Protein Data Bank entries can contain atomic coordinates spaced less than 1 Angstrom apart due to modeling errors

the verdict

SUPPORTED

the evidence backs this

Recorded sources

2 sources for · 0 against

Counts group repeated records of the same source within each side. They do not measure evidence strength or source independence.

Protein Data Bank entries can indeed contain atoms spaced less than 1 Angstrom apart resulting from modeling errors or structural anomalies.

The analysis

The claim states that Protein Data Bank entries can contain atomic coordinates spaced less than 1 Angstrom apart due to modeling errors. Papers [1] and [7] explicitly discuss identifying and correcting unrealistic close contacts and atomic clashes in PDB entries, thereby supporting the claim.

Evidence for · 2

MolProbity: More and better reference data for improved all-atom structure validation.

Recorded source metadata

Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, Verma V, Keedy DA, Hintze BJ, Chen VB, Jain S, Lewis SM, Arendall WB 3rd, Snoeyink J, Adams PD, Lovell SC, Richardson JS, Richardson DC. MolProbity: More and better reference data for improved all-atom structure validation.. 2018. https://doi.org/10.1002/pro.3330

MolProbity validation explicitly flags atomic clashes and closely spaced atoms arising from modeling errors in Protein Data Bank entries.

Source citation format

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More for · 1

An approach to creating a more realistic working model from a protein data bank entry.

Recorded source metadata

Brandon CJ, Martin BP, McGee KJ, Stewart JJ, Braun-Sand SB. An approach to creating a more realistic working model from a protein data bank entry.. 2015. https://doi.org/10.1007/s00894-014-2520-1

Semiempirical evaluations of Protein Data Bank entries frequently identify non-bonding close contacts and anomalously short distances due to structural faults.

Source citation format

The paper trail · every fact has a biography

first checked01 Aug 2026

judged → SUPPORTED · 9801 Aug 2026

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