Perturbation Response Scanning

This module defines functions for performing perturbation response scanning from PCA and normal modes.

calcPerturbResponse(model, **kwargs)

This function implements the perturbation response scanning (PRS) method described in [CA09] and [IG14]. It returns a PRS matrix, and effectiveness and sensitivity profiles.

Rows of the matrix are the average magnitude of the responses obtained by perturbing the atom/node position at that row index, i.e. prs_matrix[i,j] will give the response of residue/node j to perturbations in residue/node i.

PRS is performed using the covariance matrix from a model, e.g. a ANM instance. To use an external matrix, please provide it to a PCA instance using the PCA.setCovariance().

When an atoms instance is given, the PRS matrix will be added as data, which can be retrieved with atoms.getData('prs_matrix').

model and atoms must have the same number of atoms. atoms must be an AtomGroup instance.

[CA09]

Atilgan C, Atilgan AR, Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein. PLoS Comput Biol 2009 5(10):e1000544.

[IG14]

General IJ, Liu Y, Blackburn ME, Mao W, Gierasch LM, Bahar I. ATPase subdomain IA is a mediator of interdomain allostery in Hsp70 molecular chaperones. PLoS Comput. Biol. 2014 10:e1003624.

If turbo is True (default), then PRS is approximated by the limit of large numbers of forces and no perturbation forces are explicitly applied. If set to False, then each residue/node is perturbed repeats times (default 100) with a random unit force vector as in ProDy v1.8 and earlier.

calcDynamicFlexibilityIndex(matrix, atoms, select, **kwargs)

Calculate the dynamic flexibility index for the selected residue(s). This function implements the dynamic flexibility index (Dfi) method described in [ZNG13].

Parameters:

• matrix (ndarray, ANM, PCA, GNM) – PRS or covariance matrix, or a model from which to calculate them
• atoms (Atomic) – an Atomic object from which residues are selected
• select (str, Selection) – a selection string or selection for residues of interest
• norm (bool) – whether to normalise the covariance to a PRS matrix, default False This option is only valid when providing a model.

[ZNG13]

Gerek ZN, Kumar S, Ozkan SB, Structural dynamics flexibility informs function and evolution at a proteome scale. Evol Appl. 2013 6(3):423-33.

calcDynamicCouplingIndex(matrix, atoms, select, func_sel, **kwargs)

Calculate the dynamic coupling index for the selected residue(s). This function implements the dynamic coupling index (DCI) or functional DFI method described in [AK15].

Parameters:

• matrix (ndarray, ANM, PCA, GNM) – PRS or covariance matrix, or a model from which to calculate them
• atoms (Atomic) – an Atomic object from which residues are selected
• select (str, Selection) – a selection string or selection for residues of interest
• func_sel (str, Selection) – a selection string or selection for functional residues
• norm (bool) – whether to normalise the covariance to a PRS matrix, default False This option is only valid when providing a model.

[AK15]

Kumar A, Glembo TJ, Ozkan SB. The Role of Conformational Dynamics and Allostery in the Disease Development of Human Ferritin. Biophys J. 2015 109(6):1273-81.