Applications & Tools

List of selected computational tools and software applications that are under development.

Pymembrane

Photosynthetic Systems

Active Development

Extended open-source software tools for modeling and analyzing light harvesting processes in photosynthetic systems with MCCE and CDC calculations for structure-based Hamiltonian construction.

PythonNumPySLURMLinux/Unix

Source Code

pdbtoolkits

Chemical Informatics

Active Development

A comprehensive collection of Python tools for working with PDB (Protein Data Bank) files. This toolkit provides utilities for structural alignment, analysis, visualization of molecular structures and other useful capapilities that would be released soon.

RDKitOpenBabelPythonPandas

Source Code

Development Stack

🐍

Python

Advanced development with NumPy, Pandas

⚙️

Molecular dynamics simulations

Gromacs, Amber, OpenMM

🤖

Machine Learning

TensorFlow, Keras, PyTorch

💻

HPC Systems

SLURM, distributed computing

🧪

Chemical Informatics

RDKit, molecular analysis

📊

Visualization

ChimeraX, PyMOL, VMD

☁️

Cloud Computing

Google Colab, cloud infrastructure

📈

Version Control

Git, GitHub