Hello, ScanProsite almost does what you want, but since it only searches sequence databases, it has no notion of secondary structures and therefore cannot exclude motifs found in a secondary structure. https://prosite.expasy.org/scanprosite/
I don’t know of any tool that would search structures and not only sequences. But if your motif isn’t too short or simple, ScanProsite should return a small enough number of hits that you could then inspect structures (or AlphaFold models) manually. I hope this helps, Guillaume On 19 Oct 2021, at 20:43, Jan van Agthoven <[email protected]> wrote: Dear all, I apologize for the off-topic question. I’d like to search for a particular aa sequence motif inside the protein sequence data bank (Swiss-prot, Uniprot, etc…) with the following criteria: * It should not be inside a secondary structure. Does anyone know a program that could do that? Thanks, Jan ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
