I want to design peptide from group a group of aligned sequences targeting a specific viral region of human. What will be my approach, I need step by step guide so that in each step I can overcome the hurdles through in silico approach. Further these candidate will be synthesized and will be tested in vivo in animal models.
Thanking you.
Use Pymol or Coot for peptide design. Use builder tool in pymol to design peptides of your interest.
Better approach would be :
Your guide/head of institution writes to a director of the lab or scientist expert in peptide chemistry(as revealed in literature search) for training/collaboration in the synthesis of the desired peptides.
Also please see the link
WBW rks
Article In Silico Models for Designing and Discovering Novel Antican...
Dear Prof. Ravi K. Sharma,
Thank you so much for your valuable input. Its indeed require a good chemist to do synthesize peptide.
Thanks a lot.
Though delayed, I hope this helps.
Based on our experience of designing a candidate peptide vaccine against Japanese encephalitis virus, I would like to suggest following workflow.
Predict B-cell and T-cell epitopes of the antigenic protein/s of the virus. There are several tools available for prediction of both, B- and T-cell epitopes. Carry out MSA of antigenic protein using sequences of various isolates, sero/genotypes of the same virus. You may also consider a separate MSA of the said protein of antigenically similar viruses. Map predicted epitopes on the MSA. Take sequence variation and conservation in to account to select and prioritize candidate peptides. If 3D structure of the protein is known, you may map the predicted epitopes on the structure to check if the epitope is present on the surface as the most of the neutralising epitopes are observed to be present on the surface of the protein. You may build and model structure of the peptide(s) in silico. Based on the in silico analysis get the peptides synthesized and validate them experimentally. Please note that being flexible, the 3D structure of the peptide may vary from the conformation of the same peptide when it is part of the antigenic protein.
You can consider these articles
http://www.sciencedirect.com/science/article/pii/S1567134810002947
http://www.sciencedirect.com/science/article/pii/S0264410X0901442X
Hope will help you a lot!
Dear Urmila Kulkarni-Kale Madam,
Thank you much for your valuable suggestion. I have followed your guideline and successfully designed and now validation is underway in our laboratory.
Dear Dr. Budheswar,
Thank you very much for this wonderful update. I am very happy to know that my suggestions helped you to design peptide/s. I am eager to know outcome of experimental validation and shall be happy to help you further, if needed.
If this works and if you publish it, Research Gate deserves acknowledgements.
All the best...!
Thank you much mam for your encouraging words. Once the results come out I will let you know...
Thanking you.
With Warm Regards
Budheswar
this resource may help a lot in your peptide based drug designing and therapeutics
SATPdb: A database of structurally annotated therapeutic peptides.
http://crdd.osdd.net/raghava/satpdb/
paper link
http://nar.oxfordjournals.org/content/early/2015/11/01/nar.gkv1114.full
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology