[MDAKit / Hackathon] Contact Analysis

[IAlibay]

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

• 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.