Applications & Tools

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

Alprotein-Alpha : Alprotein: Advanced Protein Site Energy Calculator

Photosynthetic Systems
Active Development

Alprotein 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.

PythonNumPySLURMLinux/Unix

NeuralFinance

Machine Learning
Alpha Release

Neural 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.

PythonTensorFlowKerasPandasNumPy

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

Development Stack

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Python

Advanced development with NumPy, Pandas

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Molecular dynamics simulations

Gromacs, Amber, OpenMM

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Machine Learning

TensorFlow, Keras, PyTorch

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HPC Systems

SLURM, distributed computing

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Chemical Informatics

RDKit, molecular analysis

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Visualization

ChimeraX, PyMOL, VMD

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Cloud Computing

Google Colab, cloud infrastructure

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Version Control

Git, GitHub