Network construction methods

Residue information extracted from trajectories	Atom/angle tracked	Package	Correlation measurement	Name in AlloViz
Atoms’ displacements	Whole residue	dynetan	MI (Mutual Information)	dynetan
	Carbon β	pytraj	Pearson’s	pytraj_CB
	Carbon α			pytraj_CA
		MD-TASK	Pearson’s	MDTASK
		correlationplus	Pearson’s LMI (Linear MI)	correlationplus_CA_Pear correlationplus_CA_LMI
Dihedral angles	Phi Psi All backbone dihedrals (Phi and psi) Chi[1-4] All side-chain dihedrals All dihedrals		Pearson’s	correlationplus_Phi, correlationplus_Psi correlationplus_Backbone_Dihs
		AlloViz	MI with Local Non-uniformity Correction (LNC)	AlloViz_Phi, AlloViz_Psi, AlloViz_Backbone_Dihs AlloViz_Chi[1-4], AlloViz_Sidechain_Dihs AlloViz_Dihs
		CARDS	MI, Pure-disorder MI, Disorder-mediated MI, Holistic MI	CARDS_[MI, Pure_disorder_MI, Disorder_mediated_MI, Holistic_MI]_[Phi, Psi, Backbone_Dihs] CARDS_[MI, Pure_disorder_MI, Disorder_mediated_MI, Holistic_MI]_Chi[1-4] CARDS_[MI, Pure_disorder_MI, Disorder_mediated_MI, Holistic_MI]_[Sidechain_Dihs, Dihs]
		MDEntropy	MI	MDEntropy_Phi, MDEntropy_Psi MDEntropy_Backbone_Dihs
	Alpha angle			MDEntropy_AlphaAngle
Contacts				MDEntropy_Contacts
		GetContacts	Contacts occurrence	GetContacts
		PyInteraph2		PyInteraph2_Contacts
			Atomic contacts occurrence Atomic contacts strength	PyInteraph2_Atomic_Contacts_Occurrence PyInteraph2_Atomic_Contacts_Strength
Interaction energy				PyInteraph2_Energy