ArticleBMC bioinformatics2018
How large B-factors can be in protein crystal structures.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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45 citing papers in PubMed, 101 citations in OpenAlex.
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- ATLAS: protein flexibility description from atomistic molecular dynamics simulations.Nucleic acids research · 2024Article
- Using graphlet degree vectors to predict atomic displacement parameters in protein structures.Acta crystallographica. Section D, Structural biology · 2023Article
- Analyzing Current Trends and Possible Strategies to Improve Sucrose Isomerases' Thermostability.International journal of molecular sciences · 2023Review
- B-factor prediction in proteins using a sequence-based deep learning model.Patterns (New York, N.Y.) · 2023Article
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- Structural and biochemical characterization ofProcess biochemistry (Barking, London, England) · 2023Article
- Statistical learning of protein elastic network from positional covariance matrix.Computational and structural biotechnology journal · 2023Article
- Widespread occurrence of covalent lysine-cysteine redox switches in proteins.Nature chemical biology · 2022Article
- Designing Anti-Microbial Peptides Against Major β-Lactamase Enzymes in Clinically Important Gram-Negative Bacterial Pathogens: An In-Silico Study.Probiotics and antimicrobial proteins · 2022Article
- Molecular Coevolution of Nuclear and Nucleolar Localization Signals inside the Basic Domain of HIV-1 Tat.Journal of virology · 2022Article
- B-factor accuracy in protein crystal structures.Acta crystallographica. Section D, Structural biology · 2022Article
- Mutagenic Distinction between the Receptor-Binding and Fusion Subunits of the SARS-CoV-2 Spike Glycoprotein and Its Upshot.Vaccines · 2021Article
Corrections and comments
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Authors and funding
1 author at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundProtein crystal structures are potentially over-interpreted since they are routinely refined without any restraint on the upper limit of atomic B-factors. Consequently, some of their atoms, undetected in the electron density maps, are allowed to reach extremely large B-factors, even above 100 square Angstroms, and their final positions are purely speculative and not based on any experimental evidence.
resultsA strategy to define B-factors upper limits is described here, based on the analysis of protein crystal structures deposited in the Protein Data Bank prior 2008, when the tendency to allow B-factor to arbitrary inflate was limited. This B-factor upper limit (B_max) is determined by extrapolating the relationship between crystal structure average B-factor and percentage of crystal volume occupied by solvent (pcVol) to pcVol =100%, when, ab absurdo, the crystal contains only liquid solvent, the structure of which is, by definition, undetectable in electron density maps.
conclusionsIt is thus possible to highlight structures with average B-factors larger than B_max, which should be considered with caution by the users of the information deposited in the Protein Data Bank, in order to avoid scientifically deleterious over-interpretations.
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