schrodinger.application.bioluminate.reactive_residues module¶

Identify protein sequences that are likely:

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.

Oxidation sites.

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

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).

Proteolysis hot spots.

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

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 search_pre_defined:
Params st:	input structure
	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__¶: alias of builtins.type

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.bioluminate.reactive_residues', '__doc__': '\n Find the reactive residues on a protein based on sequence patterns.\n ', '__init__': <function ReactiveResidues.__init__>, 'generateCSVTable': <function ReactiveResidues.generateCSVTable>, 'iterateResidues': <function ReactiveResidues.iterateResidues>, '_checkGroupForTypes': <function ReactiveResidues._checkGroupForTypes>, 'getNumResidues': <function ReactiveResidues.getNumResidues>, '__dict__': <attribute '__dict__' of 'ReactiveResidues' objects>, '__weakref__': <attribute '__weakref__' of 'ReactiveResidues' objects>})¶

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__module__ = 'schrodinger.application.bioluminate.reactive_residues'¶

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__¶: list of weak references to the object (if defined)

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_type:
Params res:	the reactive residue
	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

__class__¶: alias of builtins.type

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.bioluminate.reactive_residues', '__doc__': '\n A container holding the data about the reactive residue\n ', '__init__': <function ResidueData.__init__>, '__dict__': <attribute '__dict__' of 'ResidueData' objects>, '__weakref__': <attribute '__weakref__' of 'ResidueData' objects>})¶

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).