ArticleScientific reports2021
Random sampling of the Protein Data Bank: RaSPDB.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Interplay between hydrogen and chalcogen bonds in cysteine.Proteins · 2023Article
- Survey of the Intermolecular Disulfide Bonds Observed in Protein Crystal Structures Deposited in the Protein Data Bank.Life (Basel, Switzerland) · 2022Article
- Developing a bioinformatics pipeline for comparative protein classification analysis.BMC genomic data · 2022Article
- Network Pharmacology and Molecular Docking to Elucidate the Potential Mechanism of Ligusticum Chuanxiong Against Osteoarthritis.Frontiers in pharmacology · 2022Article
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1 author.
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Abstract
A novel and simple procedure (RaSPDB) for Protein Data Bank mining is described. 10 PDB subsets, each containing 7000 randomly selected protein chains, are built and used to make 10 estimations of the average value of a generic feature F-the length of the protein chain, the amino acid composition, the crystallographic resolution, and the secondary structure composition. These 10 estimations are then used to compute an average estimation of F together with its standard error. It is heuristically verified that the dimension of these 10 subsets-7000 protein chains-is sufficiently small to avoid redundancy within each subset and sufficiently large to guarantee stable estimations amongst different subsets. RaSPDB has two major advantages over classical procedures aimed to build a single, non-redundant PDB subset: a larger fraction of the information stored in the PDB is used and an estimation of the standard error of F is possible.
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