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1

Connecting protein and mRNA burst distributions for stochastic models of gene expression

Elgart, Vlad, Jia, Tao, Fenley, Andrew T, Kulkarni, Rahul

Journal:

Physical Biology

Year:

2011

Language:

english

File:

PDF, 433 KB

english, 2011

2

Identification of distributed metabolic objectives in the hypermetabolic liver by flux and energy balance analysis

Ryan P. Nolan, Andrew P. Fenley, Kyongbum Lee

Journal:

Metabolic Engineering

Year:

2006

Language:

english

File:

PDF, 489 KB

english, 2006

3

Correlation as a Determinant of Configurational Entropy in Supramolecular and Protein Systems

Fenley, Andrew T., Killian, Benjamin J., Hnizdo, Vladimir, Fedorowicz, Adam, Sharp, Dan S., Gilson, Michael K.

Journal:

Journal of Physical Chemistry B

Year:

2014

Language:

english

File:

PDF, 1.38 MB

english, 2014

4

The SAMPL4 hydration challenge: evaluation of partial charge sets with explicit-water molecular dynamics simulations

Muddana, Hari S., Sapra, Neil V., Fenley, Andrew T., Gilson, Michael K.

Journal:

Journal of Computer-Aided Molecular Design

Year:

2014

Language:

english

File:

PDF, 594 KB

english, 2014

5

Entropic Insights from Millisecond Protein Simulations

Fenley, Andrew T., Gilson, Michael K.

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 58 KB

english, 2012

6

Charge State of the Globular Histone Core Controls Stability of the Nucleosome

Fenley, Andrew T., Adams, David A., Onufriev, Alexey V.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 428 KB

english, 2010

7

Atomic Stress Propagation Reveals Allosteric Pathways in Proteins

Muddana, Hari S., Fenley, Andrew T., Gilson, Michael K.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 36 KB

english, 2013

8

Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units

Ramu Anandakrishnan, Tom R.W. Scogland, Andrew T. Fenley, John C. Gordon, Wu-chun Feng, Alexey V. Onufriev

Journal:

Journal of Molecular Graphics and Modelling

Year:

2010

Language:

english

File:

PDF, 330 KB

english, 2010

9

Ed board

Muddana, Hari S., Fenley, Andrew T., Gilson, Michael K.

Journal:

Advances in Chronic Kidney Disease

Year:

2008

Language:

english

File:

PDF, 102 KB

english, 2008

10

Calculation and Visualization of Atomistic Mechanical Stresses in Biomolecules

Fenley, Andrew T., Muddana, Hari S., Gilson, Michael K.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 124 KB

english, 2014

11

Nucleosome Stability is Controlled by the Charge of its Globular Core: Implications for the Biological Function

Onufriev, Alexey V., Fenley, Andrew T., Anandakrishnan, Ramu

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 69 KB

english, 2014

12

Properties of the nucleic-acid bases in free and Watson-Crick hydrogen-bonded states: computational insights into the sequence-dependent features of double-helical DNA

A. R. Srinivasan, Ronald R. Sauers, Marcia O. Fenley, Alexander H. Boschitsch, Atsushi Matsumoto, Andrew V. Colasanti, Wilma K. Olson

Journal:

Biophysical Reviews

Year:

2009

Language:

english

File:

PDF, 288 KB

english, 2009

13

An analytical approach to computing biomolecular electrostatic potential. II. Validation and applications

Gordon, John C., Fenley, Andrew T., Onufriev, Alexey

Journal:

The Journal of Chemical Physics

Year:

2008

Language:

english

File:

PDF, 1.28 MB

english, 2008

14

Introducing Charge Hydration Asymmetry in the Realm of Continuum Solvation

Mukhopadhyay, Abhishek, Fenley, Andrew T., Tolokh, Igor S., Onufriev, Alexey V.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 35 KB

english, 2013

15

Computational Calorimetry: High-Precision Calculation of Host–Guest Binding Thermodynamics

Henriksen, Niel M., Fenley, Andrew T., Gilson, Michael K.

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 2.57 MB

english, 2015

16

Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core

Fenley, Andrew T., Anandakrishnan, Ramu, Kidane, Yared H., Onufriev, Alexey V.

Journal:

Epigenetics & Chromatin

Year:

2018

Language:

english

File:

PDF, 2.06 MB

english, 2018

17

Early Paleocene Magnetostratigraphy and Revised Biostratigraphy of the Ojo Alamo Sandstone and Lower Nacimiento Formation, San Juan Basin, New Mexico, USA

Flynn, Andrew G., Davis, Adam J., Williamson, Thomas E., Heizler, Matthew, Fenley IV, C. William, Leslie, Caitlin E., Secord, Ross, Brusatte, Stephen L., Peppe, Daniel J.

Journal:

Base of the Kiaman Its definition and global stratigraphic significance

Year:

2020

Language:

english

File:

PDF, 1.82 MB

english, 2020

18

The electrostatic response of water to neutral polar solutes: Implications for continuum solvent modeling

Muddana, Hari S., Sapra, Neil V., Fenley, Andrew T., Gilson, Michael K.

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 1.51 MB

english, 2013

19

Evaluation of Representations and Response Models for Polarizable Force Fields

Li, Amanda, Voronin, Alexey, Fenley, Andrew T, Gilson, Michael K.

Journal:

Journal of Physical Chemistry B

Year:

2016

Language:

english

File:

PDF, 2.67 MB

english, 2016

20

The Carmaphycins: New Proteasome Inhibitors Exhibiting an α,β-Epoxyketone Warhead from a Marine Cyanobacterium

Dr. Alban R. Pereira, Andrew J. Kale, Dr. Andrew T. Fenley, Tara Byrum, Dr. Hosana M. Debonsi, Dr. Michael K. Gilson, Dr. Frederick A. Valeriote, Dr. Bradley S. Moore, Dr. William H. Gerwick

Journal:

Year:

2012

Language:

english

File:

PDF, 784 KB

english, 2012

21

An analytical approach to computing biomolecular electrostatic potential. I. Derivation and analysis

Fenley, Andrew T., Gordon, John C., Onufriev, Alexey

Journal:

The Journal of Chemical Physics

Year:

2008

Language:

english

File:

PDF, 406 KB

english, 2008

22

Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method

Muddana, Hari S., Yin, Jian, Sapra, Neil V., Fenley, Andrew T., Gilson, Michael K.

Journal:

Journal of Computer-Aided Molecular Design

Year:

2014

Language:

english

File:

PDF, 1.72 MB

english, 2014

23

Bridging Simulations and Calorimetry: Computational Studies of Binding Thermodynamics and Entropy-Enthalpy Transduction

Gilson, Michael K., Fenley, Andrew T., Muddana, Hari

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 41 KB

english, 2014

24

Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril–Guest Binding Enthalpies

Fenley, Andrew T., Henriksen, Niel M., Muddana, Hari S., Gilson, Michael K.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 2.34 MB

english, 2014

25

Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics

Yin, Jian, Fenley, Andrew T., Henriksen, Niel M., Gilson, Michael K.

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 675 KB

english, 2015

26

A model for signal transduction during quorum sensing in Vibrio harveyi

Banik, Suman K, Fenley, Andrew T, Kulkarni, Rahul V

Journal:

Physical Biology

Year:

2009

Language:

english

File:

PDF, 410 KB

english, 2009

27

Analytical electrostatics for biomolecules: Beyond the generalized Born approximation

Sigalov, Grigori, Fenley, Andrew, Onufriev, Alexey

Journal:

The Journal of Chemical Physics

Year:

2006

Language:

english

File:

PDF, 572 KB

english, 2006

28

Computational modeling of differences in the quorum sensing induced luminescence phenotypes of Vibrio harveyi and Vibrio cholerae

Andrew T. Fenley, Suman K. Banik, Rahul V. Kulkarni

Journal:

Journal of Theoretical Biology

Year:

2011

Language:

english

File:

PDF, 442 KB

english, 2011

29

Charge Hydration Asymmetry: The Basic Principle and How to Use It to Test and Improve Water Models

Mukhopadhyay, Abhishek, Fenley, Andrew T., Tolokh, Igor S., Onufriev, Alexey V.

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 1.07 MB

english, 2012

30

The SAMPL4 host–guest blind prediction challenge: an overview

Muddana, Hari S., Fenley, Andrew T., Mobley, David L., Gilson, Michael K.

Journal:

Journal of Computer-Aided Molecular Design

Year:

2014

Language:

english

File:

PDF, 1.84 MB

english, 2014

31

Binding Enthalpy Calculations for a Neutral Host–Guest Pair Yield Widely Divergent Salt Effects across Water Models

Gao, Kaifu, Yin, Jian, Henriksen, Niel M., Fenley, Andrew T., Gilson, Michael K.

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 2.65 MB

english, 2015

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