Chemical Forums

Please login or register.

Login with username, password and session length

Sponsored links

Pages: [1]   Go Down

Author Topic: comparing similarity search tools  (Read 1472 times)

0 Members and 1 Guest are viewing this topic.

mana

  • Full Member
  • ****
  • Mole Snacks: +3/-2
  • Offline Offline
  • Posts: 112
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?
Logged

hypervalent_iodine

  • Chemist
  • Full Member
  • *
  • Mole Snacks: +21/-1
  • Offline Offline
  • Posts: 139
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.
Logged

Pages: [1]   Go Up
 

Mitch Andre Garcia's Chemical Forums 2003-Present.

Page created in 0.054 seconds with 23 queries.