> On Dec 9, 2020, at 07:45, Harry Powell - CCP4BB > <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > ... GDT_TS (Global Distance Test - Total Score - you can look it up on > Wikipedia
Thanks, this is helpful. Wikipedia: “The primary GDT assessment uses only the alpha carbon atoms.” Then there’s GDT_sc that incorporates side chains in a soecific way, then GDC_all. References: Zemla A (2003). "LGA: A method for finding 3D similarities in protein structures". Nucleic Acids Research. 31(13): 3370–3374. doi:10.1093/nar/gkg571. PMC 168977. PMID 12824330. Keedy, D.A.; Williams, CJ; Headd, JJ; Arendall, WB; Chen, VB; Kapral, GJ; Gillespie, RA; Block, JN; Zemla, A; Richardson, DC; Richardson, JS (2009). "The other 90% of the protein: Assessment beyond the α-carbon for CASP8 template-based and high-accuracy models". Proteins. 77 (Suppl 9): 29–49. doi:10.1002/prot.22551. PMC 2877634. PMID 19731372. Modi V, Xu QF, Adhikari S, Dunbrack RL (2016). "Assessment of template‐based modeling of protein structure in CASP11". Proteins. 84: 200–220. doi:10.1002/prot.25049. PMC 5030193. PMID 27081927. ............................... The “C-alpha-IDDT” cited in the AlphaFold abstract was published in 2013: Mariani et. al., Bioinformatics, 29(21), 2722-2728, 2013 The top scores increased after 2013. -Bryan W. Lepore ######################################################################## 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/
