Further Evidence for the Likely Completeness of the Library of Solved Single Domain Protein Structures
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Recent studies questioned whether the Protein Data Bank (PDB) contains all compact, single domain protein structures. Here, we show that all quasi-spherical, QS, random protein structures devoid of secondary structure are in the PDB and are excellent templates for all native PDB proteins up to 250 residues. Because QS templates have a similar global contour as native, TASSER can refine 98% (90%) of those whose TM-score is 0.4 (0.35) to structures greater than or equal to the 0.5 TM-score threshold (0.74 (0.64) mean TM-score) for CATH/SCOP assignment. On the basis of this and the fact that, at a TM-score of 0.4, 83% (90%) of all (internal) core secondary structure elements are recovered, a 0.40 TM-score is an appropriate fold similarity assignment threshold. Despite the claims of Taylor, Trovato, and Zhou that many of their structures lack a PDB counterpart, using fr-TM-align, at a 0.45 (0.5) TM-score threshold, essentially all (most) are found in the PDB. Thus, the conclusion that the PDB is likely complete is further supported.
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The reason SAdLSA trained on helical proteins works for β-proteins is that the global topology of β-proteins is in the training set; the chain contour of helical proteins provides a globally correct fold for β-proteins.
“The reason that SAdLSA trained on helical proteins works for β-proteins is that the global topology of β-proteins is in the training set;2,12,13 the chain contour of helical proteins provides a globally correct fold for β-proteins.13”
From AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function (2021) · cites this paper as [13]
The library of single domain protein structures is essentially complete.
“The key to why AF211 works is the fact the library of single domain protein structures is essentially complete.2,12,13”
From AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function (2021) · cites this paper as [13]
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- Authors
- Skolnick, J., Zhou, H., & Brylinski, M.
- Affiliations
- Georgia Institute of Technology (US)
- Center for the Study of Systems Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, Georgia 30318, United States
- Corresponding author
- Skolnick, Jeffrey
- Venue
- The Journal of Physical Chemistry B
- Publisher
- American Chemical Society (ACS)
- Published
- 2012-02-13
- Volume
- 116
- Issue
- 23
- Pages
- 6654-6664
- ISSN
- 1520-5207 (ISSN-L)
- 1520-6106
- PMC
- PMC3351587
- OpenAlex
- W2081208252
- Cited by
- 35
- References
- 40
- Citations by year
- 2025: 1 · 2024: 3 · 2023: 2 · 2022: 2 · 2021: 1 · 2019: 1 · 2018: 3 · 2017: 1 · 2016: 2 · 2015: 1 · 2014: 4 · 2013: 11 · 2012: 3
- FWCI
- 2.44
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- The Journal of Physical Chemistry B (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Civil War Book Review (submittedVersion)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (R01GM037408, GM-48835, R01GM048835)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- single-domain proteins, TM-score
- MeSH terms
- Algorithms, Models, Molecular, Proteins, Protein Structure, Secondary, Peptide Library, Databases, Protein
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