Mechanical Stiffness Calculations

This module defines functions for Mechanical Stiffness calculations.

prody.dynamics.mechstiff.calcMechStiff(modes, coords, kbt=1.0)

Calculate stiffness matrix calculated using ANM instance. Method described in [EB08] and [KMR17].

[KMR]

Mikulska-Ruminska K., Kulik A.J., Benadiba C., Bahar I., Dietler G., Nowak W. Nanomechanics of multidomain neuronal cell adhesion protein contactin revealed by single molecule AFM and SMD. Sci Rep 2017 7:8852.

Parameters:

• coords (numpy.ndarray.) – a coordinate set or an object with getCoords method

• n_modes (int or None, default is 20.) – number of non-zero eigenvalues/vectors to calculate. If None is given, all modes will be calculated (3x number of atoms).

Authors: Mustafa Tekpinar & Karolina Mikulska-Ruminska & Cihan Kaya

prody.dynamics.mechstiff.calcMechStiffStatistic(stiffness, rangeK, minAA=0, AA='all')

Returns number of effective spring constant with set range of amino acids of protein structure. AA can be a list with a range of analysed amino acids as: [first_aa, last_aa, first_aa2, last_aa2], minAA - eliminate amino acids that are within 20aa and rangeK is a list [minK, maxK]

prody.dynamics.mechstiff.calcStiffnessRange(stiffness)

Return the range of effective spring constant.

prody.dynamics.mechstiff.calcStiffnessRangeSel(stiffness, value, minAA=20, AA='all')

Returns minimum or maximum value of sping constant from mechanical stiffness calculations for residues that are within more than min_aa from each other. Value should be ‘minK’ or ‘maxK’. It alow to avoid residues near each other. AA is a number of residues from both terminus (N and C) of protein strcuture, it can be all or int value (than first and last AA residues will be analysed. With minAA=0 it can be used to search the highest/lowest values of interactions between N-C terminus if protein structure has a shear, zipper or SD1-disconnected mechanical clamp -it is common in FnIII/Ig like domains and determines the maximum unfolding force in AFM or SMD method.