Applications & Tools
List of selected computational tools and software applications that are under development.
Alprotein-Alpha : Alprotein: Advanced Protein Site Energy Calculator
Photosynthetic SystemsAlprotein is a powerful, modern Python package for calculating site energies and electronic properties of pigment-protein complexes using the Charge Density Coupling (CDC) method. Built with a focus on accuracy, usability, and extensibility, it provides both programmatic APIs and an intuitive graphical interface for computational biophysics research.
NeuralFinance
Machine LearningNeural Finance is a research-oriented deep learning framework for predictive modeling of financial time series. The framework integrates Long Short-Term Memory (LSTM) neural networks with technical indicators and sentiment analysis pipelines, enabling comprehensive temporal modeling of asset prices. It aims to address non-stationary characteristics of financial data, multi-scale temporal dependencies, and the integration of qualitative sentiment information, providing a platform for rigorous scientific experimentation and evaluation.
pdbtoolkits
Chemical InformaticsA 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.
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