The importance of residue-level filtering and the Top2018 best-parts dataset of high-quality protein residues.

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2022-01

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Abstract

We have curated a high-quality, "best-parts" reference dataset of about 3 million protein residues in about 15,000 PDB-format coordinate files, each containing only residues with good electron density support for a physically acceptable model conformation. The resulting prefiltered data typically contain the entire core of each chain, in quite long continuous fragments. Each reference file is a single protein chain, and the total set of files were selected for low redundancy, high resolution, good MolProbity score, and other chain-level criteria. Then each residue was critically tested for adequate local map quality to firmly support its conformation, which must also be free of serious clashes or covalent-geometry outliers. The resulting Top2018 prefiltered datasets have been released on the Zenodo online web service and are freely available for all uses under a Creative Commons license. Currently, one dataset is residue filtered on main chain plus Cβ atoms, and a second dataset is full-residue filtered; each is available at four different sequence-identity levels. Here, we illustrate both statistics and examples that show the beneficial consequences of residue-level filtering. That process is necessary because even the best of structures contain a few highly disordered local regions with poor density and low-confidence conformations that should not be included in reference data. Therefore, the open distribution of these very large, prefiltered reference datasets constitutes a notable advance for structural bioinformatics and the fields that depend upon it.

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10.1002/pro.4239

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Williams, Christopher J, David C Richardson and Jane S Richardson (2022). The importance of residue-level filtering and the Top2018 best-parts dataset of high-quality protein residues. Protein science : a publication of the Protein Society, 31(1). pp. 290–300. 10.1002/pro.4239 Retrieved from https://hdl.handle.net/10161/29455.

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Scholars@Duke

Richardson

Jane Shelby Richardson

James B. Duke Distinguished Professor of Medicine

3D structure of macromolecules; molecular graphics; protein folding and design; all-atom contacts; x-ray crystallography; structure validation.


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