Thomas R Ioerger

Summary

Affiliation: Texas A and M University
Country: USA

Publications

  1. ncbi request reprint The context-dependence of amino acid properties
    T R Ioerger
    Department of Computer Science, Texas A and M University College Station 77843, USA
    Proc Int Conf Intell Syst Mol Biol 5:157-66. 1997
  2. pmc Genome analysis of multi- and extensively-drug-resistant tuberculosis from KwaZulu-Natal, South Africa
    Thomas R Ioerger
    Department of Computer Science and Engineering, Texas A and M University, College Station, Texas, United States of America
    PLoS ONE 4:e7778. 2009
  3. pmc Variation among genome sequences of H37Rv strains of Mycobacterium tuberculosis from multiple laboratories
    Thomas R Ioerger
    Department of Computer Science and Engineering, Texas A and M University, College Station, TX 77843 3112, USA
    J Bacteriol 192:3645-53. 2010
  4. pmc The non-clonality of drug resistance in Beijing-genotype isolates of Mycobacterium tuberculosis from the Western Cape of South Africa
    Thomas R Ioerger
    Department of Computer Science and Engineering, Texas A and M University, College Station, TX, USA
    BMC Genomics 11:670. 2010
  5. ncbi request reprint Automatic modeling of protein backbones in electron-density maps via prediction of Calpha coordinates
    Thomas R Ioerger
    Department of Computer Science, Texas A and M University, College Station, TX 77843 3112, USA
    Acta Crystallogr D Biol Crystallogr 58:2043-54. 2002
  6. ncbi request reprint Conservation of cys-cys trp structural triads and their geometry in the protein domains of immunoglobulin superfamily members
    T R Ioerger
    Department of Computer Science, Texas A and M University, College Station 77843, USA
    Mol Immunol 36:373-86. 1999
  7. pmc Structures of Mycobacterium tuberculosis FadD10 protein reveal a new type of adenylate-forming enzyme
    Zhen Liu
    Department of Chemistry, Texas A and M University, College Station, Texas 77842 3012, USA
    J Biol Chem 288:18473-83. 2013
  8. doi request reprint The tuberculosis structural genomics consortium: a structural genomics approach to drug discovery
    Tracey L Musa
    Department of Biochemistry and Biophysics, Texas A and M University, College Station, Texas 77843 2128, USA
    Adv Protein Chem Struct Biol 77:41-76. 2009
  9. pmc Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries
    Michael A Dejesus
    Department of Computer Science, Texas A and M University, College Station, TX 77843, USA
    Bioinformatics 29:695-703. 2013
  10. pmc Crystal structure of Mycobacterium tuberculosis polyketide synthase 11 (PKS11) reveals intermediates in the synthesis of methyl-branched alkylpyrones
    Kuppan Gokulan
    Department of Biochemistry and Biophysics, Texas A and M University, College Station, Texas 77843, USA
    J Biol Chem 288:16484-94. 2013

Collaborators

Detail Information

Publications32

  1. ncbi request reprint The context-dependence of amino acid properties
    T R Ioerger
    Department of Computer Science, Texas A and M University College Station 77843, USA
    Proc Int Conf Intell Syst Mol Biol 5:157-66. 1997
    ..The method is shown to perform better than using the MDM78 substitution table for partial match scores...
  2. pmc Genome analysis of multi- and extensively-drug-resistant tuberculosis from KwaZulu-Natal, South Africa
    Thomas R Ioerger
    Department of Computer Science and Engineering, Texas A and M University, College Station, Texas, United States of America
    PLoS ONE 4:e7778. 2009
    ....
  3. pmc Variation among genome sequences of H37Rv strains of Mycobacterium tuberculosis from multiple laboratories
    Thomas R Ioerger
    Department of Computer Science and Engineering, Texas A and M University, College Station, TX 77843 3112, USA
    J Bacteriol 192:3645-53. 2010
    ..The resequencing of these six lab strains represents a fortuitous "in vitro evolution" experiment that demonstrates how the M. tuberculosis genome continues to evolve even in a controlled environment...
  4. pmc The non-clonality of drug resistance in Beijing-genotype isolates of Mycobacterium tuberculosis from the Western Cape of South Africa
    Thomas R Ioerger
    Department of Computer Science and Engineering, Texas A and M University, College Station, TX, USA
    BMC Genomics 11:670. 2010
    ..Although the outbreak is considered to be due to clonal transmission, the relationship among drug resistant isolates has not yet been established...
  5. ncbi request reprint Automatic modeling of protein backbones in electron-density maps via prediction of Calpha coordinates
    Thomas R Ioerger
    Department of Computer Science, Texas A and M University, College Station, TX 77843 3112, USA
    Acta Crystallogr D Biol Crystallogr 58:2043-54. 2002
    ..4-2.8 A resolution reveal that CAPRA is capable of building approximately 90% of the backbone of a protein molecule, with an r.m.s. error for Calpha coordinates of around 0.9 A...
  6. ncbi request reprint Conservation of cys-cys trp structural triads and their geometry in the protein domains of immunoglobulin superfamily members
    T R Ioerger
    Department of Computer Science, Texas A and M University, College Station 77843, USA
    Mol Immunol 36:373-86. 1999
    ..Knowledge of these geometric parameters may prove useful in the construction and validation of theoretical models of Ig, TCR, and other IgSF members...
  7. pmc Structures of Mycobacterium tuberculosis FadD10 protein reveal a new type of adenylate-forming enzyme
    Zhen Liu
    Department of Chemistry, Texas A and M University, College Station, Texas 77842 3012, USA
    J Biol Chem 288:18473-83. 2013
    ..We have also characterized the fatty acid preference of FadD10 through biological and structural analyses, and the data indicate long chain saturated fatty acids as the biological substrates of the enzyme. ..
  8. doi request reprint The tuberculosis structural genomics consortium: a structural genomics approach to drug discovery
    Tracey L Musa
    Department of Biochemistry and Biophysics, Texas A and M University, College Station, Texas 77843 2128, USA
    Adv Protein Chem Struct Biol 77:41-76. 2009
    ..The success of this pipeline is illustrated in the number of successful structure solutions as demonstrated in the case studies presented in this chapter...
  9. pmc Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries
    Michael A Dejesus
    Department of Computer Science, Texas A and M University, College Station, TX 77843, USA
    Bioinformatics 29:695-703. 2013
    ..We describe a sampling procedure based on the Metropolis-Hastings algorithm to calculate posterior probabilities of essentiality while simultaneously integrating over unknown internal parameters...
  10. pmc Crystal structure of Mycobacterium tuberculosis polyketide synthase 11 (PKS11) reveals intermediates in the synthesis of methyl-branched alkylpyrones
    Kuppan Gokulan
    Department of Biochemistry and Biophysics, Texas A and M University, College Station, Texas 77843, USA
    J Biol Chem 288:16484-94. 2013
    ....
  11. doi request reprint Structural genomics approach to drug discovery for Mycobacterium tuberculosis
    Thomas R Ioerger
    Department of Computer Science and Engineering, Texas A and M University, USA
    Curr Opin Microbiol 12:318-25. 2009
    ..We conclude by describing the high-throughput screening facilities and virtual screening facilities we have implemented for identifying small-molecule inhibitors of proteins whose structures have been solved...
  12. pmc Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors
    Manchi C M Reddy
    Department of Biochemistry and Biophysics, Texas A and M University, College Station, Texas 77843 2128, USA
    Protein Sci 17:2134-44. 2008
    ..Differences in the entrance to this access channel between human and Mtb SAHH are identified...
  13. pmc The 1.25 A resolution structure of phosphoribosyl-ATP pyrophosphohydrolase from Mycobacterium tuberculosis
    Farah Javid-Majd
    Department of Biochemistry and Biophysics, Texas A and M University, College Station, Texas 77843 2128, USA
    Acta Crystallogr D Biol Crystallogr 64:627-35. 2008
    ..The crystal structure of M. tuberculosis HisE provides insights into possible mechanisms of substrate binding and the diversity of the nucleoside-triphosphate pyrophosphatase superfamily...
  14. pmc Crystal structure of Mycobacterium tuberculosis LrpA, a leucine-responsive global regulator associated with starvation response
    Manchi C M Reddy
    Department of Biochemistry and Biophysics, Texas A and M University, College Station, Texas 77843 2128, USA
    Protein Sci 17:159-70. 2008
    ..This study provides insights into the potential role of LrpA as a global regulator in the transition of M. tuberculosis to a persistent state...
  15. ncbi request reprint Determining relevant features to recognize electron density patterns in x-ray protein crystallography
    Kreshna Gopal
    Department of Computer Science, Texas A and M University, 301 H R Bright Building, College Station TX 77843 3112, USA
    J Bioinform Comput Biol 3:645-76. 2005
    ..We show that SLIDER contributes significantly in finding the similarity between density patterns, and discuss the sensitivity of feature relevance to the underlying similarity metric...
  16. pmc Reannotation of translational start sites in the genome of Mycobacterium tuberculosis
    Michael A Dejesus
    Department of Computer Science and Engineering, Texas A and M University, College Station, TX, USA
    Tuberculosis (Edinb) 93:18-25. 2013
    ..These revised ORF definitions could be used in the reannotation of the H37Rv genome, as well as to prioritize genes for experimental start-site validation...
  17. pmc Mycobacterium tuberculosis dihydrofolate reductase is not a target relevant to the antitubercular activity of isoniazid
    Feng Wang
    Department of Biochemistry and Biophysics, Texas A and M University, College Station, Texas 77843 2128, USA
    Antimicrob Agents Chemother 54:3776-82. 2010
    ..The dfrA overexpression experiments, together with the biochemical and sequencing studies, conclusively demonstrate that DHFR is not a target relevant to the antitubercular activity of INH...
  18. doi request reprint A Multifaceted Secondary Structure Mimic Based On Piperidine-piperidinones
    Dongyue Xin
    Department of Chemistry, Texas A and M University, Box 30012, College Station, TX 77841 3012 USA
    Angew Chem Int Ed Engl 53:3594-8. 2014
    ..Thus dld-1 faf crystallized in a conformation that is estimated to be 0.91 kcal mol(-1) above the minimum energy solution state. ..
  19. pmc Evaluating minimalist mimics by exploring key orientations on secondary structures (EKOS)
    Dongyue Xin
    Department of Chemistry, Texas A and M University, Box 30012, College Station, TX 77842, USA
    Org Biomol Chem 11:7789-801. 2013
    ....
  20. pmc Structure-guided discovery of phenyl-diketo acids as potent inhibitors of M. tuberculosis malate synthase
    Inna V Krieger
    Department of Biochemistry and Biophysics, Texas A and M University, College Station, TX 77843, USA
    Chem Biol 19:1556-67. 2012
    ..A selected PDKA compound demonstrated efficacy in a mouse model of tuberculosis. The discovery of these PDKA derivatives provides chemical validation of GlcB as an attractive target for tuberculosis therapeutics...
  21. ncbi request reprint TEXTAL system: artificial intelligence techniques for automated protein model building
    Thomas R Ioerger
    Texas A and M University, College Station, Texas 77843, USA
    Methods Enzymol 374:244-70. 2003
  22. pmc Identification of new drug targets and resistance mechanisms in Mycobacterium tuberculosis
    Thomas R Ioerger
    Department of Computer Science and Engineering, Texas A and M University, College Station, Texas, United States of America
    PLoS ONE 8:e75245. 2013
    ..Pks13, AspS, and EccB3 represent novel candidates not targeted by existing TB drugs, and the availability of whole-cell active inhibitors greatly increases their potential for drug discovery. ..
  23. pmc Exploring key orientations at protein-protein interfaces with small molecule probes
    Eunhwa Ko
    Department of Chemistry, Texas A and M University, Box 30012, College Station, Texas 77842, United States
    J Am Chem Soc 135:167-73. 2013
    ..These data indicate this approach may inspire design of small molecule interface probes to perturb PPIs...
  24. pmc A Hidden Markov Model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data
    Michael A Dejesus
    Department of Computer Science, Texas A and M University, College Station, TX 77843, USA
    BMC Bioinformatics 14:303. 2013
    ....
  25. ncbi request reprint Determining protein structure from electron-density maps using pattern matching
    T Holton
    Department of Biochemistry and Biophysics, Texas A and M University, College Station, TX 77843 2128, USA
    Acta Crystallogr D Biol Crystallogr 56:722-34. 2000
    ..The system represents a new approach to protein structure determination and has the potential to greatly reduce the time required to interpret electron-density maps in order to build accurate protein models...
  26. ncbi request reprint Antibody-ligand interactions: computational modeling and correlation with biophysical measurements
    D S Linthicum
    Delaware Water Gap Science Institute, Bangor, and Department of Computer Science, Texas A and M University, College Station, TX 77843, USA
    Comb Chem High Throughput Screen 4:439-49. 2001
    ..An understanding of these parameters is essential to our use of antibodies as tools in high throughput screening of chemical libraries for the discovery of novel compounds...
  27. ncbi request reprint PHENIX: building new software for automated crystallographic structure determination
    Paul D Adams
    Lawrence Berkeley National Laboratory, One Cyclotron Road, Mailstop 4 230, Berkeley, CA 94720, USA
    Acta Crystallogr D Biol Crystallogr 58:1948-54. 2002
    ..This new software will provide the necessary algorithms to proceed from reduced intensity data to a refined molecular model and to facilitate structure solution for both the novice and expert crystallographer...
  28. ncbi request reprint Improving amino-acid identification, fit and C(alpha) prediction using the Simplex method in automated model building
    Tod D Romo
    Texas A and M Center for Structural Biology, Institute for Biosciences and Technology, Houston, TX 77030, USA
    Acta Crystallogr D Biol Crystallogr 62:1401-6. 2006
    ....
  29. ncbi request reprint Recent developments in the PHENIX software for automated crystallographic structure determination
    Paul D Adams
    Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    J Synchrotron Radiat 11:53-5. 2004
    ..Here, the features of PHENIXare reviewed and the recent advances in infrastructure and algorithms are briefly described...
  30. doi request reprint Automated structure solution with the PHENIX suite
    Peter H Zwart
    Lawrence Berkeley National Laboratory, Berkeley, CA, USA
    Methods Mol Biol 426:419-35. 2008
    ..The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI...
  31. ncbi request reprint Crystal structure of circadian clock protein KaiA from Synechococcus elongatus
    Sheng Ye
    Center for Structural Biology, Institute of Biosciences and Technology, Houston, TX 77030, USA
    J Biol Chem 279:20511-8. 2004
    ..The structure suggests that the KaiB binding site is covered in the dimer interface of the KaiA "closed" conformation, observed in the crystal structure, which suggests an allosteric regulation mechanism...
  32. pmc Discovery of novel nitrobenzothiazole inhibitors for Mycobacterium tuberculosis ATP phosphoribosyl transferase (HisG) through virtual screening
    Yoonsang Cho
    Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, USA
    J Med Chem 51:5984-92. 2008
    ..Several of these also exhibited micromolar inhibition. Furthermore, two of the compounds showed bacteriocidal activity in a whole-cell assay against Mycobacterium smegmatis...