Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.

By Cyrus A. Wilson, Julia Kreychman, Mark Gerstein. Journal of Molecular Biology, 2000

474 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/3de28cd5bd893768ac6b2b6d8a209b940d251ba0

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Citations in the corpus

Practical limits of function prediction (2000, result): “The shape of the obtained curves mirror the ones obtained in a recent and complementary study 39 using different deﬁnitions of function and EC codes.”
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. (2004, methodology): “It is difficult to evaluate the relationship between sequence homology and function, because no clear measure of functional similarity exists between any two proteins, and the definition of “function” itself is often vague (Bork et al. 1998; Wilson et al. 2000; Lan et al. 2002, 2003).”
UniqueProt: creating representative protein sequence sets (2003, background): “We need to apply yet a different battery of thresholds to infer that: (i) two proteins dwell in the same sub-cellular compartment (3, K.O.Wrzeszczynski and B.Rost, manuscript submitted); (ii) that they belong to the same groups of cellular function (4), have similar binding sites (5) or belong to si”
A census of human transcription factors: function, expression and evolution (2009, background): “Previous studies of enzymes have shown that pairs of proteins with sequence similarities above 40% tend to share the same catalytic activit”
Improved estimates of coordinate error for molecular replacement (2013, methodology): “Below 30% sequence identity, it has been shown that the expectation values produced by tools such as BLAST are better correlated than the sequence identity with the r.m.s.d. value between structures (Wilson et al., 2000).”
What is Bioinformatics? A Proposed Definition and Overview of the Field (2001, unknown): “Combined with similarity measurements, these studies provide us with an understanding of how much biological information can be accurately transferred between homologous proteins [ 55 ].”
How well is enzyme function conserved as a function of pairwise sequence identity? (2003, background): “been frequently observed that function may diverge more quickly than sequence, and homologous proteins may evolve to have different functions and possess different functional sites, especially when sequence identity falls below 40%.(17,18,20,39) Thus, the dataset constructed by Rost that contains on”
Sequence-similar, structure-dissimilar protein pairs in the PDB (2007, background): “16,17 The majority of the domain pairs in the ‘‘outlier set’’ have sequence identities 50% and many contain NMR entries or structures with resolution worse than 2.5 A˚.”
MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming (2009, background): “The biological function of protein complexes depends on their 3D structures (6,24).”
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes (2004, background): “Correct identification of orthologs and paralogs is of central importance for both the functional and evolutionary aspects of comparative genomics [12,13].”
Amino‐Acid Properties and Consequences of Substitutions (2003, methodology): “Some rough rules of thumb can be used: function is often conserved down to 40% protein sequence identity, with the broad functional class being conserved to 25% identity (Wilson et al., 2000).”
The COG database: an updated version includes eukaryotes (2003, background): “A classic case of the interplay between orthologous and paralogous relationships is seen in the globin family: all animal globins, including myoglobin, are paralogs, but they are all coorthologs of the plant leghemoglobin(s) [5].”
Improving structure-based function prediction using molecular dynamics (2009, background): “However, when sequence similarity falls below 40%, the reliability of these methods decreases (Wilson et al., 2000).”