Difference between revisions of "CSC334 Lab10"
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* Connect to the Psipred system at [http://bioinf.cs.ucl.ac.uk/psipred/ bioinf.cs.ucl.ac.uk/psipred/] | * Connect to the Psipred system at [http://bioinf.cs.ucl.ac.uk/psipred/ bioinf.cs.ucl.ac.uk/psipred/] | ||
* Click on [http://bioinf.cs.ucl.ac.uk/psipred/psiform.html CLICK HERE TO ENTER THE SERVER] | * Click on [http://bioinf.cs.ucl.ac.uk/psipred/psiform.html CLICK HERE TO ENTER THE SERVER] | ||
| − | * Copy/Paste a protein sequence in FASTA format (without the first text line). Here we are using a sequence we obtained in [[CSC334_Lab9 | Lab #9]] | + | * Copy/Paste a protein sequence in FASTA format (without the first text line). Here we are using a sequence we obtained in [[CSC334_Lab9 | Lab #9]] for the E. Coli sequence reference AAF33488: |
MESTVDTELLKTFLEVSRTRHFGRAAEALYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTTAGEKLLP | MESTVDTELLKTFLEVSRTRHFGRAAEALYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTTAGEKLLP | ||
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LTTSSAELARQQLSALNGCSWLPVNWANEKGGLHTVADSATLSRPLYAIWLQNSDKYSLICDLLKTDVLD | LTTSSAELARQQLSALNGCSWLPVNWANEKGGLHTVADSATLSRPLYAIWLQNSDKYSLICDLLKTDVLD | ||
EQ | EQ | ||
| + | |||
| + | * Accept the defaults, enter your email address, then click on '''Predict''' | ||
| + | * Wait a while | ||
| + | * Wait some more | ||
Revision as of 14:21, 13 August 2008
<meta name="keywords" content="computer science, bioinformatics, DNA, CSC334, Lab" /> <meta name="description" content="DNA Sequence Logo Lab" /> <meta name="title" content="Bioinformatics Lab" /> <meta name="abstract" content="DNA Sequence Logo" /> <meta name="author" content="thiebaut at cs.smith.edu" />
Finding the Secondary Structure of a Protein
The page on Secondary Structures in Wikipedia defines it well:
- In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure.
- Secondary structure is formally defined by the hydrogen bonds of the biopolymer, as observed in an atomic-resolution structure. In proteins, the secondary structure is defined by patterns of hydrogen bonds between backbone amide and carboxyl groups (sidechain-mainchain and sidechain-sidechain hydrogen bonds are irrelevant), where the DSSP definition of a hydrogen bond is used. In nucleic acids, the secondary structure is defined by the hydrogen bonding between the nitrogenous bases.
Goal
In this lab we use the PSIPRED system to get the secondary structure of a protein.
Steps
- Connect to the Psipred system at bioinf.cs.ucl.ac.uk/psipred/
- Click on CLICK HERE TO ENTER THE SERVER
- Copy/Paste a protein sequence in FASTA format (without the first text line). Here we are using a sequence we obtained in Lab #9 for the E. Coli sequence reference AAF33488:
MESTVDTELLKTFLEVSRTRHFGRAAEALYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTTAGEKLLP YAETLMNTWQAARKEVAHTSRHNEFSIGASASLWECMLNAWLGRLYQLQEPQSGLQFEARIAQRQSLVKQ LHERQLDLLITTEAPKMDEFSSQLLGHFTLALYCSSPARKKSELNYLRLEWGPDFQQHETGLIAADEVPV LTTSSAELARQQLSALNGCSWLPVNWANEKGGLHTVADSATLSRPLYAIWLQNSDKYSLICDLLKTDVLD EQ
- Accept the defaults, enter your email address, then click on Predict
- Wait a while
- Wait some more
