OMSF Projects
This is the current list of projects under the OMSF umbrella.
If you are interested to become a member of any of the projects, please reach out to info@omsf.io.
OpenFold is a non-profit AI research and development consortium developing free and open-source software tools for biology and drug discovery. Our mission is to bring the most powerful software ever created – AI systems with the ability to engineer the molecules of life – to everyone. These tools can be used by academics, biotech and pharmaceutical companies, or students learning to create the medicines of tomorrow, to accelerate basic biological research, and bring new cures to market that would be impossible to discover without AI. Structure Prediction
In biology, structure and function are inextricably linked. Understanding the mechanisms of biological systems, their engineering, and how to affect them therefore implies a need to know and understand their structure. The consortium is creating state-of-the-art AI-based protein modeling tools that can predict molecular structures with atomic accuracy, making this level of precision accessible in open source for both research and commercial applications for the first time. Researchers around the world will be able to use, improve, and contribute to this “predictive molecular microscope.”
This work aims to:
- Develop a permissively licensed model competitive with the performance of state-of-the-art models.
- Provide the entire training & inference stack and training datasets under the same permissive license
- Optimize the performance of this model for use on state-of-the-art and widely available GPUs.
The Open Force Field Consortium is a network of academic and industry researchers working together to advance science and infrastructure required for building the next generation of small molecule and biomolecular force fields. The shared goal of these researchers is to develop automated and systematic data-driven techniques to parameterize and assess new generations of more accurate force fields. Software and data are released under open licensing agreements to enable rapid application, validation, extension and any kind of modification by our users and contributors. In addition, the Initiative aims to build and support a strong community of users and contributors from industry and academia.
The OpenFF Initiative is funded by the OpenFF Consortium of industry partners focused on development of small molecule force fields, and the NIH grant aimed at supporting compatible biomolecular force fields.
The growing success of alchemical free energy methods in aiding structure-enabled drug discovery efforts in driving or maintaining potency and selectivity—and more recently, in quantifying the impact of mutations—is driving the development of an open source ecosystem of alchemical free energy calculation packages. However, this ecosystem is not yet interoperable, interchangeable, robust, or developing sufficiently quickly to meet the rapidly growing needs of pharma and widespread availability of inexpensive GPU computing resources. In addition, the proliferation of free energy methods makes it difficult to determine which methods will perform well on targets of interest without significant time and money investment by individual pharma companies to bring individual methods in house.
Following the 2018 Alchemical Free Energy Methods in Drug Discovery meeting in Göttingen, a series of calls including representatives of numerous pharma companies defined the need for an Open Free Energy Consortiumto address the growing demand for these tools within the biomolecular modeling community. These calls articulated three primary goals:
- Accelerate the development of robust, scalable, and flexible open source GPU-accelerated alchemical free energy packages and the associated ecosystem of essential scientific software.
- Develop infrastructure for interoperable workflow components to enable portable, interoperable, and robust free energy calculation workflows and an open component registry.
- Establish standards for free energy calculations.
Open Rosetta is the project exploring the transition pathways for the Rosetta Commons to an open source model under the OMSF umbrella, with the initial focus on the community building efforts and new developments. The Rosetta Commons are a community of over 100 labs worldwide who collectively develop Rosetta, the macromolecular modeling suite that has led the field of protein and RNA modeling and design for over two decades, and many emerging artificial intelligence based approaches recently. The Rosetta software allows tackling a variety of molecular modeling problems including protein design, protein-protein interactions, protein small molecule interactions, and protein structure prediction. The software can model biomolecules including proteins, DNA, RNA, carbohydrates, lipids; systems ranging from antibodies, enzymes, membrane proteins, systems including non-canonical amino acids, with or without the use of different types of experimental data ranging from density maps from cryoEM or crystallography, and other structural biology methods including NMR, EPR, mass-spectrometry, and cross-linking. Currently, the Rosetta suite is available under a custom license free of charge for non-commercial use through the University of Washington. Legal mechanisms enabling adoption of one of the standard open source licenses are under review.
The goal of the Rosetta Commons is to continue developing state-of-the-art tools in macromolecular modeling and design in conjunction with deep learning technology and to keep driving scientific progress that allows solving some of the biggest challenges the world is facing today. The Rosetta community believe that the open source model is not just deeply aligned with their values, but also the most efficient mechanism to harness the power of open science and collaborative mindset spanning academia, government laboratories, institutes, research centers and partner corporations to build future technologies in biomolecular modeling.
Boston Protein Design and Modeling Club
The Boston Protein Design and Modeling Club (BPDMC) unites computational protein engineers and modelers from academia and industry. Founded in 2017, it’s a hub for collaborative innovation in protein design and modeling. The club hosts monthly meetings featuring dinner, drinks, seminars, workshops, and discussions, providing a rich environment for networking and intellectual exchange. These gatherings are dynamic, rotating across various Boston locations, and invite members to delve into the latest scientific advancements while fostering lasting connections.
You can find a recordings of these monthly meetings on BPDMC’s YouTube page.