Software for distribution:

EDock-ML (Ensemble Docking with Machine Learning)

SRmapper: for aligning short reads from next-generation sequencing experiments to referenece genomes (Paul M. Gontaz, Jennifer Berger, and Chung F. Wong)

Version 0.1.5

Version 0.1.2 (Version used in the publication "SRmapper: A Fast and Sensitive Genome-Hashing Alignment Tool", Bioinformatics, 29 (2013) 316.)

ECEP2D: for simulating 1-D and 2-D gel electrophoresis of a protein after digestion by one or more enzymes (Howard Mayes and Chung F. Wong)

Version 0.1.2 (Test sequence files for teaching purposes: XP_023009855.2.fasta XP_024541079.fasta) (Video demonstration)

Other software:

    UHBD/SIESTA: coupling between the University of Houston Brownian Dynamics program (UHBD) and the quantum mechanical code SIESTA. (Mingliang Wang and Chung F. Wong)
    BDI: Brownian dynamics simulation of ions surrounding biomolecules. (Wenbin Yu, David Cerutti, Chung F. Wong, John Zhang, and J. Andrew McCammon)
    Helicity: predicting helical segments in proteins by using the helix-coil transition theory with knowledge-based potentials. (Gauri Misra and Chung F. Wong)
    GROMOS87 extension to perform molecular sensitivity analysis and to simulate energy flow in proteins. (Chung F. Wong, Qiang Wang, and Herschel Rabitz)
    RXN1D/VEDA: Extension of the RXN1D code developed in Professor John C. Light's laboratory to study the vibrational excitation and dissociation attachment of triatomic molecules upon electron impact (Chung F. Wong and John C. Light)
    VEDA: Simulate the vibrational excitation and dissociation attachment of diatomic molecules upon electron impact by using the R-matrix propagation method (Chung F. Wong and John C. Light)