Protein-protein interaction Binding Affinity Prediction

Framework for benchmarking RNA secondary structure prediction algorithms.

This repository contains different scripts used for the normal mode analysis of biomolecules with known crystal structures.

Welcome to the Open Source Computational Biology Master's

Scripts for analysing MD simulations of nanopores and DNA translocation (ionic current, translocation rate, pore hydrophobicity).

Generate realistic synthetic 3D Cryo-EM densities from structural models for testing algorithms and training ML models.

NMR spectroscopy calculations for protein structures. Jupyter Notebook tutorials are available to visualize the concepts.

Micelle Maker source code

Complete implementation with 3 methods, sensitivity analysis, and comprehensive visualizations. Reference: doi.org/10.1002/advs.202407641"

A lightweight Python library for simulating Small-Angle X-ray Scattering (SAXS) profiles from protein coordinates, with Jupyter Notebook examples.

Differentiable High-Speed AFM (HS-AFM) simulation for protein structures. JAX-powered toolkit for generating synthetic movies with realistic tip-dilation and scanning lag.

JAX-native differentiable protein folding framework integrating experimental NMR constraints (RDCs) and biophysical "self-correction." Several Jupyter Notebooks visualize the concepts.

Fast Langevin dynamics engine using the Anisotropic Network Model (ANM) for rapid protein conformational ensemble generation.

Curated Portfolio For A 100-Module Graduate Curriculum in ML/AI Ops Engineering Development of Soil Quality Laboratory Foundation Models Using A Set Of 100 Foundational Model Concepts

Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development. Jupyter Notebook tutorials are available to visualize the concepts..

Differentiable VAE framework for predicting protein structural ensembles (IDPs) consistent with SAXS and NMR data. Built on JAX/Flax.

GNN-based protein structure refinement using JAX-differentiable kinematics to fit solution-state experimental data (SAXS/NMR).

My GitHub profile README, current reading list, and courses.

FELBuilder is an automated Python pipeline that automates the complex workflow of Principal Component Analysis (PCA) and Free Energy Landscape (FEL) analysis from Molecular Dynamics (MD) trajectories.

Using graph-theory descriptors to classify the binding affinity of a protein dimer.