Olivier Lichtarge

Summary

Affiliation: Baylor College of Medicine
Country: USA

Publications

  1. pmc Evolution: a guide to perturb protein function and networks
    Olivier Lichtarge
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    Curr Opin Struct Biol 20:351-9. 2010
  2. pmc Prediction of enzyme function based on 3D templates of evolutionarily important amino acids
    David M Kristensen
    Department of Molecular and Human Genetics, Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
    BMC Bioinformatics 9:17. 2008
  3. ncbi request reprint Composite motifs integrating multiple protein structures increase sensitivity for function prediction
    Brian Y Chen
    Department of Computer Science, Rice University, Houston, TX 77005, USA
    Comput Syst Bioinformatics Conf 6:343-55. 2007
  4. pmc Evolutionary trace annotation of protein function in the structural proteome
    Serkan Erdin
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    J Mol Biol 396:1451-73. 2010
  5. ncbi request reprint The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs
    Brian Y Chen
    Department of Computer Science, Rice University, Houston, TX 77005, USA
    J Comput Biol 14:791-816. 2007
  6. pmc Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates
    R Matthew Ward
    Department of Molecular and Human Genetics, Program in Structural and Computational Biology and Molecular, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    Bioinformatics 25:1426-7. 2009
  7. ncbi request reprint Rank information: a structure-independent measure of evolutionary trace quality that improves identification of protein functional sites
    Hui Yao
    Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
    Proteins 65:111-23. 2006
  8. ncbi request reprint Cavity scaling: automated refinement of cavity-aware motifs in protein function prediction
    Brian Y Chen
    Department of Computer Science, Rice University, Houston, TX 77005, USA
    J Bioinform Comput Biol 5:353-82. 2007
  9. pmc Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities
    Eric Venner
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS ONE 5:e14286. 2010
  10. pmc Function prediction from networks of local evolutionary similarity in protein structure
    Serkan Erdin
    Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    BMC Bioinformatics 14:S6. 2013

Collaborators

Detail Information

Publications44

  1. pmc Evolution: a guide to perturb protein function and networks
    Olivier Lichtarge
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    Curr Opin Struct Biol 20:351-9. 2010
    ..These studies suggest, in principle, a scalable approach to perturb individual links in protein networks...
  2. pmc Prediction of enzyme function based on 3D templates of evolutionarily important amino acids
    David M Kristensen
    Department of Molecular and Human Genetics, Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
    BMC Bioinformatics 9:17. 2008
    ..Since experimentally determined functional sites are not common enough to define 3D templates on a large scale, this work tests a computational strategy to select relevant residues for 3D templates...
  3. ncbi request reprint Composite motifs integrating multiple protein structures increase sensitivity for function prediction
    Brian Y Chen
    Department of Computer Science, Rice University, Houston, TX 77005, USA
    Comput Syst Bioinformatics Conf 6:343-55. 2007
    ..On our data set, we observed that composite motifs simultaneously capture variations in active site conformation, diminish the problem of selecting motif structures, and enable the fusion of protein structures from diverse data sources...
  4. pmc Evolutionary trace annotation of protein function in the structural proteome
    Serkan Erdin
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    J Mol Biol 396:1451-73. 2010
    ..ETA is available at http://mammoth.bcm.tmc.edu/eta...
  5. ncbi request reprint The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs
    Brian Y Chen
    Department of Computer Science, Rice University, Houston, TX 77005, USA
    J Comput Biol 14:791-816. 2007
    ..In exhaustive comparison of all possible motifs based on the active sites of 10 well-studied proteins, we observed that optimized motifs were among the most sensitive and specific...
  6. pmc Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates
    R Matthew Ward
    Department of Molecular and Human Genetics, Program in Structural and Computational Biology and Molecular, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    Bioinformatics 25:1426-7. 2009
    ..Users may modify any search parameter, including the template. ETA thus expands the ET suite for protein structure annotation, and can contribute to the annotation efforts of metaservers...
  7. ncbi request reprint Rank information: a structure-independent measure of evolutionary trace quality that improves identification of protein functional sites
    Hui Yao
    Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
    Proteins 65:111-23. 2006
    ..In practice, as the size of the proteome continues to grow exponentially, it provides a novel and structure-free measure of ET quality that increases its accuracy for large-scale automated annotation of protein functional sites...
  8. ncbi request reprint Cavity scaling: automated refinement of cavity-aware motifs in protein function prediction
    Brian Y Chen
    Department of Computer Science, Rice University, Houston, TX 77005, USA
    J Bioinform Comput Biol 5:353-82. 2007
    ..While the optimal placement of C-spheres remains a difficult open problem, we compared two logical placement strategies to better understand C-sphere placement...
  9. pmc Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities
    Eric Venner
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS ONE 5:e14286. 2010
    ..A web server is at http://mammoth.bcm.tmc.edu/networks...
  10. pmc Function prediction from networks of local evolutionary similarity in protein structure
    Serkan Erdin
    Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    BMC Bioinformatics 14:S6. 2013
    ..In order to further increase sensitivity, we now let each protein contribute multiple templates rather than just one, and also let the template size vary...
  11. ncbi request reprint Accurate and scalable identification of functional sites by evolutionary tracing
    Olivier Lichtarge
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    J Struct Funct Genomics 4:159-66. 2003
    ..The result is an accurate method of functional site annotation that is scalable for structural proteomics...
  12. pmc ETAscape: analyzing protein networks to predict enzymatic function and substrates in Cytoscape
    Benjamin J Bachman
    Departments of Molecular and Human Genetics, Program Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    Bioinformatics 28:2186-8. 2012
    ..The plugin displays these novel functional annotations, their confidence, the molecular basis for individual matches and the set of matches that lead to a prediction...
  13. pmc De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features
    R Matthew Ward
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS ONE 3:e2136. 2008
    ....
  14. pmc Prediction and experimental validation of enzyme substrate specificity in protein structures
    Shivas R Amin
    Department of Molecular and Human Genetics and Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX 77030
    Proc Natl Acad Sci U S A 110:E4195-202. 2013
    ..We conclude that evolutionary and structural information may be combined on a Structural Genomics scale to create motifs of mixed catalytic and noncatalytic residues that identify enzyme activity and substrate specificity. ..
  15. ncbi request reprint An accurate, sensitive, and scalable method to identify functional sites in protein structures
    Hui Yao
    Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza T921, Houston, TX 77030, USA
    J Mol Biol 326:255-61. 2003
    ..This should help focus structure-function studies, rational drug design, protein engineering, and functional annotation to the relevant regions of a protein...
  16. ncbi request reprint ET viewer: an application for predicting and visualizing functional sites in protein structures
    Daniel H Morgan
    Department of Molecular and Human Genetics, One Baylor Plaza, Houston, TX 77030, USA
    Bioinformatics 22:2049-50. 2006
    ..ETV is implemented using Java to run across different operating systems using Java Web Start technology...
  17. ncbi request reprint Distinct faces of the Ku heterodimer mediate DNA repair and telomeric functions
    Albert Ribes-Zamora
    Department of Pediatrics, Hematology Oncology Section, Baylor College of Medicine, One Baylor Plaza, BCM225, Houston, Texas 77030 3411, USA
    Nat Struct Mol Biol 14:301-7. 2007
    ..We propose a 'two-face' model for Ku and that divergent evolution of these faces allowed Ku's dual role in NHEJ and telomere maintenance...
  18. ncbi request reprint Character and evolution of protein-protein interfaces
    Ivica Res
    Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    Phys Biol 2:S36-43. 2005
    ..This paper discusses methods based on multiple sequence alignments of protein homologues and phylogenetic trees...
  19. ncbi request reprint Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions
    Srinivasan Madabushi
    Program in Structural and Computational Biology and Molecular Biophysics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    J Biol Chem 279:8126-32. 2004
    ..These results define in GPCRs a canonical signal transduction mechanism where ligand binding induces conformational changes propagated through adjacent trigger, linking core, and coupling regions...
  20. pmc Rapid detection of similarity in protein structure and function through contact metric distances
    Andreas Martin Lisewski
    Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    Nucleic Acids Res 34:e152. 2006
    ..A public 'Contact Metric Internet Server' is provided...
  21. pmc Role for the regulator of G-protein signaling homology domain of G protein-coupled receptor kinases 5 and 6 in beta 2-adrenergic receptor and rhodopsin phosphorylation
    Faiza Baameur
    Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Medical School, 6431 Fannin St, Houston, TX 77030, USA
    Mol Pharmacol 77:405-15. 2010
    ....
  22. ncbi request reprint Computational and biochemical identification of a nuclear pore complex binding site on the nuclear transport carrier NTF2
    Ian Cushman
    Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    J Mol Biol 344:303-10. 2004
    ..Instead, the D23 residue is located in an evolutionarily important region in the NTF2 domain containing superfamily, that in NTF2, is involved in binding to the NPC...
  23. pmc Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity
    David M Kristensen
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    Protein Sci 15:1530-6. 2006
    ....
  24. doi request reprint Evolutionary trace for prediction and redesign of protein functional sites
    Angela Wilkins
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
    Methods Mol Biol 819:29-42. 2012
    ..Public ET servers are located at: http://mammoth.bcm.tmc.edu/...
  25. pmc Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors
    Gustavo J Rodriguez
    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 107:7787-92. 2010
    ....
  26. pmc Identification of functionally important residues/domains in membrane proteins using an evolutionary approach coupled with systematic mutational analysis
    Lavanya Rajagopalan
    Bobby R Alford Department of Otolaryngology HNS, Baylor College of Medicine, Houston, TX, USA
    Methods Mol Biol 493:287-97. 2009
    ....
  27. pmc Accounting for epistatic interactions improves the functional analysis of protein structures
    Angela D Wilkins
    Department of Molecular and Human Genetics, CIBR Center for Computational and Integrative Biomedical Research and Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030 and Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
    Bioinformatics 29:2714-21. 2013
    ..Based on prior data, we hypothesize that epistatic forces operate most strongly between residues nearby in the structure, resulting in smooth evolutionary importance across the structure...
  28. pmc Protein kinase A and phosphodiesterase-4D3 binding to coding polymorphisms of cardiac muscle anchoring protein (mAKAP)
    Abeer Rababa'h
    Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Texas Medical Center, Houston, TX 77204, USA
    J Mol Biol 425:3277-88. 2013
    ..Comparative analysis of the binding responses of mutations to mAKAP could provide important information about how these mutations modulate signaling. ..
  29. pmc Essential helix interactions in the anion transporter domain of prestin revealed by evolutionary trace analysis
    Lavanya Rajagopalan
    Department of Molecular Virology, Baylor College of Medicine, Houston, Texas 77030, USA
    J Neurosci 26:12727-34. 2006
    ..These data suggest that packing of helices and interactions between residues surrounding the "sulfate transporter motif" is essential for normal prestin activity...
  30. pmc Protein function prediction: towards integration of similarity metrics
    Serkan Erdin
    Department of Molecular and Human Genetics, 1 Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
    Curr Opin Struct Biol 21:180-8. 2011
    ..Although high sensitivity is elusive, network analyses that integrate these metrics together hold the promise of rapid gains in function prediction specificity...
  31. ncbi request reprint Evolutionary predictions of binding surfaces and interactions
    Olivier Lichtarge
    Department of Molecular and Human Genetics, 1 Baylor Plaza, Baylor College of Medicine, Houston, Texas 77030, USA
    Curr Opin Struct Biol 12:21-7. 2002
    ..Among these determinants, those residues that are on protein surfaces are especially likely to form binding sites and are the logical choice for further mutational analysis and drug targeting...
  32. pmc PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes
    Rhonald C Lua
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    Bioinformatics 26:2981-2. 2010
    ..Together with other tools in the popular PyMOL viewer, PyETV thus provides a novel tool to integrate evolutionary forces into the design of experiments targeting the most functionally relevant sites of a protein...
  33. ncbi request reprint Evolutionary identification of a subtype specific functional site in the ligand binding domain of steroid receptors
    Michele Raviscioni
    W M Keck Center for Computational and Structural Biology, Baylor College of Medicine, Houston Texas 77030, USA
    Proteins 64:1046-57. 2006
    ..This highlights the power of evolutionary information for the identification of new functional sites even in a protein family as well studied as NRs...
  34. pmc Identity and function of a large gene network underlying mutagenic repair of DNA breaks
    Abu Amar M Al Mamun
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 3411, USA
    Science 338:1344-8. 2012
    ....
  35. pmc The use of evolutionary patterns in protein annotation
    Angela D Wilkins
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    Curr Opin Struct Biol 22:316-25. 2012
    ..Here we review these methods, and the patterns they identify in case studies and in proteome-wide applications, to infer and rationally redesign function...
  36. ncbi request reprint Evolutionary trace-based peptides identify a novel asymmetric interaction that mediates oligomerization in nuclear receptors
    Peili Gu
    Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
    J Biol Chem 280:31818-29. 2005
    ..These findings shed light on an evolutionarily selected mechanism that reveals the unusual DNA-binding, dimerization, and oligomerization properties of GCNF...
  37. ncbi request reprint Lysine 270 in the third intracellular domain of the oxytocin receptor is an important determinant for G alpha(q) coupling specificity
    Ming Yang
    Department of Biochemistry and Molecular Biology, University of Texas Medical School Houston, Houston, Texas 77030, USA
    Mol Endocrinol 16:814-23. 2002
    ..Mutation of K270 also adversely affects the ability of OTR to stimulate ERK1/2 phosphorylation. Therefore, this residue plays an important role in the specificity of OTR/G alpha(q)/PLC coupling...
  38. pmc Separation of recombination and SOS response in Escherichia coli RecA suggests LexA interaction sites
    Anbu K Adikesavan
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS Genet 7:e1002244. 2011
    ..These new sites can provide new drug targets to modulate one or more RecA functions, with the potential to address the problem of evolution of antibiotic resistance at its root...
  39. ncbi request reprint Structural clusters of evolutionary trace residues are statistically significant and common in proteins
    Srinivasan Madabushi
    Structural and Computational Biology and Molecular Biophysics Program, Baylor College of Medicine, Houston, TX 77030, USA
    J Mol Biol 316:139-54. 2002
    ..This approach to combining raw sequences and structure to obtain detailed insights into the molecular basis of function should prove valuable in the context of the Structural Genomics Initiative...
  40. doi request reprint Desmosterolosis-phenotypic and molecular characterization of a third case and review of the literature
    Christian P Schaaf
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
    Am J Med Genet A 155:1597-604. 2011
    ..We compare the phenotype of our patient with previously reported cases...
  41. pmc The maternal-to-zygotic transition targets actin to promote robustness during morphogenesis
    Liuliu Zheng
    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS Genet 9:e1003901. 2013
    ..Since all morphogenesis depends on cytoskeletal remodeling, both in embryos and adults, we suggest that robustness-promoting mechanisms aimed at actin could be effective at all life stages. ..
  42. doi request reprint Regulation of ras localization and cell transformation by evolutionarily conserved palmitoyltransferases
    Evelin Young
    Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
    Mol Cell Biol 34:374-85. 2014
    ....
  43. ncbi request reprint Evolutionary traces of functional surfaces along G protein signaling pathway
    Olivier Lichtarge
    Department of Molecular and Human Genetics, Program in Structural and Computational Biology and Molecular Biophysics, Baylor Human Genome Sequencing Center, Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
    Methods Enzymol 344:536-56. 2002
  44. pmc An AT-hook domain in MeCP2 determines the clinical course of Rett syndrome and related disorders
    Steven Andrew Baker
    Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
    Cell 152:984-96. 2013
    ....