Project titles for:
Project titles for: 2008-10
- In silico analysis of Larger subunit of AGPase in Rice and Maize
- In silico Analysis of mutated in Larger subunit of AGPase in Maize
- Structural Comparison of Betaine Aldehyde Dehydrogenase-1 of Barley and Rice
- Analysis of Gene Expression Database of Skin Cancer
- Evaluation of Sequence Alignment Tools
- Phylogenetic analysis of Drb 3.2 gene
- Modelling of Smaller subunit of AGPase in Rice and Maize
- Prediction of Protein structure from sequence
- Development of Clinical Information Database of domestic animals
- To identify distant relationship between flavoprotein superfamily
- Promoters comparison in bacteria
- Transport protein features analysis
- Genome deciphering and comparative genomics of Solanaceous genome
- Computational approach in deciphering effect of gene alteration inArabidopsis Thaliana
- Simulation of conformational changes in protein
The objective of present work Comparative modeling or Homology modeling is considered the most reliable method to predict the 3-D structure of a protein. It is based on the assumption that homologous proteins share same structural organization, so that the known 3-D structure of a protein can be used as template to model the structure of an homologous protein. Modeling of side chains with accuracy should improve the recognition of protein-protein binding and the result of rigid- body docking. Model build by homology procedure is used to simulate the interaction with receptor. The best template to use is the conformation of the protein in the complex with receptor, but when the model is not available the unbound conformation can be used to create starting model. After the assembly of the complex the refinement of side chain followed by optimization procedure made the complex more similar to experimental ones in terms of conformations and protein receptor interaction. Results suggest a possible modeling procedure to apply when a model should be generated by using the unbound protein is template. Difference between unbound and bound protein conformations affects mainly the interface between protein and receptor and the bound conformation is better simulated with careful application of modeling and computational techniques.