ArticleThe journal of physical chemistry. B2012
Further evidence for the likely completeness of the library of solved single domain protein structures.
Article in The journal of physical chemistry. B, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Rapid discovery of new-to-nature protein domains by novelty-first forcing of language models.bioRxiv : the preprint server for biology · 2025Article
- On Protein Loops, Prior Molecular States and Common Ancestors of Life.Journal of molecular evolution · 2024Review
- Are Viruses Taxonomic Units? A Protein Domain and Loop-Centric Phylogenomic Assessment.Viruses · 2024Review
- Tracing the birth of structural domains from loops during protein evolution.Scientific reports · 2023Article
- A review of visualisations of protein fold networks and their relationship with sequence and function.Biological reviews of the Cambridge Philosophical Society · 2023Review
- AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function.Journal of chemical information and modeling · 2021Article
- Multistep mutational transformation of a protein fold through structural intermediates.Protein science : a publication of the Protein Society · 2018Article
- THE-DB: a threading model database for comparative protein structure analysis of the E. coli K12 and human proteomes.Database : the journal of biological databases and curation · 2018Article
- Enhanced unbiased sampling of protein dynamics using evolutionary coupling information.Scientific reports · 2017Article
- Why Is There a Glass Ceiling for Threading Based Protein Structure Prediction Methods?The journal of physical chemistry. B · 2017Article
- Evaluating the accuracy of protein design using native secondary sub-structures.BMC bioinformatics · 2016Article
- Biophysics of protein evolution and evolutionary protein biophysics.Journal of the Royal Society, Interface · 2014Article
- On the role of physics and evolution in dictating protein structure and function.Israel journal of chemistry · 2014Article
- Template-based structure modeling of protein-protein interactions.Current opinion in structural biology · 2014Review
- Protein folding and de novo protein design for biotechnological applications.Trends in biotechnology · 2014Review
- Article
- An evolution-based approach to De Novo protein design and case study on Mycobacterium tuberculosis.PLoS computational biology · 2013Article
- eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures.BMC research notes · 2013Article
- EvoDesign: De novo protein design based on structural and evolutionary profiles.Nucleic acids research · 2013Article
- Interplay of physics and evolution in the likely origin of protein biochemical function.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.