Project titles for:
Project titles for: 2007-09
- Comparison of software for Analysis of Molecular Marker Data
- In silico Prediction of miRNA in Rice Genome
- Web Tools for Bioinformatics
- In silico Structure Prediction of enzyme Arsenite methyltransferase
- Comparison of various software for QTL Analysis
- QSAR studies of Tuberculosis Inhibitors
- Determination of common transcription factor binding site in promoter region of abiotic stress resistance gene in rice
- SNP Mining in Rice Genome
- Protein Modelling of Betaine Aldehyde Dehydrogenase-2 in Rice
- Data Mining of Chemical Substructures for Biological Efficacy
- Plant Disease Database mined from PubMed
- Comparison of Protein Structure Prediction Methods
- Virtual High Throughput Screening for Influenza Virus Inhibitors
- Combinatorial Libraries for Screening against Tuberculosis Inhibitors
Arsenic Methyltransferase (EC 2.1.1.137) is an enzyme responsible for the di- and tri-methylation of the inorganic arsenic. As arsenic is very toxic to the body so its removal is very necessary. This enzyme is found to be taking part in arsenic removal from the body but the structure of the enzyme is not known, so the proper mechanism of the arsenic removal is still not understood properly. The peptide sequence of Arsenite Methyltransferase with sequence id Q9HBK9 was obtained from SWISSPROT sequence database. Low complexity regions were masked as it is a eukaryotic protein. The structural features of protein like helices, sheets, loops and putative domain boundaries were predicted using PSIPRED, DOMPRED and DOMAIN3D servers. The sequence was submitted to HMM based fully automated server SAM-T08 which returned five models, one final model and four intermediate models. Final model was first of all checked for sequence identity with target sequence it was found to be 100% similar with target sequence. This assured that the server had not made any alteration in our target sequence. After that, secondary structural features of the model were compared with that of predicted features by PSI-PRED server. The model was found to have around 95% amino acids present in the same region. Model was also found to have hydrophobic and hydrophilic amino acid distributed biologically. Model was verified using various verification servers. Model was having good Ramachandran statistics and coarse packing. Model was having nearly all its bond angles and bond length accurate and deviated normally from standard conditions. When possible domains were detected using Domain 3D server then model was found to have same number (2 domains) of 31 domains as was predicted in target sequence by DOMPRED server. Model was searched against Protein Data Bank using DALI and MAMMOTH servers. The servers fetched the most of methyltransferases in top results with minimum RMSD. That was a good poof of models accurate prediction. Also ProFunc server had predicted function of model as methyltransferase. Finally model was refined using chimera program and “complete a structure” program from WHAT IF server. This serer has corrected all missing side chains of model. The hydrogen bonds and water molecules were added using chimera by preparing a file for docking.