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Back to SimpleMetrics page. Page created 23 April 2020 by Vikram K. Mulligan, Flatiron Institute (vmulligan@flatironinstitute.org).

PeptideInternalHbondsMetric

The PeptideInternalHbondsMetric counts hydrogen bonds between residues that are within a residue selection, or, if no residue selection is provided, wihin a pose. Unlike the HbondMetric, the PeptideInternalHbondsMetric omits from the count any hydrogen bonds that are between residues that are within a user-specified distance in terms of covalent connectivity. This is particularly useful for finding long-range backbone hydrogen bonds in peptide macrocycles, for example.

Autogenerated Tag Syntax Documentation:

A metric for counting the number of hydrogen bonds that are internal to a cyclic peptide or other residue selection. Note that this metric does not count intra-residue hydrogen bonds.

References and author information for the PeptideInternalHbondsMetric simple metric:

PeptideInternalHbondsMetric SimpleMetric's citation(s): Mulligan VK, Workman S, Sun T, Rettie S, Li X, Worrall LJ, Craven TW, King DT, Hosseinzadeh P, Watkins AM, Renfrew PD, Guffy S, Labonte JW, Moretti R, Bonneau R, Strynadka NCJ, and Baker D. (2021). Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1. Proc Natl Acad Sci USA 118(12). doi: 10.1073/pnas.2012800118.

<PeptideInternalHbondsMetric name="(&string;)" custom_type="(&string;)"
        backbone_backbone="(true &bool;)" backbone_sidechain="(false &bool;)"
        sidechain_sidechain="(false &bool;)"
        exclusion_distance="(1 &non_negative_integer;)"
        hbond_energy_cutoff="(-0.25 &real;)" scorefxn="(&string;)"
        residue_selector="(&string;)" />
  • custom_type: Allows multiple configured SimpleMetrics of a single type to be called in a single RunSimpleMetrics and SimpleMetricFeatures. The custom_type name will be added to the data tag in the scorefile or features database.
  • backbone_backbone: If true, backbone-backbone hydrogen bonds are counted. True by default.
  • backbone_sidechain: If true, backbone-sidechain hydrogen bonds are counted. False by default.
  • sidechain_sidechain: If true, sidechain-sidechain hydrogen bonds are counted. False by default.
  • exclusion_distance: Hydrogen bonds between residues that are N positions apart in terms of covalent connectivity will not be counted if this is set higher than 0. Set to 1 by default to exclude hydrogen bonds between neighbouring residues.
  • hbond_energy_cutoff: The maximum energy of a hydrogen bond, if that hydrogen bond is to be counted. Defaults to -0.25
  • scorefxn: The scorefunction to use for computing hydrogen bonds. If not provided, the default scoring function is used.
  • residue_selector: An optional residue selector that selects the peptide. If provided, hydrogen bonds within this selection will be counted. If not, the entire pose will be considered. The name of a previously declared residue selector or a logical expression of AND, NOT (!), OR, parentheses, and the names of previously declared residue selectors. Any capitalization of AND, NOT, and OR is accepted. An exclamation mark can be used instead of NOT. Boolean operators have their traditional priorities: NOT then AND then OR. For example, if selectors s1, s2, and s3 have been declared, you could write: 's1 or s2 and not s3' which would select a particular residue if that residue were selected by s1 or if it were selected by s2 but not by s3.

See Also