Protein Secondary Structure, Bioinformatics Tools, and Multiple Sequence Alignments Finding Similar Sequences Predicting Secondary Structures Predicting.

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Presentation transcript:

Protein Secondary Structure, Bioinformatics Tools, and Multiple Sequence Alignments Finding Similar Sequences Predicting Secondary Structures Predicting Protein Folds (Tertiary Structures)

Tools for Identifying Protein Domains based only on Primary Sequence: PROSITE

What is the local sequence preference:  -helix or  -strand or random?

Tools for finding Similar Proteins: FASTA Also identifies reported crystal structures

Alternative Site: BLAST identifies Similar Proteins

Sequence Alignment Matrix Sequence A: VATTPDKSWLTV Sequence B: ASTPERASWLGTA VATTPDK-SWLTV- |*||** ||| -ASTPERASWLGTA score 39 VATTPDK-SWL-TV |*||** ||| |* -ASTPERASWLGTA score 45

Multiple Sequence Alignment Sequence A: LTLTLTLT Sequence B: HAHAHAHAH Sequence C: THTHTHTHT LTLTLTLT- HAHAHAHAH score -4 -LTLTLTLT HAHAHAHAH score 0 -LTLTLTLT- | | | | THTHTHTHT- | | | | -HAHAHAHAH The third sequence from a homologous protein allows alignment It’s a very good idea to have more than one template!

Multiple Sequence Alignment Can also display helices, beta-sheets; buried vs exposed; Look for a consensus of different methods, etc

Conclusions Bioinformatics Tools: Can be based on Statistical Analysis, or Scoring, or Physics Sequence matching is the realm of computer science more than chemistry/biochemistry Biochemistry/Chemistry is fundamental to 3D structure prediction