Software from Our Group

  • 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.
  • SDAP is a Web server that integrates a database of allergenic proteins with various bioinformatics and computational tools to perform structural studies related to allergens and characterization of their epitopes.
  • FANTOM (Energy refinement and Monte Carlo simulations of proteins).
  • GETAREA (Web interface to solvent accessible surface area calculations).
  • MASIA (Pattern search and analysis in multiple aligned sequences of proteins).
  • DIAMOD (Self-correcting distance geometry calculations of protein and DNA structures).
  • NOAH (Structure-based automatic assignment of multidimensional NOESY spectra).
  • PCPMer is a software tool for automatic motif detections of a protein family and identification of related family members in protein sequence database base. Both PCPMer software and manual are available for download.

    PCPMer download link : pcpmer-3.5.6.tar.gz
    PCPMer manual download link : PCPMer_guide.pdf


    1. Please download pcpmer-3.5.6.tar.gz software and unzip it using following command

    tar -zxvf pcpmer-3.5.6.tar.gz

    This will create a pcpmer-3.5.6 directory. Change dir to pcpmer-3.5.6 using command cd pcpmer-3.5.6

    Inorder to compile the software, please use following command


    This will compile and install PCPMer. For more information please refer to PCPMer manual.

  • 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.
  • 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.
  • EpiSearch is designed to map conformational epitopes on a protein surface.  Please check back soon.  The link to this program will be updated once the corresponding manuscript has been published.