Abhishek Tiwari:Softwares

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Developed Softwares/Tools/Programs

HBAT(Hydrogen Bond Analysis Tool)

HBAT is a tool to automate the analysis of strong and weak hydrogen bonds present in a PDB file. This tool can be implemented in active site interaction analysis, structure based drug design and molecular dynamics simulations. HBAT is written using PERL and TK languages. It is a user-friendly desktop tool, which offers the user freedom to select several parameters. The program generates an MSOFFICE Excel compatible output file for statistical analysis, provides distance-angle distributions across various geometry ranges while tabulation of frequencies for each residue, ligand, water, and also nucleic acids can be done easily for any kind of interaction. Cooperativity in hydrogen bond geometry can also be studied in a defined region of the structure. HBAT could prove to be highly useful in structure based drug design especially for analysing intermolecular interactions in docking and dynamics studies.


Availability http://202.41.85.161/~grd/HBAT.html


MeltDNA

Availability http://meltdna.sourceforge.net/


Project Peptide

Project Peptide has developed fallowing tools

   * PDBMAT (PDB Manipulation Tool)
   * PMSAT (Peptide MS Analysis Tool)
   * HBNGraph (Hydrogen Bond Network Graph)

HBNGraph is a Peptide sub-project to develop Graph Theory based tools to visualize Hydrogen Bonding Networks along with cooperativity and anti -cooperativity. HBNGraph includes DOT language scripting utility for AT&T Graphviz(dot/dotty) Framework based visualization.

PMSAT is a Peptide sub-project to develop an integrated software tool for Mass Spectroscopy analysis of peptides. PMSAT-Peptide MS Analysis Tool determines the peptide composition for the query mass and also generates fragmentation pattern for Peptide Sequence. It finds utility in checking whether the denovo sequence established accurately matches the values obtained from the mass spectra. This software determines the likely amino acid composition and not the sequence. It will also find

   *Peptide masses from enzymatic digestion of protein
   *AA compositions fitting parent or fragment mass and immonium ions
   *Isotope patterns of peptides

PDBMAT is a Peptide sub-project to develop a tool to manipulate PDB files like file format conversion, hydrogen adding & removing and other utilities.

Availability http://peptide.sourceforge.net/

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