Identifying inter- and intra-molecular contacts is the basis of many
simulation analyses. A pair of atoms is often defined as “in contact”
when they fall within a specified cut-off distance of each other.
Native contact analysis identifies the contacts present in a reference
structure, and then tracks the existence of these contacts across a
trajectory; evolution of the fraction of native contacts can be used to
analyse protein folding, binding or other conformational changes.
MDAnalysis features a Native contacts analysis module() that allows
this fraction of native contacts to be calculated over a trajectory.
However, the native contact approach is limited - a reference structure
must be defined, only contacts present in the reference structure are
considered, and only the total fraction of contacts is tracked,
not individual pairs.
MDAnalysis also features a hydrogen bond analysis module() which does
allow the identification of all contacts across all frames, without
the need for a reference structure, but is geared towards the
the identification of hydrogen bonds. A more generalised analysis
could be useful to many MDAnalysis users.
Where to start
Look at the existing Native Contact and Hydrogen bond analysis modules
to see how existing contact analysis is performed
Create a class using AnalysisBase (see the guide on User Guide on
custom trajectory analysis() that identifies all contacts in each frame,
e.g. generalising the approach used by hbond_analysis.
Additional features could include e.g. tools to allow extraction of
timeseries data for a specified contact pair from the full contact/frame
array.
Overview
Identifying inter- and intra-molecular contacts is the basis of many simulation analyses. A pair of atoms is often defined as “in contact” when they fall within a specified cut-off distance of each other.
Native contact analysis identifies the contacts present in a reference structure, and then tracks the existence of these contacts across a trajectory; evolution of the fraction of native contacts can be used to analyse protein folding, binding or other conformational changes. MDAnalysis features a Native contacts analysis module() that allows this fraction of native contacts to be calculated over a trajectory. However, the native contact approach is limited - a reference structure must be defined, only contacts present in the reference structure are considered, and only the total fraction of contacts is tracked, not individual pairs.
MDAnalysis also features a hydrogen bond analysis module() which does allow the identification of all contacts across all frames, without the need for a reference structure, but is geared towards the the identification of hydrogen bonds. A more generalised analysis could be useful to many MDAnalysis users.
Where to start
AnalysisBase(see the guide on User Guide on custom trajectory analysis() that identifies all contacts in each frame, e.g. generalising the approach used byhbond_analysis.