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1

Optimizing Solute–Water van der Waals Interactions To Reproduce Solvation Free Energies

Nerenberg, Paul S., Jo, Brian, So, Clare, Tripathy, Ajay, Head-Gordon, Teresa

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 1.41 MB

english, 2012

2

Optimizing Protein–Protein van der Waals Interactions for the AMBER ff9x/ff12 Force Field

Chapman, Dail E., Steck, Jonathan K., Nerenberg, Paul S.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 838 KB

english, 2014

3

Perturbing the folding energy landscape of the bacterial immunity protein Im7 by site-specific N-linked glycosylation

Mark M. Chen, Alice I. Bartlett, Paul S. Nerenberg, Claire T. Friel, Christian P. R. Hackenberger, Collin M. Stultz, Sheena E. Radford and Barbara Imperiali

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 1.38 MB

english, 2010

4

Do collagenases unwind triple-helical collagen before peptide bond hydrolysis? Reinterpreting experimental observations with mathematical models

Paul S. Nerenberg, Ramon Salsas-Escat, Collin M. Stultz

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 314 KB

english, 2008

5

Metal Preference At The Second Metal Binding Site Of E. coli NikR

Phillips, Christine M., Nerenberg, Paul S., Drennan, Catherine L., Stultz, Collin M.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 40 KB

english, 2009

6

Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2)

Schauperl, Michael, Nerenberg, Paul S., Jang, Hyesu, Wang, Lee-Ping, Bayly, Christopher I., Mobley, David L., Gilson, Michael K.

Journal:

Communications Chemistry

Year:

2020

File:

PDF, 2.18 MB

2020

7

Optimizing Protein−Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides

Nerenberg, Paul S., Head-Gordon, Teresa

Journal:

Journal of Chemical Theory and Computation

Year:

2011

Language:

english

File:

PDF, 1.36 MB

english, 2011

8

Cleavage Site Specificity and Conformational Selection in Type I Collagen Degradation

Salsas-Escat, Ramon, Nerenberg, Paul S., Stultz, Collin M.

Journal:

Year:

2010

Language:

english

File:

PDF, 2.39 MB

english, 2010

9

Building capacity for undergraduate education and training in computational molecular science: A collaboration between the MERCURY consortium and the Molecular Sciences Software Institute

McDonald, Ashley Ringer, Nash, Jessica A., Nerenberg, Paul S., Ball, K. Aurelia, Sode, Olaseni, Foley, Jonathon J., Windus, Theresa L., Crawford, T. Daniel

Journal:

International Journal of Quantum Chemistry

Year:

2020

File:

PDF, 1.84 MB

2020

10

NCCN Molecular Testing White Paper: Effectiveness, Efficiency, and Reimbursement

Engstrom, Paul F., Bloom, Mara G., Demetri, George Daniel, Febbo, Phillip G., Goeckeler, William, Ladanyi, Marc, Loy, Bryan, Murphy, Kate, Nerenberg, Michael, Papagni, Paul, Robson, Mark, Sweetman, Ro

Journal:

Journal of the National Comprehensive Cancer Network

Year:

2011

Language:

english

File:

PDF, 724 KB

english, 2011

11

The Contribution of Interchain Salt Bridges to Triple-Helical Stability in Collagen

Gurry, Thomas, Nerenberg, Paul S., Stultz, Collin M.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 996 KB

english, 2010

12

Homogeneous and Heterogeneous Tertiary Structure Ensembles of Amyloid-β Peptides

Ball, K. Aurelia, Phillips, Aaron H., Nerenberg, Paul S., Fawzi, Nicolas L., Wemmer, David E., Head-Gordon, Teresa

Journal:

Year:

2011

Language:

english

File:

PDF, 6.37 MB

english, 2011

13

Does Cytosine Methylation Stabilize the BI Substate of DNA?

Garcia Castillo, Jesse, Romero, Jessica, Fries, Roxanne A., Macy, Georgia A., Nerenberg, Paul S.

Journal:

Biophysical Journal

Year:

2018

File:

PDF, 43 KB

2018

14

Benchmarking Electronic Structure Methods for Accurate Fixed-Charge Electrostatic Models

Zhou, Alex, Schauperl, Michael, Nerenberg, Paul S.

Journal:

Journal of Chemical Information and Modeling

Year:

2019

File:

PDF, 727 KB

2019

15

Using Molecular Dynamics Simulations to Understand IR Spectroscopy Results in Green Fluorescent Protein

Huggins, Nia, Ng, Tracey, Cruz, Nicole, Brewer, Scott H., Phillips-Piro, Christine M., Nerenberg, Paul S.

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 52 KB

2020

16

Unraveling Complex Protein Environments in Green Fluorescent Protein using the Unnatural Amino Acid 4-cyano-L-phenylalanine

Papoutsis, Brianna M., Lee, ByungUk, Wong, Nathan, Nerenberg, Paul, Brewer, Scott H., Phillips-Piro, Christine M.

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 42 KB

2020

17

Differential Unfolding of α1 and α2 Chains in Type I Collagen and Collagenolysis

Paul S. Nerenberg, Collin M. Stultz

Journal:

Journal of Molecular Biology

Year:

2008

Language:

english

File:

PDF, 1.14 MB

english, 2008

18

Disordered Structural Ensembles of Vasopressin and Oxytocin and Their Mutants

Yedvabny, Eugene, Nerenberg, Paul S., So, Clare, Head-Gordon, Teresa

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 1.48 MB

english, 2015

19

New developments in force fields for biomolecular simulations

Nerenberg, Paul S, Head-Gordon, Teresa

Journal:

Current Opinion in Structural Biology

Year:

2018

Language:

english

File:

PDF, 801 KB

english, 2018

20

How Much Pre-Polarization is Ideal for Fixed-Charge MD Simulations?

Nerenberg, Paul S., Steck, Jonathan K., Wych, David C.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 37 KB

english, 2014

21

Computational Characterization of the Disordered Ensembles of Vasopressin and Oxytocin

Nerenberg, Paul S., Yedvabny, Eugene, Ball, K. Aurelia, So, Clare, Head-Gordon, Teresa

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 58 KB

english, 2014

22

Evaluation and Improvement of the Amber ff99SB Force Field with an Advanced Water Model

Nerenberg, Paul S., So, Clare, Tripathy, Ajay, Head-Gordon, Teresa

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 39 KB

english, 2011

23

Physical Basis of Metal-Binding Specificity in Escherichia coli NikR

Phillips, Christine M., Nerenberg, Paul S., Drennan, Catherine L., Stultz, Collin M.

Journal:

Journal of the American Chemical Society

Year:

2009

Language:

english

File:

PDF, 3.98 MB

english, 2009

24

Embedding Aβ42 in Heterogeneous Membranes Depends on Cholesterol Asymmetries

Liguori, Nicoletta, Nerenberg, Paul S., Head-Gordon, Teresa

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 2.08 MB

english, 2013

25

Seasonal alteration in taste detection and recognition threshold in seasonal affective disorder: the proximate source of carbohydrate craving

Paul A Arbisi, Allen S Levine, Jill Nerenberg, Julie Wolf

Journal:

Psychiatry Research

Year:

1996

Language:

english

File:

PDF, 1.15 MB

english, 1996

26

TIPPing practice away from anticoagulation in pregnancy

Gibson, Paul S, Nerenberg, Kara A

Journal:

Year:

2014

Language:

english

File:

PDF, 122 KB

english, 2014

27

Systematic Optimization of Water Models Using Liquid/Vapor Surface Tension Data

Qiu, Yudong, Nerenberg, Paul S., Head-Gordon, Teresa, Wang, Lee-Ping

Journal:

Journal of Physical Chemistry B

Year:

2019

File:

PDF, 1.53 MB

2019

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