Structural genomics is the largest contributor of novel structural leverage

By Rajesh Nair, Jinfeng Liu, Ta-tsen Soong, T. Acton, J. Everett, Andrei Kouranov, András Fiser, Adam Godzik, Lukasz Jaroszewski, Christine A. Orengo and 2 more. 2009

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The Protein Structural Initiative (PSI) at the US National Institutes of Health (NIH) is funding four large-scale centers for structural genomics (SG). These centers systematically target many large families without structural coverage, as well as very large families with inadequate structural coverage. Here, we report a few simple metrics that demonstrate how successfully these efforts optimize structural coverage: while the PSI-2 (2005-now) contributed more than 8% of all structures deposited into the PDB, it contributed over 20% of all novel structures (i.e. structures for protein sequences with no structural representative in the PDB on the date of deposition). The structural coverage of the protein universe represented by today’s UniProt (v12.8) has increased linearly from 1992 to 2008; structural genomics has contributed significantly to the maintenance of this growth rate. Success in increasing novel leverage (defined in Liu et al. in Nat Biotechnol 25:849–851, 2007) has resulted from systematic targeting of large families. PSI’s per structure contribution to novel leverage was over 4-fold higher than that for non-PSI structural biology efforts during the past 8 years. If the success of the PSI continues, it may just take another ~15 years to cover most sequences in the current UniProt database.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Protein 3D Structure Computed from Evolutionary Sequence Variation (2011, background): “In spite of significant progress in the field of structural genomics over the last decade [20], only about half of all well-characterized protein families (PFAM-A, 12,000”
De Novo Structure Prediction of Globular Proteins Aided by Sequence Variation-Derived Contacts (2014, background): “Until recently, however, accurate prediction of residue-residue contacts from sequence information has been a significant problem due to methods having a high rate of false positives [15], and the relative shortage of homologous sequences [16].”
Improved Technologies Now Routinely Provide Protein NMR Structures Useful for Molecular Replacement (2011, background): “Additionally, both the number of structures deposited in the Protein Data Bank (PDB) and the coverage of structure space are increasing rapidly (Liu et al., 2007; Burley et al., 2008; Nair et al., 2009).”
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3D Protein Structure Predicted from Sequence (2011, unknown): “In spite of significant progress in the field of structural genomics over the last decade [18], only about half of all well-‐characterized protein families (PFAM-‐A, 12,000 families), have a 3D stru”
An estimated 5% of new protein structures solved today represent a new Pfam family (2013, background): “…how close we are to the goal of structurally covering the proteinsequence space; that is, of having the structure of a homologue for each (or, more realistically, most) of the protein sequences available (Chothia, 1992; Yan & Moult, 2005; Chandonia & Brenner, 2006; Levitt, 2007; Nair et al., 2009).”