Nature of the protein universe

By Michael Levitt. 2009

311 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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In Molecular Biology

Citations in the corpus

Critical assessment of methods of protein structure prediction (CASP) — round x (2013, background): “…databank, and these span about 1393 folds, so that a homology model can be produced for in excess of half of all protein domains of known sequence.4,5 Homology models vary greatly in accuracy depending on a number of factors, and for that reason CASP has encouraged the development of methods…”
Protein structure prediction from sequence variation (2012, background): “Of course, new families will also join the known universe of sequences, at a rate that is hard to predict 56 , but it is likely that the absolute number of correctly predictable protein folds will rise sharply into the many thousands over the next few years.”
Outcome of a Workshop on Applications of Protein Models in Biomedical Research (2009, background): “The coverage issue was addressed in a recent comprehensive analysis of the current sampling of the protein universe (Levitt, 2008).”
Unexpected features of the dark proteome (2015, methodology): “A recent survey of 8 million protein sequences by Levitt (6) concluded that, eventually, the number of folds may increase linearly with sequences.”
Fundamentals and Methods for T- and B-Cell Epitope Prediction (2017, background): “First of all, prediction of conformational B-cell epitopes generally requires the knowledge of protein three-dimensional (3D) structure and this information is only available for a fraction of proteins [117].”
Recognizing protein substructure similarity using segmental threading. (2010, background): “It has been well established that the number of folds in the protein universe is limited (Chothia, 1992; Levitt, 2009; Orengo et al., 1994).”
Templates are available to model nearly all complexes of structurally characterized proteins (2012, background): “In model organisms such as Escherichia coli or yeast, the Protein Data Bank (PDB) offers valid templates for a significant part of their soluble proteins (10), including those in known PPI (85% in E. coli and 39% in yeast, according to our results).”
Grammar of protein domain architectures (2019, background): “…and the fraction of multidomain proteins increase with the organismal complexity (defined as the number of unique cell types in an organism): Eukaryotes have more multidomain proteins than prokaryotes (4, 9, 20 – 25), and animals have more multidomain proteins than unicellular eukaryotes (26).”
Protein Modelling: What Happened to the “Protein Structure Gap”? (2013, unknown): “The computational modeling of a protein’s structure has therefore attracted substantial interest in the field of structural bioinformatics to complement experimental structural biology efforts to characterize the protein universe (Baker and Sali, 2001; Levitt, 2009).”
Protein-protein docking: from interaction to interactome. (2014, unknown): “Modeling templates are available for a significant part of soluble proteins in genomes (73), including those in known protein interactions (61,74).”
The evolutionary origin of orphan genes (2011, background): “Convergence to a subset of folds would explain why structure-oriented searches suggest that the discovery of new domains is approaching saturatio”