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PSI in the Spotlight

May 2012

SBKB [doi:10.1038/sbkb.2011.80]

PSI solves first structure for 1000th Pfam family

Protein Structure Initiative (PSI) centers, which developed technologies for high throughput protein structure determination have, from very beginning of the PSI specifically targeted novel and uncharacterized proteins. In 2005 the structural coverage of protein families was officially adopted as one of PSI goals and the four PSI production centers (JCSG, MCSG, NESG and NYSG(X)RC) jointly selected a group of structurally uncharacterized PFAM families to target them for structure determination. Between these two overlapping goals, PSI centers solved first structures for over 1000 protein families, i.e. 18% of all families with at least one structurally characterized member, far exceeding the PSI overall contributions to the PDB, which constitute about 6% of all structures. This statistic includes families characterized by structural biology even before PSI existence, so counting only families characterized structurally after PSI was established in 2000, PSI centers contributed 25% of all first representatives (while contributing 8% of all structures solved during that time). Since PSI centers entered a full production mode and specifically started to target novel protein families in 2005, this percentage increased to 34% (with 10% overall contributions). PSI contribution is especially significant in characterizing protein families with unknown functions (DUFs), with PSI characterizing 70% of such families.

Highlights of PSI characterized PFAM families:

  • PSI is characterizing large and very large families: 9 families of over 10,000 members , 292 over 1000 and 900 over 100 (protein counts according to the PFAM server)
  • PSI centers doesn't target only bacterial families: 588 families characterized by PSI are present in eukaryotic genomes and 60 are present only in eukaryotic or archaeal genomes; 315 families present in all kingdoms of life (central machinery of life)
  • bacterial families targeted by PSI have broad distribution and, even if indirectly, are relevant for human biology: 213 families are part of the core human microbiome (present in all gut metagenome samples)

The milestone of 1000 structures was achieved on 2/22/2011 by deposition of the ChbC transporter (3qnq) by the NYCOMPS center. As of 4/12/2012, the number of families characterized by PSI centers stands at 1026.For more information, please contact Adam Godzik at JCSG.

Save the Date — PSI:Biology Enabling Technologies Workshop is back for 2012

Back by popular demand, the PSI:Biology Program will hold the next installment of the “Enabling Technologies” Workshop, presenting the latest technologies and ideas to surpass experimental bottlenecks to protein production and structure determination. This one-day workshop will be held on December 12, 2012 in the Building 49 Auditorium at the NIH campus, Bethesda, MD, USA.

Check back with the SBKB for the latest information on program details, website, abstract submission, and registration.

TargetDB and PepcDB retired

TargetDB and PepcDB, the SBKB's experimental data tracking resources, were retired on April 2, 2012. All legacy data, new contributions, and most of the functionalities can be found at the new TargetTrack database at http://sbkb.org/tt/. Please contact the TT staff at target-help@sbkb.org immediately if you require help.

Updates to the SBKB

Current data totals as of 16 April 2012:

 

  • 19 M rows of annotations in SBKB database about 80041 PDB structures and 295,791 SG structure determination targets in TargetTrack .
  • 22.7 M comparative protein models for 3.7 million UniProt sequences in Protein Model Portal .
  • 1015 experimental protocols referenced in TargetTrack .
  • 274 technology reports in the Tech Portal .
  • 1,697 PSI publications in the Pubs Portal , with 1164 of them having >5 citations.

 

Coming to a Conference Near You

The PSI SBKB regularly attends national and international scientific conferences to talk about the PSI and the SBKB portal with the greater biological community. Meet PSI, SBKB, and PSI:Biology-Materials Repository representatives at our posters and booths at these upcoming conferences:

Experimental Biology 2012
April 21, 2012 - April 25, 2012
San Diego, CA, USA

42nd Mid-Atlantic Macromolecular Crystallography Meeting
May 31, 2012 - June 2, 2012
Charlottesvile, VA, USA

Margaret Gabanyi

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