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1

Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family

Dennis R Livesay, Dang H Huynh, Sargis Dallakyan, Donald J Jacobs

Journal:

Chemistry Central Journal

Year:

2008

Language:

english

File:

PDF, 7.35 MB

english, 2008

2

At the crossroads of biomacromolecular research: highlighting the interdisciplinary nature of the field

Dennis R Livesay

Journal:

Chemistry Central Journal

Year:

2007

Language:

english

File:

PDF, 126 KB

english, 2007

3

Predicting protein functional sites with phylogenetic motifs

David La, Brian Sutch, Dennis R. Livesay

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 452 KB

english, 2005

4

Conserved quantitative stability/flexibility relationships (QSFR) in an orthologous RNase H pair

Dennis R. Livesay, Donald J. Jacobs

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 1.27 MB

english, 2006

5

New insight into long-range nonadditivity within protein double-mutant cycles

Andrei Y. Istomin, M. Michael Gromiha, Oleg K. Vorov, Donald J. Jacobs, Dennis R. Livesay

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 427 KB

english, 2008

6

Unifying mechanical and thermodynamic descriptions across the thioredoxin protein family

James M. Mottonen, Minli Xu, Donald J. Jacobs, Dennis R. Livesay

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2009

Language:

english

File:

PDF, 1.33 MB

english, 2009

7

On the role of structural class of a protein with two-state folding kinetics in determining correlations between its size, topology, and folding rate

Andrei Y. Istomin, Donald J. Jacobs, Dennis R. Livesay

Journal:

Protein Science

Year:

2007

Language:

english

File:

PDF, 460 KB

english, 2007

8

Predicting functional sites with an automated algorithm suitable for heterogeneous datasets

David La, Dennis R Livesay

Journal:

BMC Bioinformatics

Year:

2005

Language:

english

File:

PDF, 1.64 MB

english, 2005

9

How accurate and statistically robust are catalytic site predictions based on closeness centrality?

Eric Chea, Dennis R Livesay

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 776 KB

english, 2007

10

Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na+symporter family

Dennis R Livesay, Patrick D Kidd, Sepehr Eskandari, Usman Roshan

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 1.54 MB

english, 2007

11

Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities

Usman Roshan, Satish Chikkagoudar, Dennis R Livesay

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 341 KB

english, 2008

12

Protein dynamics: dancing on an ever-changing free energy stage

Dennis R Livesay

Journal:

Current Opinion in Pharmacology

Year:

2010

Language:

english

File:

PDF, 183 KB

english, 2010

13

Elucidating Quantitative Stability/Flexibility Relationships Within Thioredoxin and its Fragments Using a Distance Constraint Model

Donald J. Jacobs, Dennis R. Livesay, Jeremy Hules, Maria Luisa Tasayco

Journal:

Journal of Molecular Biology

Year:

2006

Language:

english

File:

PDF, 1007 KB

english, 2006

14

pH dependence of antibody: hapten association

Dennis Livesay, Scott Linthicum, Shankar Subramaniam

Journal:

Molecular Immunology

Year:

1999

Language:

english

File:

PDF, 292 KB

english, 1999

15

Bimolecular Reaction Simulation Using Weighted Ensemble Brownian Dynamics and the University of Houston Brownian Dynamics Program

Rojnuckarin, Atipat, Livesay, Dennis R., Subramaniam, Shankar

Journal:

Biophysical Journal

Year:

2000

Language:

english

File:

PDF, 249 KB

english, 2000

16

Conferring Thermostability to Mesophilic Proteins through Optimized Electrostatic Surfaces

Torrez, Michael, Schultehenrich, Michael, Livesay, Dennis R.

Journal:

Biophysical Journal

Year:

2003

Language:

english

File:

PDF, 364 KB

english, 2003

17

WaveMap: Interactively Discovering Features From Protein Flexibility Matrices Using Wavelet-based Visual Analytics

Scott Barlowe, Yujie Liu, Jing Yang, Dennis R. Livesay, Donald J. Jacobs, James Mottonen, Deeptak Verma

Journal:

Computer Graphics Forum

Year:

2011

Language:

english

File:

PDF, 1.24 MB

english, 2011

18

Molecular Partition Functions For Amino Acids And Beyond

Wang, Hui, Farchild, Michael, Livesay, Dennis R., Jacobs, Donald J.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 66 KB

english, 2009

19

Helix/Coil Nucleation: A Local Response to Global Demands

Vorov, Oleg K., Livesay, Dennis R., Jacobs, Donald J.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 380 KB

english, 2009

20

Allosteric Response Is both Conserved and Variable across Three CheY Orthologs

Mottonen, James M., Jacobs, Donald J., Livesay, Dennis R.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 1.65 MB

english, 2010

21

Nonadditivity in Conformational Entropy upon Molecular Rigidification Reveals a Universal Mechanism Affecting Folding Cooperativity

Vorov, Oleg K., Livesay, Dennis R., Jacobs, Donald J.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 505 KB

english, 2011

22

The evolutionary origins and catalytic importance of conserved electrostatic networks within TIM-barrel proteins

Dennis R. Livesay, David La

Journal:

Protein Science

Year:

2005

Language:

english

File:

PDF, 1.69 MB

english, 2005

23

[Methods in Molecular Biology] Protein Dynamics Volume 1084 || Analysis of Protein Conformational Transitions Using Elastic Network Model

Livesay, Dennis R.

Year:

2014

Language:

english

File:

PDF, 568 KB

english, 2014

24

[Methods in Molecular Biology] Protein Dynamics Volume 1084 ||

Livesay, Dennis R.

Year:

2014

Language:

english

File:

PDF, 7.42 MB

english, 2014

25

Elucidating the Effects of Mutation upon C-Type Lysozyme through Quantitative Stability/Flexibility Relationships

Verma, Deeptak, Jacobs, Donald J., Livesay, Dennis R.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 35 KB

english, 2011

26

Assessing Mechanical And Thermodynamic Response Upon Allosteric Perturbation

Mottonen, James M., Jacobs, Donald J., Livesay, Dennis R.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 85 KB

english, 2009

27

Towards Comprehensive Analysis of Protein Family Quantitative Stability/flexibility Relationships

Verma, Deeptak, Jacobs, Donald J., Guo, Jun-tao, Livesay, Dennis R.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 40 KB

english, 2010

28

Is Rigidity Conserved Across the Class A Beta-Lactamase Family?

Verma, Deeptak, Livesay, Dennis R.

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 69 KB

english, 2012

29

Fast Prediction of Protein Thermodynamics

Wang, Hui, Du, Chuanbin, Livesay, Dennis R., Jacobs, Donald J.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 37 KB

english, 2010

30

Predicting Protein Mutant Stability With A Combined Experimental/theoretical Approach

Verma, Deeptak, Jacobs, Donald J., Livesay, Dennis R.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 54 KB

english, 2009

31

Redistribution of Flexibility in Stabilizing Antibody Fragment Mutants Follows Le Chatelier's Principle

Li, Tong, Tracka, Malgorzata B., Uddin, Shahid, Casas-Finet, Jose, Jacobs, Donald J., Livesay, Dennis R.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 41 KB

english, 2014

32

Using Motif-Based Methods in Multiple Genome Analyses: A Case Study Comparing Orthologous Mesophilic and Thermophilic Proteins †

La, David, Silver, Melanie, Edgar, Robert C., Livesay, Dennis R.

Journal:

Year:

2003

Language:

english

File:

PDF, 667 KB

english, 2003

33

Elucidating the Conformational Dependence of Calculated p K a Values

Livesay, Dennis R., Jacobs, Donald J., Kanjanapangka, Julie, Chea, Eric, Cortez, Hector, Garcia, Jorge, Kidd, Patrick, Marquez, Mario Pulido, Pande, Swati, Yang, David

Journal:

Journal of Chemical Theory and Computation

Year:

2006

Language:

english

File:

PDF, 697 KB

english, 2006

34

Conservation of Electrostatic Properties within Enzyme Families and Superfamilies †

Livesay, Dennis R., Jambeck, Per, Rojnuckarin, Atipat, Subramaniam, Shankar

Journal:

Year:

2003

Language:

english

File:

PDF, 588 KB

english, 2003

35

[IEEE Sixth IEEE Symposium on BioInformatics and BioEngineering (BIBE'06) - Arlington, VA (2006.10.16-2006.10.18)] Sixth IEEE Symposium on BioInformatics and BioEngineering (BIBE'06) - Improving progressive alignment for phylogeny reconstruction using parsimonious guide-trees

Roshan, Usman, Livesay, Dennis, Chikkagoudar, Satish

Year:

2006

Language:

english

File:

PDF, 315 KB

english, 2006

36

Topology Improves Phylogenetic Motif Functional Site Predictions

Kc, Dukka B, Livesay, Dennis R

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 1.66 MB

english, 2011

37

[IEEE 2013 IEEE Pacific Visualization Symposium (PacificVis) - Sydney, Australia (2013.02.27-2013.03.1)] 2013 IEEE Pacific Visualization Symposium (PacificVis) - A visual analytics approach to exploring protein flexibility subspaces

Barlowe, Scott, Yang, Jing, Jacobs, Donald J., Livesay, Dennis R., Alsakran, Jamal, Zhao, Ye, Verma, Deeptak, Mottonen, James

Year:

2013

Language:

english

File:

PDF, 964 KB

english, 2013

38

A virtual pebble game to ensemble average graph rigidity

González, Luis C, Wang, Hui, Livesay, Dennis R, Jacobs, Donald J

Journal:

Algorithms for Molecular Biology

Year:

2015

Language:

english

File:

PDF, 3.63 MB

english, 2015

39

Reduced Lateral Mobility of Lipids and Proteins in Crowded Membranes

Goose, Joseph E., Sansom, Mark S. P., Livesay, Dennis R.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 3.97 MB

english, 2013

40

Coupling between Catalytic Loop Motions and Enzyme Global Dynamics

Kurkcuoglu, Zeynep, Bakan, Ahmet, Kocaman, Duygu, Bahar, Ivet, Doruker, Pemra, Livesay, Dennis R.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 2.49 MB

english, 2012

41

On Conduction in a Bacterial Sodium Channel

Furini, Simone, Domene, Carmen, Livesay, Dennis R.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.19 MB

english, 2012

42

Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged

Verma, Deeptak, Jacobs, Donald J., Livesay, Dennis R., Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 3.20 MB

english, 2012

43

Collective Dynamics Underlying Allosteric Transitions in Hemoglobin

Vesper, Martin D., de Groot, Bert L., Livesay, Dennis R.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.45 MB

english, 2013

44

The HAMP Signal Relay Domain Adopts Multiple Conformational States through Collective Piston and Tilt Motions

Zhu, Lizhe, Bolhuis, Peter G., Vreede, Jocelyne, Livesay, Dennis R.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.95 MB

english, 2013

45

Assembly of the Transmembrane Domain of E. coli PhoQ Histidine Kinase: Implications for Signal Transduction from Molecular Simulations

Lemmin, Thomas, Soto, Cinque S., Clinthorne, Graham, DeGrado, William F., Dal Peraro, Matteo, Livesay, Dennis R.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 3.18 MB

english, 2013

46

Convergent Transmission of RNAi Guide-Target Mismatch Information across Argonaute Internal Allosteric Network

Joseph, Thomas T., Osman, Roman, Livesay, Dennis R.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 893 KB

english, 2012

47

Identification of Key Hinge Residues Important for Nucleotide-Dependent Allostery in E. coli Hsp70/DnaK

Ung, Peter Man-Un, Thompson, Andrea D., Chang, Lyra, Gestwicki, Jason E., Carlson, Heather A., Livesay, Dennis R.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 4.17 MB

english, 2013

48

Binding Free Energy Landscape of Domain-Peptide Interactions

Staneva, Iskra, Wallin, Stefan, Livesay, Dennis R.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 636 KB

english, 2011

49

Unbiased Simulations Reveal the Inward-Facing Conformation of the Human Serotonin Transporter and Na+ Ion Release

Koldsø, Heidi, Noer, Pernille, Grouleff, Julie, Autzen, Henriette Elisabeth, Sinning, Steffen, Schiøtt, Birgit, Livesay, Dennis R.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.06 MB

english, 2011

50

Enhancing Human Spermine Synthase Activity by Engineered Mutations

Zhang, Zhe, Zheng, Yueli, Petukh, Margo, Pegg, Anthony, Ikeguchi, Yoshihiko, Alexov, Emil, Livesay, Dennis R.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.36 MB

english, 2013