schrodinger.application.bioluminate.reactive_residues module

Identify protein sequences that are likely:

  1. Deamidation sites.

Standard rules exist for determining deamidation sites, i.e. X-Asn-Y and X-Gln-Y are considered the hottest deamidation targets, with Y=Gly, Ala, Ser, and with the rate determined to some extent by the nature of X (higher for X = polar). There seems to be some correlation with flexibility at the region, as well.

  1. Oxidation sites.

Identification of potential oxidation sites would start with highlighting the His, Met, Cys, Trp and Tyr residues.

  1. Glycosylation sites (most common).

N-linked: Asn. Consensus sequence: Asn-X-Ser/Thr (X=! Pro) O-linked: Ser and Thr. No consensus sequence. We do not identify these. At greater detail, there is some indication that Asn-X-Ser/Thr-Y can be considered and the tendency toward glycosylation is impacted by Y. (See, e.g. Mellquist et al Biochemistry (1998) 12, 6833-7).

  1. Proteolysis hot spots.

These would be Asp residues. The cleavage can occur at either the N or C-terminal end.

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class schrodinger.application.bioluminate.reactive_residues.ReactiveResidues(st, search_pre_defined=True, custom_patterns=[])

Bases: object

Find the reactive residues on a protein based on sequence patterns.

__init__(st, search_pre_defined=True, custom_patterns=[])
Params st:input structure
Params search_pre_defined:
 whether or not search the pre-defined patterns for reactive sites
Params custom_patterns:
 input custom patterns defining the reactive sites
generateCSVTable()

Analyze the given structure and return the results summary in a CSV table

iterateResidues()

Iterate over all residues and yield ResidueData objects (or None if the residue is not reactive) Note that one residue can be multiple reactive types and yielded multiple times

getNumResidues()

return the total number of residues in the sequences that will be analyzed.

class schrodinger.application.bioluminate.reactive_residues.ResidueData(res, res_type, alpha_carbon, neighbor_alphas, custom_color, sasa_by_atom)

Bases: object

A container holding the data about the reactive residue

__init__(res, res_type, alpha_carbon, neighbor_alphas, custom_color, sasa_by_atom)
Params res:the reactive residue
Params res_type:
 the name for the type of the reactive residue
Params alpha_carbon:
 Ca atom index of the reactive residue
Params neighbor_alphas:
 Ca atom indices of previous and next residue to the reactive residue
Params custom_color:
 color for custom pattern
Params sasa_by_atom:
 SASA of all atoms of the given structure