|
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
|