Vicente M. Reyes

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S. cerevisae tRNA introns interrupt the gene at a constant position in the anticodon loop. Pre-tRNAs are matured by an endonuclease and a ligase. The endonuclease alone can accurately release the intron from the pre-tRNA. Here, we investigate the mechanism of splice site selection by the endonuclease. We propose that it initially recognizes features in the(More)
The ongoing global effort of genome sequencing is making large scale comparative proteomic analysis an intriguing task. The Encyclopedia of Life (EOL; http://eol.sdsc.edu) project aims to provide current functional and structural annotations for all available proteomes, a computational challenge never seen before in biology. Using an integrative genome(More)
We have developed an analytical, ligand-specific and scalable algorithm that detects a 'signature' of the 3D binding site of a given ligand in a protein 3D structure. The said signature is a 3D motif in the form of an irregular tetrahedron whose vertices represent the backbone or side-chain centroids of the amino acid residues at the binding site that(More)
Sheth, Vrunda, "Visualization of protein 3D structures in reduced representation with simultaneous display of intra and inter-molecular interactions" (2009). i This thesis is dedicated to my beloved family, to my parents for their never ending encouragement and confidence in me and to my sisters for their motivation and guidance. ii DISSERTATION AUTHOR(More)
We describe two complementary methods to quantify the degree of burial of ligand and/or ligand binding site (LBS) in a protein-ligand complex, namely, the 'cutting plane' (CP) and the 'tangent sphere' (TS) methods. To construct the CP and TS, two centroids are required: the protein molecular centroid (global centroid, GC), and the LBS centroid (local(More)
Due to increased activity in high-throughput structural genomics efforts around the globe, there has been a steady accumulation of experimentally solved protein 3D structures lacking functional annotation, thus creating a need for structure-based protein function assignment methods. Computational prediction of ligand binding sites (LBS) is a(More)
ii This thesis is dedicated to my beloved family, to my parents for their never-ending encouragement, love and confidence in me and to my brother for his motivation and guidance. iii ACKNOWLEDGEMENTS I feel it as a unique privilege, combined with immense happiness, to acknowledge the contributions and support of all the wonderful people who have been(More)
Three-dimensional objects can be represented using cartesian, spherical or cylindrical coordinate systems, among many others. Currently all protein 3D structures in the PDB are in cartesian coordinates. We wanted to explore the possibility that protein 3D structures, especially the globular type (spheroproteins), when represented in spherical coordinates(More)
Transformation of protein 3D structures from their all-atom representation (AAR) to the double-centroid reduced representation (DCRR) is a prerequisite to the implementation of both the tetrahedral three-dimensional search motif (3D SM) method for predicting specific ligand binding sites (LBS) in proteins, and the 3D interface search motif tetrahedral pair(More)