Software

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 access the services online.

Structural Database of Allergenic Proteins

Investigations regarding sequence and structural determinants of allergenicity, allergens motifs, and database mining for the identification of potential allergens.

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.

Docking@UTMB

The Watowich lab has developed this web interface, to AutoDock Vina, for virtual docking trials. This server performs docking between a user-provided protein and either a user-provided ligand or several pre-compiled small molecule virtual libraries.

FANTOM

This is software for efficient molecular modeling of proteins in torsional angle space.

Flavitrack

This software 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.

GETAREA

GETAREA is a web interface to solvent accessible surface area calculations.

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.

M-Value

This site permits the prediction of m-values for osmolyte-induced protein folding and unfolding. The m-value is an experimentally determined quantity derived from the Linear Extrapolation Method, and is a measure of the osmolyte efficacy in folding or unfolding a protein. It is also a measure of the cooperativity of folding/unfolding in the presence of the osmolyte, and it arises from the free energy contributions of protein groups that either become exposed upon unfolding or buried upon folding the protein.

MASIA/DIAMOD

MASIA is a pattern search and analysis of multiple aligned sequences of proteins.

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.

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.

PCPMer

This is a software tool for automatic motif detections of a protein family and identifications of related family members in protein sequence databases.

PMB

PMB is more than a wrapper for the CNS program. It includes several improvements for refining crystal structures, particularly in the case of low resolution data.