Software


Check us out on GitHub

These are oldschool utilities written in C. They're probably not terribly useful anymore, but back in the day reviewers flexed their authority by demanding the publication of source code.

Membrane ANM

Source C code from the paper Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter GltPh (Lezon & Bahar.  Biophys J 102:1331 (2012)) can be found on my membrane ANM page. The software is useful for calculating equilibrium dynamics of proteins that are embedded in coarse-grained membranes, and for incorporating rigid blocks into ANM calculations.

For those who are more comfortable working in python, or on a non-nix operating system, these methods are also incorporated into the ProDy software package as membrANM.

Parallel ANM

Source C code from the paper Modeling global changes induced by local perturbations to the HIV-1 capsid. (Bergman & Lezon. J Mol Graphics Modelling 71:218-226 (2017)) can be found on the ANMMPI page. This software is useful for constructing ENMs of very large protein complexes, such as the HIV capsid.