Hi I think the fastest solution to your problem might be restricting the region of the complete protein structure from AlphaFold you use for the alignment. Perhaps selecting just your domain of interest, or maybe a slightly wider region maybe including a linker will do the trick.
I suspect the structure of this BH3 domain might be so simple (Is it just a single alpha-helix?) that it's to easy for structural alignment software to find that motif in other parts of the protein. How to do this and whether it's an appropriate approach depends on what software you're using and what question you're trying to answer Hope this helps Aderik ________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Thripthi Shenoy <[email protected]> Sent: Wednesday, February 11, 2026 5:27 AM To: [email protected] <[email protected]> Subject: [ccp4bb] Query regarding the structure-based sequence alignment CAUTION: This email originated outside of the University. Do not click links unless you can verify the source of this email and know the content is safe. Check sender address, hover over URLs, and don't open suspicious email attachments. Greetings to all, I am currently working on understanding the structure-based sequence alignment of the crystal structure of NOXA BH3 domain and the complete protein structure obtained from AlphaFold. According to my understanding, the BH3 binding domain from the crystal structure should get aligned with the BH3 domain in the entire protein structure. However, this is not the case and the identical amino acids of the BH3 domains are not getting aligned. I would be grateful to know if this is a correct approach to proceed with the structure based protein alignment. Thanking you in advance With regards, Thripthi S. ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## 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/
