Victor Wong

Under Construction

Summer Intern

Victor is currently a student at The University of Pennsylvania who is interning in the Hoatlin lab during the summer of 2006. He enjoys table tennis, go cart racing, miniature golf and other miniaturized sports.

Building a Protein Model

Searching for Sequence Homologs

1. Acquire sequence for the protein that you want to model (target sequence)
2. Go to NCBI BLAST
3. Click on position-specific iterated and pattern-hit initiated BLAST (PSI- and PHI-BLAST)
4. Enter your target sequence into the box labelled Search
5. Change the database to "swissprot" in the Choose Database box
6. Hit BLAST!
7. Hit Format!
8. Run PSI-BLAST iteration 3 or 4 times.
9. Save sequences with high identity percentages
   • Save as either a FASTA file or copy and paste each sequence into MacVector

Note: If you already know which homologs you are using and have the accession codes, it is possible to find the sequences at PubMed.

Searching for a Template Sequence

1. Go to NCBI BLAST
2. Click on position-specific iterated and pattern-hit initiated BLAST (PSI- and PHI-BLAST)

Aligning Homolog Sequences

MacVector

1. Open all sequences
2. Open Analyze and then click on ClustalW alignment
3. Save Alignment as a FASTA file

ClustalW

1. Paste all of your sequences into one FASTA file
2. Select an online alignment program (CLUSTALW or TCoffee) depending on the number of sequences you are using and the total length of the sequences
3. Upload your alignment

Submitting Your Alignments

1. Go to Swiss-Model
2. Click on Alignment Interface
3. Set Alignment Input Format as ClustalW
4. Upload or Paste your file
5. Choose your Target and Template Sequence

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