D. Livesay

发表

Predicting protein functional sites with phylogenetic motifs

Brian T. Sutch, David La, D. Livesay, 2004, Proteins.

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

D. Jacobs, D. Livesay, S. Dallakyan, 2008, Chemistry Central journal.

A critical evaluation of correlated mutation algorithms and coevolution within allosteric mechanisms.

Dennis R Livesay, A. Fodor, D. Livesay, 2012, Methods in molecular biology.

Protein Dynamics

D. Livesay, Dennis R. Livesay, 2014, Methods in Molecular Biology.

Unifying mechanical and thermodynamic descriptions across the thioredoxin protein family

Dennis R Livesay, Minli Xu, Donald J Jacobs, 2009, Proteins.

Mutations in Antibody Fragments Modulate Allosteric Response Via Hydrogen-Bond Network Fluctuations.

D. Jacobs, D. Livesay, Amit Srivastava, 2016, Biophysical journal.

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

Dennis R Livesay, Donald J Jacobs, D. Jacobs, 2005, Proteins.

Optimized electrostatic surfaces parallel increased thermostability: a structural bioinformatic analysis.

Dennis R Livesay, D. Livesay, E. Alsop, 2003, Protein engineering.

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

Dennis R Livesay, M Michael Gromiha, Donald J Jacobs, 2008, Proteins.

Allosteric response is both conserved and variable across three CheY orthologs.

Dennis R Livesay, Donald J Jacobs, D. Jacobs, 2010, Biophysical journal.

Ensemble properties of network rigidity reveal allosteric mechanisms.

Dennis R Livesay, Deeptak Verma, Donald J Jacobs, 2012, Methods in molecular biology.

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

Dennis R Livesay, Donald J Jacobs, D. Jacobs, 2007, Protein science : a publication of the Protein Society.

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

Satish Chikkagoudar, Dennis R. Livesay, Usman Roshan, 2008, BMC Bioinformatics.

A Spectrum of Phylogenetic-Based Approaches for Predicting Protein Functional Sites

D. Livesay, K. C. D. Bahadur, D. K. C., 2009 .

Bimolecular reaction simulation using Weighted Ensemble Brownian dynamics and the University of Houston Brownian Dynamics program.

A Rojnuckarin, S. Subramaniam, A. Rojnuckarin, 2000, Biophysical journal.

Predicting Protein Functional Sites with Phylogenetic Motifs: Past, Present and Beyond

Dukka B Kc, David La, D. Livesay, 2011 .

THE EFFECTS OF POLLING DATA ON INDEPENDENT VOTING BEHAVIOR A Dissertation by

D. Livesay, Katherine A. Witsman, Barbara Chaparro, 2016 .

A flexible approach for understanding protein stability

G. G. Wood, D. Jacobs, D. Livesay, 2004, FEBS letters.

Probalign: multiple sequence alignment using partition function posterior probabilities

Dennis R. Livesay, Usman Roshan, Usman Roshan, 2006, Bioinform..

Variations within Class-A β-Lactamase Physiochemical Properties Reflect Evolutionary and Environmental Patterns, but not Antibiotic Specificity

Donald J. Jacobs, Dennis R. Livesay, Deeptak Verma, 2013, PLoS Comput. Biol..

PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences

Satish Chikkagoudar, Dennis R. Livesay, Usman Roshan, 2010, Nucleic Acids Res..

Rigidity Emerges during Antibody Evolution in Three Distinct Antibody Systems: Evidence from QSFR Analysis of Fab Fragments

Tong Li, Malgorzata B. Tracka, Shahid Uddin, 2015, PLoS Comput. Biol..

Conformational Entropy of an Ideal Cross-Linking Polymer Chain

Donald J. Jacobs, Dennis R. Livesay, Oleg K. Vorov, 2008, Entropy.

Flexibility Correlation between Active Site Regions Is Conserved across Four AmpC β-Lactamase Enzymes

Dennis R. Livesay, D. Livesay, J. R. Brown, 2015, PloS one.

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

Donald J. Jacobs, Dennis R. Livesay, Deeptak Verma, 2012, PLoS Comput. Biol..

A case study comparing quantitative stability-flexibility relationships across five metallo-β-lactamases highlighting differences within NDM-1.

Dennis R Livesay, Deeptak Verma, Donald J Jacobs, 2014, Methods in molecular biology.

Using motif-based methods in multiple genome analyses: a case study comparing orthologous mesophilic and thermophilic proteins.

Dennis R Livesay, David La, R. Edgar, 2003, Biochemistry.

Topology Improves Phylogenetic Motif Functional Site Predictions

Dennis R. Livesay, Dukka Bahadur, D. Livesay, 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

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

Dennis R. Livesay, Eric Chea, D. Livesay, 2007, BMC Bioinformatics.

Improved phylogenetic motif detection using parsimony

Dennis R. Livesay, Usman Roshan, David La, 2005, Fifth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'05).

MINER: software for phylogenetic motif identification

Dennis R. Livesay, David La, David La, 2005, Nucleic Acids Res..

Predicting functional sites with an automated algorithm suitable for heterogeneous datasets

Dennis R. Livesay, David La, David La, 2005, BMC Bioinformatics.

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

Dennis R Livesay, David La, David La, 2005, Protein science : a publication of the Protein Society.

Improving position-specific predictions of protein functional sites using phylogenetic motifs

Dennis R. Livesay, Dukka Bahadur, D. Livesay, 2008, Bioinform..

Prediction of Enzyme Catalytic Sites from Sequence Using Neural Networks

Amar Raheja, Dennis R. Livesay, Swati Pande, 2007, 2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology.

Improving progressive alignment for phylogeny reconstruction using parsimonious guide-trees

Satish Chikkagoudar, Dennis R. Livesay, Usman Roshan, 2006, Sixth IEEE Symposium on BioInformatics and BioEngineering (BIBE'06).

Kinetic and thermodynamic characterization of dihydrotestosterone-induced conformational perturbations in androgen receptor ligand-binding domain.

D. Jacobs, D. Livesay, C. Yengo, 2009, Molecular endocrinology.

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

Dennis R Livesay, D. Livesay, 2010, Current opinion in pharmacology.

pH dependence of antibody: hapten association.

D. Livesay, S. Subramaniam, S. Linthicum, 1999, Molecular immunology.

A virtual pebble game to ensemble average graph rigidity

D. Jacobs, D. Livesay, Luis C. González, 2015, Algorithms for Molecular Biology.

Redistribution of Flexibility in Stabilizing Antibody Fragment Mutants Follows Le Châtelier’s Principle

Malgorzata B. Tracka, Shahid Uddin, Donald J. Jacobs, 2014, PloS one.

Thermodynamic stability and flexibility characteristics of antibody fragment complexes.

Dennis R Livesay, Deeptak Verma, Donald J Jacobs, 2013, Protein and peptide letters.

Calculating Ensemble Averaged Descriptions of Protein Rigidity without Sampling

Donald J. Jacobs, Dennis R. Livesay, D. Jacobs, 2012, PloS one.

Nonadditivity in conformational entropy upon molecular rigidification reveals a universal mechanism affecting folding cooperativity.

Donald J. Jacobs, Dennis R. Livesay, D. Jacobs, 2011, Biophysical journal.

Predicting the melting point of human C-type lysozyme mutants.

Dennis R Livesay, Deeptak Verma, Donald J Jacobs, 2010, Current protein & peptide science.

Helix/coil nucleation: a local response to global demands.

Dennis R Livesay, Donald J Jacobs, D. Jacobs, 2009, Biophysical journal.

Improving protein flexibility predictions by combining statistical sampling with a mean-field virtual Pebble Game

Donald J. Jacobs, Dennis R. Livesay, Luis C. González, 2011, BCB '11.

Conserved sequence and structure association motifs in antibody-protein and antibody-hapten complexes.

Dennis R Livesay, Shankar Subramaniam, D. Livesay, 2004, Protein engineering, design & selection : PEDS.

Elucidating the Conformational Dependence of Calculated pKa Values.

Patrick D. Kidd, D. Jacobs, D. Livesay, 2006, Journal of chemical theory and computation.

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, Usman Roshan, Patrick D. Kidd, 2007, BMC Bioinformatics.

Conferring thermostability to mesophilic proteins through optimized electrostatic surfaces.

D. Livesay, M. Torrez, Michael Schultehenrich, 2003, Biophysical journal.

Elucidating quantitative stability/flexibility relationships within thioredoxin and its fragments using a distance constraint model.

Dennis R Livesay, M. L. Tasayco, Donald J Jacobs, 2006, Journal of molecular biology.