Abhishek Tiwari:Softwares
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Developed Softwares/Tools/Programs
HBAT(Hydrogen Bond Analysis Tool)
The program HBAT, is a tool to automate the analysis of potential hydrogen bonds and similar type of weak interactions like halogen bonds and non-canonical pi interactions in macromolecular structures, available in Brookhaven Protein Database (PDB) file format. HBAT is written using PERL and TK languages. The program generates an MSOFFICE Excel compatible output file for statistical analysis. HBAT identify potential interactions based on geometrical criteria. A series of analysis reports like frequency tables, geometry distribution tables, furcations list are generated. A user friendly GUI offers freedom to select several parameters and options. Graphviz based visualization of hydrogen bond networks in 2D helps to study the cooperativity and anticooperativity geometry in hydrogen bond. HBAT supports post docking interaction analysis between PDB files for any target/receptor (in PDB files) and docked ligands/poses (in SDF). This tool can be implemented in active site interaction analysis, structure based drug design and molecular dynamics simulations.
Availability http://202.41.85.161/~grd/HBAT.html or http://sourceforge.net/projects/hbat
MeltDNA
Prediction of DNA duplex stability and thermodynamics is invaluable for many molecular biology applications involving sequence dependent hybridization reactions. Sequence dependent stability of duplex DNA plays a major role in fundamental processes of the living cell, such as replication, transcription, and recombination. Many techniques in molecular biology depend on the oligonucleotide melting temperature (Tm), and several formulas have been developed to estimate Tm. We have developed a Perl based tool to predict DNA duplex hybridization & melting thermo- dynamics. This tool consider all factors those determine thermodynamic values like-Base composition,NN parameters, salt dependency (Na+, Mg++), internal mismatch, dangling ends ,loops etc. For improve NN model based calculations we introduced fusion matrices. MeltDNA provides better prediction accuracy for DNA duplex hybridization especially its ability to handle the structural features in DNA duplex like loops, loop size etc. It has got wide applicability in primer selection in PCR, probe selection in Microarrays, DNA secondary structure stability prediction, DNA computing etc.
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/
Java Molecular Descriptor Library (JMDL)
More than 500 molecular descriptors including logP from different method (AlogP, BlogP, KlogP, MlogP, XlogP and others) can be calculated using JMDL which is coded in Java.
Availability Currently under development
Open Source Links
- SourceForge.net http://sourceforge.net/
- GNU http://www.gnu.org/
- The Free Software Foundation http://www.fsf.org/
- Open Source Initiative (OSI) http://www.opensource.org/
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