semvec/pypi-packages huggingface dataset:
findcontacts 0.1.0
A package to caculate residue-residue contacts from MD trajectories
License: BSD 2-clause

The presence of a contact between two residues in a macromolecular system (proteins nucleic acids etc.) 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 heavily depends on MDTraj simulation analysis program (1)


How to cite:

Please add the following citations:

(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/)