Packs stuff in boxes

Protein-protein interaction Binding Affinity Prediction

Framework for benchmarking RNA secondary structure prediction algorithms.

Welcome to the Open Source Computational Biology Master's

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

Differentiable FRET distance distribution modeling in JAX

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.

Differentiable Cryo-EM map fitting in JAX

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

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

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

Micelle Maker source code

Differentiable HDX-MS prediction in JAX

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

Integrative Refinement Engine for Differentiable Biophysics in JAX

Differentiable EPR/DEER distance distribution modeling in JAX

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

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