CAMEO3D
Continuous Automated Model EvaluatiOn (CAMEO) is a community-wide project to continuously evaluate the accuracy and reliability of protein structure prediction servers in a fully automated manner.{{cite journal|last1=Haas|first1=J|last2=Roth|first2=S|last3=Arnold|first3=K|last4=Kiefer|first4=F|last5=Schmidt|first5=T|last6=Bordoli|first6=L|last7=Schwede|first7=T|title=The Protein Model Portal--a comprehensive resource for protein structure and model information|journal=Database |date=2013|volume=2013|pages=bat031|pmid=23624946|pmc=3889916|doi=10.1093/database/bat031}} CAMEO is a continuous and fully automated complement to the bi-annual CASP experiment.{{cite journal|last1=Moult|first1=J|last2=Fidelis|first2=K|last3=Kryshtafovych|first3=A|last4=Schwede|first4=T|last5=Tramontano|first5=A|title=Critical assessment of methods of protein structure prediction (CASP)--round x|journal=Proteins|date=February 2014|volume=82 Suppl 2|pages=1–6|pmid=24344053|doi=10.1002/prot.24452|pmc=4394854}}
Currently,{{clarify|when did it begin doing it this way? what methodology was used previously?|date=December 2020}} CAMEO evaluates predictions for predicted three-dimensional protein structures (3D), ligand binding site predictions in proteins (LB), and model quality estimation tools (QE).
Workflow
CAMEO performs blind assessment of protein structure prediction techniques based on the weekly releases of newly determined experimental structures by the Protein Databank (PDB). The amino acid sequences of soon to be released protein structures are submitted to the participating web-servers. The web-servers return their predictions to CAMEO, and predictions received before the experimental structures have been released are included in the assessment of prediction accuracy. In contrast to the CASP experiment, the comparison between prediction and reference data is fully automated, and therefore requires numerical distance measures which are robust against relative domain movements.{{cite journal|last1=Mariani|first1=V|last2=Biasini|first2=M|last3=Barbato|first3=A|last4=Schwede|first4=T|title=lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests.|journal=Bioinformatics|date=1 November 2013|volume=29|issue=21|pages=2722–8|pmid=23986568|doi=10.1093/bioinformatics/btt473|pmc=3799472}}
History
CAMEO was developed{{when|date=December 2020}} as part of the Protein Model Portal{{cite journal|last1=Arnold|first1=K|last2=Kiefer|first2=F|last3=Kopp|first3=J|last4=Battey|first4=JN|last5=Podvinec|first5=M|last6=Westbrook|first6=JD|last7=Berman|first7=HM|last8=Bordoli|first8=L|last9=Schwede|first9=T|title=The Protein Model Portal|journal=Journal of Structural and Functional Genomics|date=March 2009|volume=10|issue=1|pages=1–8|pmid=19037750|pmc=2704613|doi=10.1007/s10969-008-9048-5}} module of the Structural Biology Knowledge Base{{cite journal|last1=Gabanyi|first1=MJ|last2=Adams|first2=PD|last3=Arnold|first3=K|last4=Bordoli|first4=L|last5=Carter|first5=LG|last6=Flippen-Andersen|first6=J|last7=Gifford|first7=L|last8=Haas|first8=J|last9=Kouranov|first9=A|last10=McLaughlin|first10=WA|last11=Micallef|first11=DI|last12=Minor|first12=W|last13=Shah|first13=R|last14=Schwede|first14=T|last15=Tao|first15=YP|last16=Westbrook|first16=JD|last17=Zimmerman|first17=M|last18=Berman|first18=HM|title=The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods.|journal=Journal of Structural and Functional Genomics|date=July 2011|volume=12|issue=2|pages=45–54|pmid=21472436|doi=10.1007/s10969-011-9106-2|pmc=3123456}} as part of the Protein Structure Initiative. CAMEO is being developed by the computational structural biology group at the SIB Swiss Institute of Bioinformatics and the Biozentrum, University of Basel.{{cn|date=December 2020}}
Earlier projects with similar aims were EVA and LiveBench.{{cn|date=December 2020}}
See also
References
{{reflist|1}}
External links
- [http://cameo3d.org/ CAMEO home page]
- [http://www.proteinmodelportal.org/ Protein Model Portal]