Unfolding of α1 and α2 Chains in Type I Collagen and Collagenolysis. Journal of Molecular Biology 2008; 382:246-256. [DOI]

  23. Nerenberg PS, Salsas-Escat R, Stultz CM. Do collagenases unwind triple-helical collagen prior to peptide bond hydrolysis? Reinterpreting experimental observations with mathematical models. Proteins 2008; 70:1154-1161. [DOI]

  24. Nerenberg PS, Salsas-Escat R, Stultz CM. Collagen – A Necessary Accomplice in the Metastatic Process. Cancer Genomics and Proteomics 2007; 4:319-328. [Link]