Many research groups within the SCSB have developed software packages and web-based services of interest to the community. Please follow the links below to download the programs for your own use or to use these services.
Bioinformatics The Bioinformatics program at UTMB. Their special interest is in Computational Genomics and Proteomics, and the Analysis of Biomedical Information using state of the art computational methods. The site offers a variety of links to bioinformatics tools.
COREX BEST The Hilser lab provides public access to the COREX/BEST algorithm through a web-based resource. The COREX/BEST algorithm uses the high resolution structure of any protein (provided by the user) and generates a statistical thermodynamic ensemble.
PMB PMB is more than a wrapper for the CNS program. PMB includes several improvements for refining crystal structures, particularly in the case of low resolution data.
FANTOM This is software for efficient molecular modeling of proteins in torsional angle space.
GETAREA GETAREA is a web interface to solvent accessible surface area calculations
Structure Database of Allergens Investigations regarding sequence and structural determinants of allergenicity, allergens motifs, and database mining for the identification of potential allergens.
MORASS The MORASS program uses a full hybrid matrix eigenvalue/eigenvector solution to the Bloch equations to derive cross-relaxation rates and interproton distances. MORASS analyzed 2D NMR NOESY data from oligonucleotides and proteins to evaluate cross-relaxation rates from which interproton distances are obtained. These are output in a format suitable for use as distance constraints in molecular dynamics calculations. MORASS2.5 is the most current version available.
PCPMer This is a software tool for automatic motif detections of a protein family and identifications of related family members in protein sequence databases.
MASIA/DIAMOD MASIA is a pattern search and analysis of multiple aligned sequences of proteins.
InterProSurf InterProSurf is designed to predict the most likely sites on proteins to interact with other proteins, such as toxin elements, cell receptors and other proteins that make up virus capsids.
MPACK MPACK is a homology modeling package that integrates several packages from our group: PCPmer to identify conserved regions, EXDIS to extract angle and distance constraints, DIAMOD to generate protein models from geometric constraints, and FANTOM to optimize the protein geometry with the ECEPP force field.
Flavitrack contains over 475 complete genomic sequences from almost 40 different flaviviruses, as well as related information on known mutations and literature references. In addition, each sequence has been assigned a unique identifier, i.e., a "license plate", which summarizes its date and place of isolation, phenotype, and lethality. This enables us to run very large sequence alignments and interpret the data with regard to vector and symptom specificity within viral subclasses and strain evolution.