Predicting functions from protein sequences—where are the bottlenecks?

By Peer Bork, Eugene V. Koonin. 1998

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Citations in the corpus

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses (2018, background): “Relationships between more rootward OGs and their nested children OGs at more specific taxonomic levels were explicitly tracked and ascertained to be consistent, with exceptions only for mosic proteins with multi-domain combinations, where individual domains might have evolved independently (26,27).”
Protein Molecular Function Prediction by Bayesian Phylogenomics (2005, unknown): “Unfortunately, large-scale automated methods for function annotation have resulted in widespread annotation errors that reside in current databases [2,18,57,63–65].”
Practical limits of function prediction (2000, background): “14 The heterogeneity of the database annotations and the fact that most sequence annotations have probably been derived by similarity 5 can be misleading at this step but are difﬁcult to avoid.”
Who's your neighbor? New computational approaches for functional genomics (2000, methodology): “The primary methodology applied to these genome sequences involved database search using sequence comparison programs, such as BLAST, and subsequently methods that allow the detection of subtle sequence conservation, such as PSI-BLAST or HMMe”
More than the sum of their parts: On the evolution of proteins from peptides (2003, unknown): “1b): (1) Collagen is composed of three parallel polyproline type II helices, each formed by hundreds of proline- and hydroxyproline-rich Gly-XY repeats.”
Prediction of protein function from protein sequence and structure (2003, unknown): “1998; Bork & Koonin, 1998; Doerks et al .”