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Author Topic: comparing similarity search tools  (Read 1993 times)

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comparing similarity search tools
« on: July 03, 2018, 07:20:40 PM »

Hi all
I'm trying to learn about similarity search for drug design and I'm very confused ???
What is the differences btw some similarity search such as BLAST, FASTA and Smith-Waterman Process with chemspider, CHEMBL, PDB and Drug bank?
Is the first group for just receptor (I have seen that they are in homology search, for example for unknown genes) and the second for organic compounds such as drugs or nondrugs compounds which can sit on the active site of receptor?


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Re: comparing similarity search tools
« Reply #1 on: July 03, 2018, 08:06:40 PM »

I'm reasonably sure BLAST and FASTA are for looking up protein and nucleic acid sequences, not drug compounds. The Smith-Waterman process is an algorithm used for genetic similarity searches. PDB is a protein database.

ChEMBL is a database that you can use to look up drugs based on their target, or chemical structure. I haven't used ChemSpider or Drug Bank, though I believe the latter serves a similar function to ChEMBL.

Most of these also have Wikipedia pages, which you should probably look up for more information about them.

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