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Proteomics Tools
This workshop focuses on computational techniques that allow for structure-function prediction, including: secondary structure analysis, topology prediction, functional domain identification, and protein-protein interaction prediction.
We will start with a protein sequence and learn how to:
- find genomic context of a protein sequence (UCSC BLAT, EBI Integr8)
- search for homologous sequences (NCBI Protein BLAST, EBI MPsrch)
- create a multiple sequence alignment (ClustalW, TCoffee, Vector NTI AlignX)
- search for presence of conserved domains (NCBI CDD, EBI InterProScan)
- analyze primary structure such as, hydrophobicity, hydrophylicity, antigenicity, repeat sequence detection etc. (ExPASy Primary structure analysis, Protein Lounge, Vector NTI BioAnnotator)
- predict secondary structure (ExPASy Secondary structure prediction)
- predict post translational modification such as phosphorylation, glycosylation, etc. (ExPASy Post-translational modification prediction)
- search for interacting partners (STRING, Protein Lounge)
- predict domain driven protein-protein interactions (Scansite)
Participants will learn how to answer questions like:
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How do I identify the protein encoded by the largest ORF in my sequence?
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Does my protein of interest have any conserved domains?
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How similar is my protein of interest to other proteins?
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How do I align a set of sequences?
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What is the predicted secondary structure of my protein of interest?
This class is approved for AMA Category 2 CME credit.
If you have questions, contact the HSLS Molecular Biology Information Service:
Class PowerPoint Presentation
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Wednesday, November 11
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1 p.m. - 3:30 p.m.
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(Falk Library, Classroom 2)
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Instructor: Ansuman Chattopadhyay, PhD
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