I would say that in a small survey (~5-6) of bacterial enzymes from our lab, AlphaFold2 predicted exactly the constructs that were discovered by limited proteolysis and/or sequence alignment for currently unpublished structures.
It’s a useful tool but I’ve also had two cases where it incorrectly predicted the sequences of helices in a helical bundle—frameshift errors in the sequence, which were confirmed by SeMet SAD data. Caveat emptor. Diana ************************************************** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu<mailto:diana.tomch...@utsouthwestern.edu> (214) 645-6383 (phone) (214) 645-6353 (fax) On Apr 4, 2022, at 2:06 PM, Scott Classen <sclas...@lbl.gov<mailto:sclas...@lbl.gov>> wrote: EXTERNAL MAIL Hello CCP4, Has anyone successfully used the available ML/AI protein folding tools to guide crystallization construct design? Maybe you had a protein or domain that was resistant to crystallization efforts and the folding algorithms predicted some loops or termini that were disordered? Then you trimmed or modified them in some way to aid in crystallization? Or if you haven’t done this yourself, are you aware of anyone who has? Thanks, Scott ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. ALS-ENABLE TomAlberTron Beamline 8.3.1 SIBYLS Beamline 12.3.1 Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 mobile 510.206.4418 desk 510.495.2697 beamline 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying. ________________________________ UT Southwestern Medical Center The future of medicine, today. ######################################################################## 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/
