evedesign 0.0.3

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evedesign: unified framework for accessible biosequence design

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What is evedesign?

evedesign is a unified open-source framework for biosequence design that formalizes conditional design problems in a method-agnostic way. The framework allows users to seamlessly build and execute complex multiobjective design workflows, including supervised and unsupervised models, from a standardized set of specifications and operations. An interactive web-based user interface facilitates end-to-end biomolecular design for a broad scientific audience and is publicly available at https://evedesign.bio.

This repository implements the core interfaces for standardizing the interaction with biomolecular models, generation of nucleotide sequences, and many other utility functions for structure handling, sequence space embeddings, etc.

Please also check evedesign-server for automated pipeline execution from declarative design specifications and the REST API, as well as evedesign-ui for the interactive user interface.

Reference

Our preprint describing the core concepts behind the evedesign framework will be posted here shortly.

Installation

Use the following command to install evedesign with support for all currently implemented models. You can remove any of the options if you do not need the respective model.

pip install evedesign[evmutation2,esm2,mpnn,umap] 

Getting started

Please refer to some of our examples how to use evedesign. We are planning to extend these further in the near future.

To implement your own models in the framework, please have a look at our existing reference implementations (e.g. EVmutation2, ESM-2, ProteinMPNN, Gibbs sampler) as well as the underlying model interfaces and description of molecular systems and instances.

We are happy to help if you have any questions!

Roadmap and contributing

We plan to continuously add more models, restraints, oracles and samplers to the framework, e.g. de novo 3D structure generation with BoltzGen or BindCraft.

We are actively looking for further contributors to develop our framework jointly with the community. If you are interested or feel like an important model is missing from the framework, please get in contact with us!

License

evedesign is released under the MIT license.

Contact

For general questions or inquiries about evedesign please reach out to [e-mail].