Biology: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.[1] CAMEO is a continuous and fully automated complement to the bi-annual CASP experiment.[2] Currently, 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.[3]
History
CAMEO was developed[when?] as part of the Protein Model Portal[4] module of the Structural Biology Knowledge Base[5] 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.[citation needed]
Earlier projects with similar aims were EVA and LiveBench.[citation needed]
See also
- Protein structure prediction software
References
- ↑ Haas, J; Roth, S; Arnold, K; Kiefer, F; Schmidt, T; Bordoli, L; Schwede, T (2013). "The Protein Model Portal--a comprehensive resource for protein structure and model information". Database 2013: bat031. doi:10.1093/database/bat031. PMID 23624946.
- ↑ Moult, J; Fidelis, K; Kryshtafovych, A; Schwede, T; Tramontano, A (February 2014). "Critical assessment of methods of protein structure prediction (CASP)--round x". Proteins 82 Suppl 2: 1–6. doi:10.1002/prot.24452. PMID 24344053.
- ↑ Mariani, V; Biasini, M; Barbato, A; Schwede, T (1 November 2013). "lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests.". Bioinformatics 29 (21): 2722–8. doi:10.1093/bioinformatics/btt473. PMID 23986568.
- ↑ Arnold, K; Kiefer, F; Kopp, J; Battey, JN; Podvinec, M; Westbrook, JD; Berman, HM; Bordoli, L et al. (March 2009). "The Protein Model Portal". Journal of Structural and Functional Genomics 10 (1): 1–8. doi:10.1007/s10969-008-9048-5. PMID 19037750.
- ↑ Gabanyi, MJ; Adams, PD; Arnold, K; Bordoli, L; Carter, LG; Flippen-Andersen, J; Gifford, L; Haas, J et al. (July 2011). "The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods.". Journal of Structural and Functional Genomics 12 (2): 45–54. doi:10.1007/s10969-011-9106-2. PMID 21472436.
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