Braun Research Lab · UTMB

Software & Tools

Bioinformatics software and web servers developed by the Braun Research Lab for structural biology, allergen analysis, and epitope prediction.

Software tools

MPACK

A homology modeling package integrating PCPMer (conserved region identification), EXDIS (angle/distance constraints), DIAMOD (protein model generation), and FANTOM (geometry optimization with ECEPP force field).

SDAP

Web server integrating a database of allergenic proteins with bioinformatics tools for structural studies related to allergens and characterization of their epitopes. Covers sequences, 3D structures, and IgE epitopes of over 900 allergens.

FANTOM

Energy refinement and Monte Carlo simulations of proteins in torsional angle space. Used for efficient optimization of protein geometry.

GETAREA

Web interface for solvent accessible surface area calculations for macromolecules. Based on the algorithm of Fraczkiewicz & Braun (J. Comp. Chem. 19, 319–333, 1998).

MASIA/DIAMOD

An expert system combining Self-Correcting Distance Geometry calculations with a pattern recognition algorithm to model 3D structures of proteins. Contributors: Catherine H. Schein, Werner Braun.

NOAH

Structure-based automatic assignment of multidimensional NOESY spectra for NMR structure determination.

PCPMer

Automatic motif detection in protein families and identification of related family members. Available for download: pcpmer-3.5.6.tar.gz · Manual (PDF)

Install: tar -zxvf pcpmer-3.5.6.tar.gz && cd pcpmer-3.5.6 && ./configure && make

Flavitrack

Contains over 475 complete genomic sequences from almost 40 different flaviviruses, with information on known mutations and literature references. Each sequence has a unique identifier summarizing date/place of isolation, phenotype, and lethality.

InterProSurf

Predicts the most likely sites on proteins to interact with other proteins, including toxin elements, cell receptors, and proteins forming virus capsids.

EpiSearch

Maps conformational epitopes on a protein surface using phage display peptide sequences as input.

AllergenPred

CNN-based web server to predict the allergenic potential of a protein from its FASTA sequence. Score >50 = allergenic.

Cross-React

Structural bioinformatics method for predicting allergen cross-reactivity using 3D conformational epitope information.