Re: [ccp4bb] looking for proteins with no homologues in pdb
You can download such proteins/sequences from the CASP website: https://predictioncenter.org/ At the JCSG, we participated for many years in the annual CASP competition, where we would use/hold our novel experimental crystal structures (before PDB deposition, almost all our ~1500 targets/PDB depositions had < 20% sequence identity to existing PDB entries, from novel Pfam/CATH) as tests by protein structure prediction/modeling groups around the world participating in CASP to try to predict before PDB release, thereby allowing a direct comparison with the prediction algorithm and the experimental structure. Best, Debanu -- Debanu Das On Mon, Jun 7, 2021 at 1:11 PM Scott Horowitz wrote: > For testing purposes, we want to solve structures of proteins that are not > in the PDB and have no significant sequence homologues in the PDB (i.e. a > blast of the pdb will get no significant hits). Does anyone happen know a > good way to find such proteins efficiently? Having an interesting function > isn't needed. > > Thanks, > Scott > > Scott Horowitz, Ph.D. > > Assistant Professor > > Department of Chemistry & Biochemistry > > Knoebel Institute for Healthy Aging > > University of Denver > > > > ECS Building > > 2155 E. Wesley Ave > > Denver, CO 80208 > > Phone: 303-871-4326 > > Fax: 303-871-7915 > > Zoom Room: https://udenver.zoom.us/my/scotthorowitz > > Email: scott.horow...@du.edu > > Office: Room 561 Lab: Room 505 > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] looking for proteins with no homologues in pdb
One short cut would be to focus on Pfam families that do not yet have a 3D representative. They can be browsed eg https://pfam.xfam.org/family/browse?browse=a or you can also install Pfam locally as MySQL for programmatic access. Choosing Families rather than Domains would make it easier to get proteins matching only a single Pfam entry If you wanted to be more stringent you could exclude any families that were in Clans that had a structural representative. Dan Prof Daniel Rigden (He/Him) Department of Biochemistry and Systems Biology Institute of Systems, Molecular and Integrative Biology Room 101, Biosciences Building University of Liverpool Crown St., Liverpool, L69 7ZB (+44) 151 795 4467 www.liverpool.ac.uk/integrative-biology/staff/daniel-rigden/ From: CCP4 bulletin board on behalf of Scott Horowitz Sent: 07 June 2021 21:00:42 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] looking for proteins with no homologues in pdb For testing purposes, we want to solve structures of proteins that are not in the PDB and have no significant sequence homologues in the PDB (i.e. a blast of the pdb will get no significant hits). Does anyone happen know a good way to find such proteins efficiently? Having an interesting function isn't needed. Thanks, Scott Scott Horowitz, Ph.D. Assistant Professor Department of Chemistry & Biochemistry Knoebel Institute for Healthy Aging University of Denver ECS Building 2155 E. Wesley Ave Denver, CO 80208 Phone: 303-871-4326 Fax: 303-871-7915 Zoom Room: https://udenver.zoom.us/my/scotthorowitz Email: scott.horow...@du.edu Office: Room 561 Lab: Room 505 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
[ccp4bb] looking for proteins with no homologues in pdb
For testing purposes, we want to solve structures of proteins that are not in the PDB and have no significant sequence homologues in the PDB (i.e. a blast of the pdb will get no significant hits). Does anyone happen know a good way to find such proteins efficiently? Having an interesting function isn't needed. Thanks, Scott Scott Horowitz, Ph.D. Assistant Professor Department of Chemistry & Biochemistry Knoebel Institute for Healthy Aging University of Denver ECS Building 2155 E. Wesley Ave Denver, CO 80208 Phone: 303-871-4326 Fax: 303-871-7915 Zoom Room: https://udenver.zoom.us/my/scotthorowitz Email: scott.horow...@du.edu Office: Room 561 Lab: Room 505 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
