Research Topics
Genomes and Genes | Olivier LichtargeSummaryAffiliation: Baylor College of Medicine Country: USA Publications
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Detail Information
Publications
Function prediction from networks of local evolutionary similarity in protein structureSerkan 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...- Evolution: a guide to perturb protein function and networksOlivier 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... - Prediction of enzyme function based on 3D templates of evolutionarily important amino acidsDavid 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... 
Composite motifs integrating multiple protein structures increase sensitivity for function predictionBrian 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...- Evolutionary trace annotation of protein function in the structural proteomeSerkan 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... - The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifsBrian 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... - Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templatesR 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..ETA thus expands the ET suite for protein structure annotation, and can contribute to the annotation efforts of metaservers. AVAILABILITY: The ETA Server is a web application available at (http://mammoth.bcm.tmc.edu/eta/)... - Rank information: a structure-independent measure of evolutionary trace quality that improves identification of protein functional sitesHui 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... - Cavity scaling: automated refinement of cavity-aware motifs in protein function predictionBrian 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... - Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similaritiesEric 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... - De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural featuresR Matthew Ward
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
PLoS ONE 3:e2136. 2008.... - Accurate and scalable identification of functional sites by evolutionary tracingOlivier 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... - Distinct faces of the Ku heterodimer mediate DNA repair and telomeric functionsAlbert 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... - An accurate, sensitive, and scalable method to identify functional sites in protein structuresHui 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... - ET viewer: an application for predicting and visualizing functional sites in protein structuresDaniel H Morgan
Department of Molecular and Human Genetics, One Baylor Plaza, Houston, TX 77030, USA
Bioinformatics 22:2049-50. 2006..AVAILABILITY: The ETV is available for download from our website at http://mammoth.bcm.tmc.edu/traceview/index.html. This webpage also links to sample trace results and a user manual that describes ET Viewer functions in detail... - Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarityDavid M Kristensen
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
Protein Sci 15:1530-6. 2006.... - Rapid detection of similarity in protein structure and function through contact metric distancesAndreas 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... - Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functionsSrinivasan 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... - 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 phosphorylationFaiza 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.... - Character and evolution of protein-protein interfacesIvica 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... - Computational and biochemical identification of a nuclear pore complex binding site on the nuclear transport carrier NTF2Ian 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... 
Evolutionary trace for prediction and redesign of protein functional sitesAngela 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/...- Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptorsGustavo 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.... - Identification of functionally important residues/domains in membrane proteins using an evolutionary approach coupled with systematic mutational analysisLavanya Rajagopalan
Bobby R Alford Department of Otolaryngology HNS, Baylor College of Medicine, Houston, TX, USA
Methods Mol Biol 493:287-97. 2009.... - Protein function prediction: towards integration of similarity metricsSerkan 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... - Evolutionary predictions of binding surfaces and interactionsOlivier 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... - PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexesRhonald 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... - Evolutionary identification of a subtype specific functional site in the ligand binding domain of steroid receptorsMichele 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... - Essential helix interactions in the anion transporter domain of prestin revealed by evolutionary trace analysisLavanya 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... - Identity and function of a large gene network underlying mutagenic repair of DNA breaksAbu Amar M Al Mamun
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 3411, USA
Science 338:1344-8. 2012.... - The use of evolutionary patterns in protein annotationAngela 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... - ETAscape: analyzing protein networks to predict enzymatic function and substrates in CytoscapeBenjamin 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..AVAILABILITY: The ETA Network Plugin is available publicly for download at http://mammoth.bcm.tmc.edu/networks/... - Evolutionary trace-based peptides identify a novel asymmetric interaction that mediates oligomerization in nuclear receptorsPeili 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... - Separation of recombination and SOS response in Escherichia coli RecA suggests LexA interaction sitesAnbu 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... - Lysine 270 in the third intracellular domain of the oxytocin receptor is an important determinant for G alpha(q) coupling specificityMing 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... - Desmosterolosis-phenotypic and molecular characterization of a third case and review of the literatureChristian 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... - Structural clusters of evolutionary trace residues are statistically significant and common in proteinsSrinivasan 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... - Evolutionary traces of functional surfaces along G protein signaling pathwayOlivier 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