In Press

Changes in lysozyme flexibility upon mutation are frequent, large and long-ranged. Verma D, Jacobs DJ, Livesay DR. PLoS Computational Biology, In press.

Calculating ensemble averaged descriptions of protein rigidity without sampling. Gonzalez LC, Livesay DR, Jacobs DJ. PLoS One, In press.

Improving protein flexibility predictions by combining statistical sampling with a mean-field virtual pebble game. Gonzalez LC, Livesay DR, Jacobs DJ. ACM Conference on Bioinformatics, Computational Biology and Biomedicine, In press.

2012

A critical evaluation of correlated mutation algorithms and coevolution within allosteric mechanisms. Livesay DR, Kreth KE, Fodor AA (2012). Methods Mol Biol, 796:385-398. PubMed | Reprint

Ensemble properties of network rigidity reveal allosteric mechanisms. Jacobs DJ, Livesay DR, Mottonen JM, Vorov OK, Istomin AY, Verma D (2012). Methods Mol Biol, 796:279-304. PubMed | Reprint

2011

WaveMap: Interactively discovering features from protein flexibility matrices using wavelet-based visual analytics. Barlow S, Liu Y, Yang J, Livesay DR, Jacobs DJ, Mottonen J, Verma D (2011). Computer Graphics Forum, 30:1001-1010. Abstract | Reprint

Nonadditivity in conformational entropy upon molecular rigidification reveals a universal mechanism affecting folding cooperativity. Vorov OK, Livesay DR, Jacobs DJ (2011). Biophysical Journal, 100:1129-1138. PubMed | Reprint

Predicting protein functional sites with phylogenetic motifs: Past, present and beyond. Livesay DR, KC DB, La D (2011). In Protein function prediction for the omics era, Kihara D (Ed.), Springer. ISBN: 978-94-007-0880-8. Available here

Topology improves phylogenetic motif functional site predictions. KC DB, Livesay DR (2011). IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8:226-233. PubMed | Reprint

2010

Protein dynamics: Dancing on an ever-changing free energy stage. Livesay DR (2010). Current Opinion in Pharmacology, 10:706-708 (also section editor). PubMed | Reprint

Predicting the melting point of human c-type lysozyme mutants. Verma D, Jacobs DJ, Livesay DR (2010). Current Protein and Peptide Science, 11:562-572. PubMed | Reprint

Allosteric response is both conserved and variable across three CheY orthologs. Mottonen JM, Jacobs DJ, Livesay DR (2010). Biophysical Journal, 99:2245-2254. PubMed | Reprint

PLAST-ncRNA: Partition function local alignment search tool for non-coding RNA sequences. Chikkagoudar S, Livesay DR, Roshan U (2010). Nucleic Acids Research, 38:W59-W63. PubMed | Reprint

2009

Helix/coil nucleation: A local response to global demands. Vorov OK, Livesay DR, Jacobs DJ (2009). Biophysical Journal, 97:3000-3009. PubMed | Reprint

Kinetic and thermodynamic characterization of dihydrotestosterone-induced conformational perturbations in androgen receptor ligand binding domain. Jasuja R, Ulloor J, Yengo CM, Choong K, Istomin AY, Livesay DR, Jacobs DJ, Swerdloff RS, Miksovska J, Larsen RW, Bhasin S (2009). Molecular Endocrinology, 23:1231-1241. PubMed | Reprint

Unifying mechanical and thermodynamic descriptions across the thioredoxin protein family. Mottonen JM, Xu M, Jacobs DJ, Livesay DR (2009). PROTEINS: Structure, Function, & Bioinformatics, 75:610-627. PubMed | Reprint

A spectrum of phylogenetic-based approaches for predicting protein functional sites. KC DB, Livesay DR (2009). In Bioinformatics for Systems Biology, Krawetz S (Ed.), Humana Press. ISBN: 978-1-934115-02-2. Available here

2008

Improving position specific predictions of protein functional sites using phylogenetic motifs. KC DB, Livesay DR (2008). Bioinformatics, 24:2308-2316. PubMed | Reprint

Conformational entropy of an ideal cross-linking polymer chain. Vorov OK, Livesay DR, Jacobs DJ (2008). Entropy, 10:285-308. PubMed | Reprint

Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family. Livesay DR, Huynh, D, Dallakyan S, Jacobs DJ (2008). Chemistry Central Journal, 2:17. PubMed | Reprint

Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities. Roshan U, Chikkagoudar S, Livesay DR (2008). BMC Bioinformatics, 9:61. PubMed | Reprint

New insight into long-range nonadditivity within protein double-mutant cycles. Istomin AY, Gromiha MM, Vorov OK, Jacobs DJ, Livesay DR (2008). PROTEINS: Structure, Function, & Bioinformatics, 70:915-924. PubMed | Reprint

2007

On the role of structural class of a protein with two-state folding kinetics in determining correlations between its size, topology, and folding rate. Istomin AY, Jacobs DJ, Livesay DR (2007). Protein Science, 16:2564-2569. PubMed | Reprint

Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na+ symporter family. Livesay DR, Kidd PD, Eskandari S, Roshan U (2007). BMC Bioinformatics, 8:397. PubMed | Reprint

How accurate and statistically robust are catalytic site predictions based on closeness centrality? Chea E, Livesay DR (2007). BMC Bioinformatics, 8:153. PubMed | Reprint | Erratum

eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities. Chikkagoudar S, Roshan U, Livesay DR (2007). Nucleic Acids Research, 35:W675-W677. PubMed | Reprint

At the crossroads of biomacromolecular research: highlighting the interdisciplinary nature of the field. Livesay DR (2007). Chemistry Central Journal, 1:4. PubMed | Reprint

Prediction of enzyme catalytic sites from sequence using neural networks. Pande S, Raheja A, Livesay DR (2007). IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB07:247-253. Abstract | Reprint

2006

Probalign: multiple sequence alignment using partition function posterior probabilities. Roshan U, Livesay DR (2006). Bioinformatics, 22:2715-2721. PubMed | Reprint

Improving progressive alignment for phylogeny reconstruction using parsimonious guide-trees. Roshan U, Livesay DR, Chikkagoudar S (2006). IEEE 6th Symposium on Bioinformatics and Bioengineering, BIBE06:159-164. Abstract | Reprint

Probing the conformational dependence of calculated pKa values. Livesay DR, Jacobs DJ, Kanjanapangka J, Chea E, Cortez H, Garcia J, Kidd P, Marquez MP, Pande S, Yang D (2006). Journal of Chemical Theory & Computation, 2:927-938. Abstract | Reprint

Elucidating quantitative stability/flexibility relationships within thioredoxin and its fragments using a distance constraint model. Jacobs DJ, Livesay DR, Hules J, Tasayco ML (2006). Journal of Molecular Biology, 358:882-904. PubMed | Reprint

Conserved quantified stability/flexibility relationships (QSFR) in an orthologous RNase H pair. Livesay DR, Jacobs DJ (2006). PROTEINS: Structure, Function, & Bioinformatics, 62:130-143. PubMed | Reprint

2005

MINER: software for phylogenetic motif identification. La D, Livesay DR (2005). Nucleic Acids Research, 33:W267-W270. PubMed | Reprint

Improved phylogenetic motif identification using parsimony. Roshan U, Livesay DR, La D (2005). IEEE 5th Symposium on Bioinformatics and Bioengineering, BIBE05:19-26. Abstract | Reprint

Accurate functional site prediction using an automated algorithm suitable for heterogeneous datasets. La D, Livesay DR (2005). BMC Bioinformatics, 6:116. PubMed | Reprint

Probing the evolutionary origins and catalytic importance of conserved electrostatic networks in TIM-barrel proteins. Livesay DR, La D (2005). Protein Science, 14:1158-1170. PubMed | Reprint

Predicting protein functional sites with phylogenetic motifs. La D, Sutch B, Livesay DR (2005). PROTEINS: Structure, Function, & Bioinformatics, 58:309-320. PubMed | Reprint

2004

A flexible approach for understanding protein stability. Livesay DR, Dallakayan S, Wood GG, Jacobs DJ (2004). FEBS Letters, 576:468-476. PubMed | Reprint

Conserved sequence and structure association motifs in antibody-protein and antibody-hapten complexes. Livesay DR, Subramaniam S (2004). Protein Engineering Design & Selection, 17:463-472. PubMed | Reprint

2003

Optimized electrostatic surfaces parallel increased thermostability: a structural bioinformatic analysis. Alsop E, Silver MA, Livesay DR (2003). Protein Engineering, 16:871-874. PubMed | Reprint

Conferring thermostability to mesophilic proteins through optimized electrostatic surfaces. Torrez M, Schultehenrich M, Livesay DR (2003). Biophysical Journal, 85:2845-2853. PubMed | Reprint

Using motif-based methods in multiple genome analyses: a case study comparing orthologous mesophilic and thermophilic proteins. La D, Silver MA, Edgar RC, Livesay DR (2003). Biochemistry, 42:8988-8998. PubMed | Reprint

Conservation of electrostatic properties within enzyme families and superfamilies. Livesay DR, Jambeck P, Rojnuckarin A, Subramaniam S (2003). Biochemistry, 42:3464-3473. PubMed | Reprint

2000

Reaction rate prediction with weighted ensemble Brownian dynamics and the University of Houston Brownian Dynamics program. Rojnuckarin A, Livesay DR, Subramaniam S (2000). Biophysical Journal, 79:686-693. PubMed | Reprint

1999

pH dependence of antibody-hapten association. Livesay DR, Linthicum SD, Subramaniam S (1999). Molecular Immunology, 36:397-410. PubMed | Reprint