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.

2. Oxidation sites.

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

3. 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).

4. 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