Projects/Repositories

FreeDTS

FreeDTS is software to perform computational research on biomembranes at messocpic length-scale. In FreeDTS, a membrane is represented by a dynamically triangulated surface equipped with vertex-based inclusions to integrate the effects of integral and peripheral membrane proteins. Several algorithms are included into the software that allow for simulation of framed membrane with constant tension, vesicles with various fixed volume or constant pressure difference, confined membranes into the fixed region of the space, constant fixed global curvature and application for external forces on regions of the membrane. In addition, the software allows one to turn off the shape evolution of the membrane and only explore inclusions organization. This allows to take realistic membrane shapes obtained from Cryo-ET and obtain heterogeneous organization of biomolecules which can be backmapped to finer simulations models. URL The article describing FreeDTS is published in Nature Communications and available here.

TS2CG

TS2CG does conversions of triangulated surfaces to (coarse grain) membrane models for molecular simulation. It also works as a backmapping algorithm from dynamically triangulated surfaces simulations to CG molecular dynamics simulations or to take electron microscopy tomography data and build structures for molecular dynamics simulations.

TS2CG is an algorithm to backmap a triangulated surface (TS) structure to a corresponding coarse-grained (CG) model. TS2CG is implemented in C++ and includes two separate scripts. Pointillism and CG Membrane Builder. URL

SiMBols

SiMBols is a python package designed to make similarity measures easily accessible for biological systems and to compare spatio-temporal data. The package offers a unified approach to calculate the Frechet distance, the weak Frechet distance, the Hausdorff distance, dynamic time warping, Wasserstein distance, Kullback-Leibler divergence, longest common subsequence and an approach based on difference distance matrices. SiMBols is developed and maintained by Fabian Schuhmann. URL