More Related Content
Similar to Homology modeling of proteins (ppt)
Homology modeling of proteins (ppt)
- 1.
- 2.
- 3.
- 4.
- 5. Why? Goal Characterize and identifythe large number of protein sequences that are being discovered. 3D structure Design of drugs, design of site- directed mutations, to understand how proteins function and interact with each other. Experimental structure Developing a structural model for a protein for which there is no solved experimental structure available. Homology modeling 3D structure of a target protein based on the similarity between template and target sequences. Predicts the 3D structure of a protein through the sequence alignment of template proteins. Significance To studying membrane proteins that are hard to crystallize like GPCR as it provides a higher degree of understanding of receptor- ligand interaction.
- 6. What is HomologyModeling?
- 7. Accuracy and Applicationof Protein Structure
- 8. Does the sequencesimilarity implies structural similarity?
- 9.
- 10. Structure prediction by Homology Modeling Identify related structures Selecttemplate Align target sequence with template sequence Build a model for the target (Using information from the template structures) Evaluate the Model Model OK? END YES NO
- 11. Homology Modeling Steps YES 1. • Templaterecognition and initial alignment 2. • Alignment correction 3. • Backbone generation 4. • Loop modeling 5. • Side-chain modeling 6. • Model optimization 7. • Model validation
- 12.
- 13.
- 14. To obtain thelist of hits-the modeling templates & corresponding alignments COMPARES QUERY SEQUENCE TO ALL THE SEQUENCES OF KNOWN STRUCTURES IN PDB USING TWO MATRICES: A RESIDUE EXCHANGE MATRIX, AN ALIGNMENT MATRIX.
- 15.
- 17.
- 18. 4. Loop optimization Thered loop is modeled with the green residues as anchor residues. The insertion of 2 residues results in a longer loop.
- 19.
- 20.
- 21.
- 22.
- 23.
- 24.
- 25. References • Insight IImanual http://www.csc.fi/chem/progs/insightII.phtml.en#manual • Structural Bioinformatics, Philip E Bourne, Helge Weissig • Bioinformatics Sequence and Genome Analysis, David W Mount http://ncisgi.ncifcrf.gov/~ravichas/HomMod/ http://www.biochem.vt.edu/modeling/homology.html http://www.cmbi.kun.nl/gv/articles/text/gambling0.html
- 26.
- 27.
Editor's Notes
- #9 % of sequence identity vs alignment length
- #21 MD SIMULATION
- #28 [email protected]