the goal of the worldwide structural genomics initiative is to determine the 3d structures of proteins on a genomic scale .
since 2001 , these efforts have resulted in more than 6772 structure depositions to the pdb ( 1 ) , 3251 of which are from the national institutes of health - sponsored protein structure initiative centers . in order to determine these structures in a high - throughput manner ,
the psi centers have developed advanced technologies to facilitate these processes , including protein production , crystallization , structure determination , refinement and analysis . the protein structure initiative structural genomics knowledgebase ( psi sgkb ) ( http://kb.psi-structuralgenomics.org )
was launched in early 2008 with the goal of making the results of the psi initiative widely available to the broad community of biologists ( 2 ) .
the psi sgkb provides access to the annotated protein structures , the models that can be leveraged from them , associated functional predictions , experimental protocols and tracking information .
the new resource integrates this structural information with relevant scientific information from external data resources in a coherent and contextual format .
the psi sgkb also provides the descriptions of a vast array of technologies , protein production protocols and software applications . by making all of these products accessible to the greater community
, it is anticipated that the psi sgkb will become an enabling resource for biologists , biochemists , functional genomicists , pharmacologists , educators and physicians .
the psi sgkb is a portal that provides integrated access to the psi centers , external biological databases , the pdb and a set of widely distributed resources , some of which are portals themselves .
these resources include : experimental data tracking : targetdb ( http://targetdb.rcsb.org ) ( 3 ) and pepcdb ( http://pepcdb.rcsb.org ) ( 4 ) were established to track the progress of targets that are being worked on by the worldwide structural genomics centers .
targetdb gives the status of each target and pepcdb provides information about the protocols used for protein production and the reasons for stopping work on any one target .
data are regularly collected , tracked and made available via the targetdb and pepcdb web sites .
pepcdb now provides access to the general protocols for the most successful experimental trial as well as any specific details associated with the trial .
cross - references are provided to the research collaboratory for structural biology ( rcsb ) pdb ( 5 ) , pfam ( 6 ) , superfamily ( 7 ) , tigr families ( 8) , prodom ( 9 ) , iproclass ( 10 ) and prosite ( 11 ) .
sequence family ( e.g. big and mega assignments ) and target classification details ( e.g. biomedical , community - nominated ) are now collected from psi centers .
as pepcdb grows , this resource will become an indispensable and truly unique resource for biologists who are expressing and purifying proteins for their own experiments .
materials repository : the psi materials repository ( psi mr ) ( http://www.hip.harvard.edu/psimr/index.htm ) has been established at harvard university .
these data include the information required to ensure the interoperability of this repository with targetdb and pepcdb .
the information collected for each psi clone will also be stored in a searchable database . using this database
, researchers will be able to select and order clones online for a minimal fee that covers processing , handling and shipping .
homology modeling : for every structure determined by the psi centers , hundreds of models could be made using a variety of established methods .
this has been done by all of the psi centers . at a workshop held in 2005 at rutgers university
, it was proposed that a portal for models should be launched ( 12 ) .
this would allow access to a variety of models predicted by different methods for any target protein . the protein modeling portal [ pmp ; http://www.proteinmodelportal.org ; ( 13 ) ] has been established at the swiss institute of bioinformatics ( biozentrum university of basel ) and is headed by torsten schwede .
the pmp currently provides access to several million pre - built models from the four psi centers and publicly available model databases [ i.e. modbase ( 14 ) and swiss - model repository ( 15 ) ] .
the pmp can be accessed from the psi sgkb through web service queries , or by directly searching the portal for models of specific or similar protein sequences or models built on specific template structures .
the psi sgkb links to the pmp pages which display information on individual models ( or sets of models ) , as well as functional annotation of the target protein sequence .
annotation : many different annotations are possible for every target , including structure determination and validation details ; sequence information , including possible family and domain assignments ; structure information , including surface characteristics ; cavities ; potential and actual active sites ; fold classifications ; protein  protein and protein  ligand interactions ; and structure  function relationships .
the psi sgkb links to the psi interactive services , summaries and galleries of annotation information , with several of these resources integrated directly into psi sgkb search reports . in addition , the search reports link to approximately 50 additional annotation resources of sequence , structure and function such as uniprot ( 16 ) , national center for biotechnology information ( ncbi ) ( 17,18 ) , class , architecture , topology , and homologous superfamily ( cath ) ( 19 ) , structural classification of proteins ( scop ) ( 20 ) , and gene ontology ( go ) ( 21 ) . a complete list of annotation sources is maintained on an annotation resources page ( http://kb.psi-structuralgenomics.org/kb/annotation-resources.html ) .
the  workshop on the biological annotation of novel proteins ( 7 and 8 march 2008 ; http://annotation-workshop.rutgers.edu/ ) was convened to collect detailed recommendations and requirements for future annotation information to be incorporated into the psi sgkb .
technology development : each psi center has developed a variety of cutting edge technologies for all stages of the structure determination pipeline ( 22 ) .
additionally , the descriptions of these technologies are an important resource for the broader biological community for use in other research
. established at lawrence berkeley laboratory under the leadership of paul adams , the technology portal ( https://isswprod.lbl.gov/psikbportal/ ) currently provides access to summaries of key psi technologies with links to the responsible psi center and/or related publication .
metrics : a quantitative assessment of the productivity of the psi centers is available via metrics , such as the numbers of distinct and novel structures .
the metrics were articulated in a psi steering subcommittee on goals and milestones report ( http://targetdb.rcsb.org/metrics/milestones.html ) .
publications : all articles published by psi scientists are collected into a central publications resource ( http://olenka.med.virginia.edu/psi ) developed by wladek minor at the university of virginia .
lists of citations are categorized as structural or methodological , and include the pubmed identifier and the number of times the article has been cited . with this final piece of information ,
the resource calculates and tracks the following ( with current values at the time this manuscript was prepared ) : total number of articles published by all centers ( 1036 ) , number of articles cited more than five times ( 561 ) , total number of citations ( 16 077 ) , average number of times a structural ( 10.7 ) or methodological ( 20.5 ) paper has been cited and total impact of the articles by journal impact rating ( 4985 ) .
these statistics are essential to track the impact of the psi efforts , since outreach and the dissemination of psi - catalyzed research are central to the psi mission .
integrating information from each psi center with external resources is a key focus of the psi sgkb .
this integration already exists in resources like the rcsb pdb , which contain annotations about folds from cath ( 19 ) and scop ( 20 ) , function via gene ontology ( 21 ) and sequence via uniprot ( 16 ) .
the psi sgkb takes this integration a large step further . in the current psi sgkb release ,
it is possible to perform a single query to extract information from the pdb , pepcdb , targetdb , the pmp , the technology portal , the publications resource , the mr and other biological annotation resources ( figure 1 ) .
for example , a user can type in a sequence or a pdb i d code to extract reports containing structural information and annotations , protein production protocols , predicted models , available dna clone materials and related target status , without having to go to each individual module .
keyword searches query technology information , publication information ( including title and abstracts for structural genomics - related target and structure publications ) , the mr and all indexed pages from the psi centers . 

the psi sgkb portal database is comprised of i d codes , sequences , external urls and annotations .
pdb i d , sequence , or keyword queries made to the psi sgkb access other psi data portals ( targetdb , pepcdb , pmp , technology portal , publications resource , mr , psi center websites ) , pdb and 50 other external biological resources ( a selection is shown ) . a functional view of the psi sgkb resource .
the psi sgkb portal database is comprised of i d codes , sequences , external urls and annotations .
pdb i d , sequence , or keyword queries made to the psi sgkb access other psi data portals ( targetdb , pepcdb , pmp , technology portal , publications resource , mr , psi center websites ) , pdb and 50 other external biological resources ( a selection is shown ) .
the scope and potential outreach of the psi sgkb was expanded recently when it joined forces with the nature publishing group to create a psi sgkb gateway .
the gateway enhances the psi sgkb 's powerful query feature with articles and resources that highlight research findings , new technologies , and general structural biology news .
a research library catalogs articles relevant to structural biology and genomics . a description of a particularly interesting molecule is featured monthly .
the functional sleuth section presents information about molecules of unknown function to challenge biologists to provide further insights about these molecules .
news alerts and really simple syndication ( rss ) feeds will help alert the scientific community about the progress of structural genomics .
new developments include the construction of a pipeline to collect and calculate an expanded set of annotations .
a simplified matrix presentation will be provided for the new annotations and will highlight the structures requiring further functional characterization .
another planned capability will be the use of data mining to fully exploit these annotations .
national institute of general medical sciences . funding for open access charge : the psi sgkb is supported by the national institutes of health ( nih ) as a sub - grant under prime agreement award number : 3u54gm074958 - 04s1 .
 the protein structure initiative structural genomics knowledgebase ( psi sgkb , http://kb.psi-structuralgenomics.org ) has been created to turn the products of the psi structural genomics effort into knowledge that can be used by the biological research community to understand living systems and disease . 
 this resource provides central access to structures in the protein data bank ( pdb ) , along with functional annotations , associated homology models , worldwide protein target tracking information , available protocols and the potential to obtain dna materials for many of the targets . 
 it also offers the ability to search all of the structural and methodological publications and the innovative technologies that were catalyzed by the psi 's high - throughput research efforts . in collaboration with the nature publishing group , 
 the psi sgkb provides a research library , editorials about new research advances , news and an events calendar to present a broader view of structural biology and structural genomics . by making these resources 
 freely available , the psi sgkb serves as a bridge to connect the structural biology and the greater biomedical communities . 
INTRODUCTION
ARCHITECTURE
SEARCH CAPABILITIES
THE NPG PSI SGKB GATEWAY
FUTURE DEVELOPMENTS
FUNDING