3D structure for proteins

Question

[sa1987]

hi

i have a set of protein names.i want to now if they have structure or not..the list is very long so i want to submit it in one go and find out.

can anyone help me out

Answer 1

[LLTommy]

Well I am sure they all do have a structure, the question is rather if we know the exact 3d structure ;) So. Check out PDBe (https://www.ebi.ac.uk/pdbe/) if you don't know it already, that might be a great resource to start. I never used their API but they have one, so with some scripting you might be able to check your data in 'one go'.

[sa1987]

thank you ..i l try with it

Answer 2

[Elisabeth Gasteiger]

What do your "protein names" look like? If you have UniProt accession numbers or gene names, you can use the UniProt IDmapping tool at http://www.uniprot.org/uploadlists to map your identifiers or gene names to PDB.

Please don't hesitate to contact the UniProt helpdesk if you have any UniProt-specific questions.

Answer 3

[fishgolden]

If you have NCBI sequence identifier or can retrieve amino acid sequences from the name of proteins, you can use blastp in NCBI website. https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome Select "Protein Data Bank protein" at the "Database" section. It can process multiple sequences at once (but might have some limitation).