A package to caculate residue-residue contacts from MD trajectories
Project description
The presence of a contact between two residues in macromolecular systems, such as proteins and nucleic acids, is established when the minimum interresidue heavy atom pair distance falls within a specified cutoff (4-5 Å) for a given majority (for example, 75% or above snapshots) of the simulation time.
This program depends on MDTraj simulation analysis package (1): mdtraj.load() is used for trajectory/topology inputs and inter-atomic distances are calculated using mdtraj.distance()
While citing, please add:
(1) McGibbon, R., et al. "MDTraj: a modern open library for the analysis of molecular dynamics trajectories." Biophysical journal 109.8 (2015): 1528-1532.
(2) Madhu, M. K., et al. "Delineating the Biased Signaling Mechanism in Mutated Variants of β2-Adrenergic Receptor Using Molecular Dynamics Simulations"
Copyright: Computational Biophysics and Soft Matter Group (https://home.iiserb.ac.in/~rkm/)
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