Homology-based inference sets the bar high for protein function prediction

BMC Bioinformatics

Volumn 14, Issue SUPPL.3, 2013, Pages

  Hamp, Tobias ^a   Kassner, Rebecca ^a   Seemayer, Stefan ^a   Vicedo, Esmeralda ^a   Schaefer, Christian ^a   Achten, Dominik ^a   Auer, Florian ^a   Boehm, Ariane ^a   Braun, Tatjana ^a   Hecht, Maximilian ^a   Heron, Mark ^a   Hönigschmid, Peter ^a   Hopf, Thomas A ^a   Kaufmann, Stefanie ^a   Kiening, Michael ^a   Krompass, Denis ^a   Landerer, Cedric ^a   Mahlich, Yannick ^a   Roos, Manfred ^a   Rost, Burkhard ^a,b  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^b Howard Hughes Medical Institute   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LOWER LIMITS; PREDICTION METHODS; PROTEIN FUNCTION PREDICTION; PROTEIN FUNCTIONS;

PROTEINS;

PROTEIN;

ALGORITHM; ARTICLE; GENETICS; PHYSIOLOGY; SEQUENCE HOMOLOGY;

ALGORITHMS; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

MLCS; MLOWN;

EID: 84879185985     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-S3-S7     Document Type: Article

References (16)

1. Consortium TU Ongoing and Future Developments at the Universal Protein Resource. Nucleic Acids Research 2011, 39:D214-219. 3013648, 21051339, Consortium TU.
2. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. Gene Ontology: Tool for the Unification of Biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29. 10.1038/75556, 3037419, 10802651.
3. Rentzsch R, Orengo CA. Protein function prediction--the power of multiplicity. Trends Biotechnol 2009, 27:210-219. 10.1016/j.tibtech.2009.01.002, 19251332.
4. Radivojac P, Clark WT, Friedberg I. A Large-scale Evaluation of Computational Protein Function Prediction. Nature Methods 2012,
5. Wass MN, Sternberg MJ. ConFunc--Functional Annotation in the Twilight Zone. Bioinformatics 2008, 24:798-806. 10.1093/bioinformatics/btn037, 18263643.
6. Jones CE, Schwerdt J, Bretag TA, Baumann U, Brown AL. GOSLING: A Rule-Based Protein Annotator Using BLAST and GO. Bioinformatics 2008, 24:2628-2629. 10.1093/bioinformatics/btn486, 18796479.
7. Hawkins T, Luban S, Kihara D. Enhanced Automated Function Prediction Using Distantly Related Sequences and Contextual Association by PFP. Protein Science 2006, 15:1550-1556. 10.1110/ps.062153506, 2242549, 16672240.
8. Martin DM, Berriman M, Barton GJ. GOtcha: A New Method for Prediction of Protein Function Assessed by the Annotation of Seven Genomes. BMC Bioinformatics 2004, 5:178. 10.1186/1471-2105-5-178, 535938, 15550167.
9. Chitale M, Hawkins T, Park C, Kihara D. ESG: Extended Similarity Group Method for Automated Protein Function Prediction. Bioinformatics 2009, 25:1739-1745. 10.1093/bioinformatics/btp309, 2705228, 19435743.
10. Sokolov A, Ben-Hur A. Hierarchical Classification of Gene Ontology Terms Using the GOstruct Method. Journal of Bioinformatics and Computational Biology 2010, 8:357-376. 10.1142/S0219720010004744, 20401950.
11. Clark WT, Radivojac P. Analysis of Protein Function and its Prediction from Amino Acid Sequence. Proteins 2011, 79:2086-2096. 10.1002/prot.23029, 21671271.
12. Altschul SF, Madden TL, Schaeffer AA, Zhang J, Zhang Z, et al. Gapped Blast and PSI-Blast: A New Generation of Protein Database Search Programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
13. Ming K, Witten I. Issues in Stacked Generalization. Journal of Artificial Intelligence Research 1999, 10:271-280. http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.16.1519 http://dl.acm.org/citation.cfm?id=1622868.
14. Eyrich VA, Przybylski D, Koh IY, Grana O, Pazos F, et al. CAFASP3 in the Spotlight of EVA. Proteins 2003, 53(Suppl 6):548-560.
15. Koh IY, Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, et al. EVA: Evaluation of Protein Structure Prediction Servers. Nucleic Acids Research 2003, 31:3311-3315. 10.1093/nar/gkg619, 169025, 12824315.
16. Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B, Sali A. Reliability of Assessment of Protein Structure Prediction Methods. Structure 2002, 10:435-440. 10.1016/S0969-2126(02)00731-1, 12005441.