bioserver@tripod

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 thermodynamics. 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.
Download from SourceForge.net
http://meltdna.sourceforge.net

Peptide
Peptide is a project to develop an integrated software tool for Mass Spectroscopy analysis of peptides.
Download from SourceForge.net
http://peptide.sourceforge.net

PDBMAT
PDBMAT (PDB Manipulation Tool) is an integrated environment for analyzing and manipulating PDB files. PDBMAT includes different modules and freely available programs for hydrogen adding, hydrogen trimming, protein secondary structure prediction, hydrogen bond listing, file format conversion and extract required section.Many more utilities are under development.