Download Comparing protein structure and sequence similarities

Comparing protein structure and
sequence similarities
Sumi Singh
Sp 2015
Learning goals
• To get a good understanding of vector space
model.
• To be able to compute similarity between
documents.
• To be able to rank the output documents based
on their similarity to query document.
Dataset
• Proteins are made up of amino acid sequences of
various lengths. The average length being 300
amino acid long. There are total 20 possible
amino acids.
• The representation of proteins is in a specific
format called PDB format (discussed later).
• PDB stands for protein database and is very large
online repository of proteins.
Protein Data Bank (PDB)
•
Protein Data Bank (PDB) is a large online database that keeps various information
on proteins including sequence information.
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Web address: http://www.rcsb.org/pdb/home/home.do
PDB ID: A 4-character PDB ID is assigned to each new structure at the time of
deposition. The IDs are automatically assigned and do not have meaning. However,
they serve as the unique, immutable identifier of each entry in the Protein Data
Bank. As such, they are used throughout the scientific literature (e.g. in journal
articles and in other databases) to refer to entries in the Protein Data Bank. Hence,
if the PDB ID of an entry in the Protein Data Bank is known, it is the most direct
way to retrieve it from the database.
How to get protein file using PDB id? Go to the link below for access details
http://www.rcsb.org/pdb/static.do?p=download/http/index.html
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Use the link below with wget to get the uncompressed PDB file for a given
protein
http://www.rcsb.org/ pdb/files/xxxx.pdb
Where xxxx is the 4 character PDB id of a protein.
What to extract
• Protein is made up of amino acids. There are
ONLY 20 possible amino acids.
• These amino acids are represented by their
three letter abbreviation.
• To get the sequence information of a protein,
you need to extract the amino acid from the
PDB file for each protein.
Sequence information-How to extract
• For each PDB file corresponding to a given
protein, get all the amino acid THREE letter
codes from column 18-20 that satisfy the
following criteria:
– The record name is ATOM (column 1-6)
– The atom name if CA ( column 13-16)
• There will be several repeating amino acids
How to use the extracted information
• Save the extracted sequence in a sequence
repository, to ensure availability for future
matches.
• Use vector space model to represent each protein
with features as amino acid.
• Use a distance/similarity measure to calculate the
similarity of an unknown protein with the proteins
stored locally.
Requirements of submission
• A GUI that gives user option to enter a PDB ID.
• Checks if the sequence of protein with that ID is in the local
directory/repository.
• If not get the PDB file for that protein from the online
database and extract the sequence information, save it.
• Perform the pair wise similarity calculation with the rest of
the proteins in the local repository.
• Display ranked output with respect to similarity.
References
• Vector space model:
http://nlp.stanford.edu/IR-book/pdf/06vect.pdf
• Distance measure:
http://nlp.stanford.edu/IR-book/pdf/07system.pdf
• PDB format:
http://www.wwpdb.org/documentation/fileformat/format33/v3.3.html
• Contact:
[email protected]