The AMIA Project

The AMIA Project develops open-source tools for the automated structural and dynamic analysis of protein mutations, helping researchers prioritise potential drug resistance variants efficiently and reproducibly.

At the heart of the project is AMIA (Automated Mutation Introduction and Analysis) — a fully automated bioinformatics pipeline designed to streamline the study of mutation effects on protein structure, stability, and interactions. AMIA enables comprehensive computational analysis by integrating widely used structural biology tools into a single, user-friendly workflow.

AMIA simplifies complex tasks such as introducing mutations into protein structures, calculating changes in molecular interactions and energy states, and analyzing dynamic behavior through molecular dynamics (MD) simulations. The pipeline includes:

• Automated mutation introduction using PyMOL and custom Python scripts
• Interaction and stability analysis with FoldX and contact distance tools
• Trajectory-based analysis of MD simulations (e.g., RMSD, RMSF, PCA, hydrogen bonds) via the dedicated TrajAna module, built on top of MDAnalysis

AMIA supports input from commonly used tools such as PyMOL, FoldX, GROMACS, and leverages libraries like Biopython, Pandas, and Matplotlib to facilitate analysis, data handling, and visualisation.

Get Started

If you’re new to AMIA, the following resources will help you get up and running:

• Installation Guide — Learn how to set up AMIA and its dependencies
• Workflow Tutorial — Walk through a complete AMIA analysis, from mutation input to trajectory insights
• Documentation — Explore detailed API docs and usage examples

Community & Contributions

AMIA is an open-source, community-driven project. Whether you're a computational biologist, structural bioinformatician, or drug resistance researcher, your input helps shape the development of AMIA.

• Join the Community — Ask questions, request features, or report bugs
• Contribute — Help improve the pipeline through code, documentation, or feedback
• AMIA Modules — Extend AMIA with custom scripts or integrate it into your own research pipelines

Citing AMIA

If you use AMIA in your research, please cite it appropriately. Citation information and badges are available on our Citation page.

Funding & Support

AMIA is freely available to the scientific community and designed to run on both high-performance clusters and local machines. To support its continued development, consider contributing code or supporting us through collaborative research initiatives.

This project is supported by funding from the Poliomyelitis Research Foundation