Hi David, do you think that alphafold2 dis/order prediction is better than specific disorder predictors?
i.e. http://dis.embl.de <http://dis.embl.de/> , which we've used for construct design https://prdos.hgc.jp <https://prdos.hgc.jp/> , which I haven't really tried yet https://iupred2a.elte.hu <http://iupred2a.elte.hu/> (which a colleague here likes because it also tries to predict likelihood of protein interactions) Or perhaps it's just because you were going to run alphafold2 anyway? best wishes, Mark Mark J van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. +34 91 585 4616 (internal 432092) > On 4 Apr 2022, at 21:30, David Briggs <david.bri...@crick.ac.uk> wrote: > > Hi Scott, > > I've used AF2 order/disorder prediction (based up pLDDT score) to decided > upon construct boundaries. We turned a non-expressing construct into a > reasonably well expressing construct based on the AF2 prediction. > > It's part of my construct design process now. > > HTH, > > Dave > > -- > Dr David C. Briggs > Senior Laboratory Research Scientist > Signalling and Structural Biology Lab > The Francis Crick Institute > London, UK > == > about.me/david_briggs > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Scott Classen > <sclas...@lbl.gov> > Sent: Monday, April 4, 2022 8:06:38 PM > To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > Subject: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide > crystallization? > > > External Sender: Use caution. > > 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 > <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7C%7C103751dae7354cae203408da166e4c3d%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637846960235320373%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=nCktCLks%2FamL94hkPtR35IEak0gE608EjHuW3cPF6II%3D&reserved=0> > The Francis Crick Institute Limited is a registered charity in England and > Wales no. 1140062 and a company registered in England and Wales no. 06885462, > with its registered office at 1 Midland Road London NW1 1AT > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <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/
