Timeline for Get protein names corresponding to PDB ID
Current License: CC BY-SA 4.0
11 events
| when toggle format | what | by | license | comment | |
|---|---|---|---|---|---|
| Nov 5, 2020 at 12:52 | vote | accept | David | ||
| Nov 4, 2020 at 16:41 | answer | added | Mr_Z | timeline score: 5 | |
| Oct 31, 2020 at 18:35 | comment | added | David | @MatteoFerla Thanks. Will check that out. | |
| Oct 31, 2020 at 17:48 | comment | added | Matteo Ferla | In which case, going from PDB to Uniprot using SIFTS https://www.ebi.ac.uk/pdbe/docs/sifts/quick.html is the best bet as the Uniprot entries will have all the synonyms you could have for. | |
| Oct 31, 2020 at 16:11 | answer | added | fra | timeline score: 2 | |
| Oct 31, 2020 at 15:40 | comment | added | David | @marcin — Thanks, but the problem with the HEADER and COMPOUND fields is that they are such utter unparsable anarchy. I could write a script to get these fields from all my pdb files, but take for example 102L — I would get as HEADER "HYDROLASE(O-GLYCOSYL)" (useless) and as COMPOUND "HOW AMINO-ACID INSERTIONS ARE ALLOWED IN AN ALPHA-HELIX OF T4 LYSOZYME ENTEROBACTERIA PHAGE T4" where the name of the protein — Lysozyme — is buried. The prehistoric format of pdb files is the problem, but surely someone, somewhere has done something with them. | |
| Oct 31, 2020 at 15:34 | comment | added | David | @Michael — Could you clarify please. A script tTo do what on what? And why in PyMol? | |
| Oct 31, 2020 at 13:20 | comment | added | marcin | Perhaps you could use ftp.wwpdb.org/pub/pdb/derived_data/index/entries.idx which contains HEADER and COMPOUND fields extracted from all PDB entries. | |
| Oct 31, 2020 at 13:08 | comment | added | M__♦ | Have you tried writing a PyMol script? | |
| Oct 31, 2020 at 12:03 | review | First posts | |||
| Oct 31, 2020 at 13:08 | |||||
| Oct 31, 2020 at 12:01 | history | asked | David | CC BY-SA 4.0 |