2025-11-17T13:41:39-08:00 2024-12-31 371420474 Fontanello Duffield & Otake LLP 111 Pine Street Suite 1750 San Francisco CA 94111 990 2024-01-01 862536664 Open Molecular Software Foundation OPEN 7074693852 200 B Street STE F Davis CA 95616 Karmen Condic-Jurkic Sec/Treas/ED 2025-11-17 true true Antonio Tellez Jr P01716904 4159830200 2024 2025-03-06 01:10:19Z David Mobley 200 B Street STE F Davis CA 95616 5422298 false X omsf.io X 2021 DE OMSF's mission is to advance the molecular sciences through the development of high-quality, open-source tools for molecular modeling and facilitating collaboration between industry and academia. 5 4 17 46 0 1966947 3661343 1030840 1758353 127 271 2331 2997914 5422298 170000 1007681 0 92581 1701381 0 0 2124724 2563463 2387305 5272525 610609 149773 2573781 3509895 1553910 2340251 1019871 1169644 OMSF's mission is to advance the molecular sciences through the development of high-quality, open-source tools for molecular modeling and facilitating collaboration between industry and academia. false false 4972344 1007681 OMSF welcomed three new projects in 2024 OpenADMET, Alchemistry and Virtual Winter School of Computational Chemistry (VWSCC). Alchemistry and VWSCC are focused on community building efforts in the field of (bio)molecular modeling, more specifically, through organizing events for education, training and networking purposes. OpenADMET is the project with the mission to build open predictive models of safety and toxicity for small molecules to improve humanitys ability to more reliably, cheaply, and effectively treat disease, launched jointly with UCSF and Octant Bio. The OpenADMET project is funded by an ARPA-H grant (the primary awardee is UCSF). The number of staff members and core contributors continued to grow, and we had 27 staff members in 2024. OMSF successfully organized its second annual symposium in Leiden (Netherlands) and successfully gathered more than 100 attendees which included our staff members, industry partners and other members of the molecular modeling community. The list of our hosted projects, their missions and activities is provided below together with our program services and community-oriented efforts. Hosted ProjectsOpenADMETOpenADMET is an open effort to build predictive models of ADMET properties and understand the mechanisms by which they arise. This means systematically characterizing the proteins and mechanisms that give rise to these properties (protein structures and scaled functional and genetic assays), understanding how small molecules interact with these mechanisms (through high-throughput nanoscale chemistry to explore/exploit chemical space), and integrative computational models (AI/ML ligand/structural, mechanistic, and physiological modeling). OMSF is focused on AI/ML ligand and structural modeling, while UCSF and Octant Bios primary role is generation of high-quality datasets. The project was launched on Oct 1, 2024, and this effort is funded by an ARPA-H grant and Gates Foundation. More information about the project and its activities can be found on their website:https://openadmet.org/. OpenFold ConsortiumOpenFold is a non-profit AI research and development consortium developing free and open-source software tools for biology and drug discovery. OpenFolds 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. This project aims to:Collaboratively 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. In 2024, the OpenFold Consortium started working on reproducing the AlphaFold3 model and releasing the resulting code, weights and data under permissive licenses. The consortium has grown from 10 to 14 industry members between 2023 and 2024. The list of current OpenFold members, links to software repositories and latest news about their activities can be found on their website (https://openfold.io). Open Force Field ConsortiumThe Open Force Field Consortium (OpenFF) 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 Sage 2.2 release delivered targeted improvements to critical pharmaceutical chemistries. Independent validation demonstrated that OpenFF outperforms leading commercial packages on challenging BACE1 scaffold-hopping transformations, confirming the force field's competitive accuracy. A major new feature is the preview release of a graph neural network model for ultra-fast, conformation-independent charge assignment that operates 10-100x faster than traditional methods with improved accuracy and elimination of conformer-dependent errors. This method scales seamlessly to large biomolecules including proteins and polymers, enabling self-consistent parameterization across all molecular types including non-natural amino acids. Infrastructure development released the production-ready Alchemiscale platform completing over 100,000 binding free energy calculations on free academic compute resources and being adopted extensively by OpenFF, OpenFE, and the ASAP Antiviral Drug Discovery Consortium for routine force field testing. The YAMMBS automated benchmarking system enabled testing of 75+ different force field fits over the past year while identifying and correcting systematic errors through continuous validation of molecular geometries and energetics. Significant progress was made toward the self-consistent protein + small molecule force field ("Rosemary"), with the team generating requisite peptide quantum chemical data and achieving performance matching AMBER ff14SB on specific benchmarks; a recent breakthrough in fitting strategy using trajectory reweighting has dramatically accelerated progress, putting the release on track for the upcoming project year to enable truly accurate protein-ligand binding with fully consistent parameterization. Additional technical developments included completion of virtual site infrastructure, advancement of automated chemical perception using BESMARTS for data-driven typing decisions, development of a direct polarizability model (AM1-BCC-dPol), biopolymer loading infrastructure for diverse polymers and materials applications, and maintenance of stable toolkit API enabling consistent workflow integration. The team also significantly enhanced documentation with centralized examples and live demonstration sessions that showcase the ease and versatility of OpenFF tools. Open Force Field had 17 industry members in 2024. You can find more information about the Consortiums activities, members, resulting publications and software repositories on their website: https://openforcefield.org.Open Free Energy ConsortiumOpen Free Energy Consortium (OpenFE) provides essential tools for drug discovery and design, supporting free energy calculations that are robust and scalable without commercial license fees. OpenFE bridges a gap in the landscape of free energy simulation software, developing stable, reliable, and openly licensed software. The project's flagship accomplishment was the launch of openfe v1.0 in April 2024, marking the first stable release with guaranteed maintenance of functionality and behavior. Validation efforts demonstrated promising accuracy, with partner testing showing comparable performance to industry-standard proprietary methods across 12 transformations, while a comprehensive benchmarking study successfully evaluated 211 ligands across 9 diverse protein systems. Major technical developments expanded the toolkit's capabilities to include charge-changing transformations between ligands with different net charges, core atom element changes, spectator molecule support for cofactors, and automated post-simulation analysis for identifying problematic calculations through energetics and structural assessments. Significant usability improvements included comprehensive documentation redesign, enhanced CLI tools for streamlined network planning and results gathering, tutorial development, and a remarkable 10-60x performance improvement in the LOMAP atom mapping tool. A critical achievement involved identifying and addressing a major AmberTools partial charge assignment bug that was causing large variability in free energy predictionsthe team traced this issue to inconsistent conformer selection across different computing environments and unstable partial charge assignments, then worked collaboratively with upstream developers to implement fixes that benefit the entire computational chemistry community. In 2023, Open Free Energy had 17 industry partners. The list of OpenFE products, industry partners, and software repositories can be found on their website: https://openfree.energy. Open RosettaOpen 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 coll 4972344 true true false false false false false false false false false false false false false false false false false false true true false false false false false true false true false false false false false false false false true false false false false false false false false true 2 0 true 17 true false false false false false false false 0 false false false false false false false X 5 4 false false false false true true false true true false false true true true true false true true true false CA X Karmen Condic-Jurkic 7074693852 200 B Street STE F Davis CA 95616 Marcus Wieder ML Scientist 40.00 0.00 208101 0 0 Julia Koehler Project Director 40.00 0.00 176313 0 10365 Jennifer Wei Software Scientist 40.00 0.00 140000 0 8717 Irfan Alibay Software Scientist 40.00 0.00 145061 0 0 David Swenson Software Scientist 40.00 0.00 132875 0 10336 Karmen Condic-Jurkic Sec/Treas/ED 40.00 0.00 X X 46667 0 55431 David Mobley President 2.00 0.00 X X 0 0 0 Brian Weitzner Director 0.50 0.00 X 0 0 0 Clara Christ Director 0.20 0.00 X 0 0 0 Jeffrey Gray Director 0.20 0.00 X 0 0 0 849017 84849 16 false true false David Lee Dotson 200 B Street STE F Davis CA 95616 Contract Services 109944 1 2373140 867425 420778 80000 3661343 Program Revenue 1758353 1758353 1758353 271 271 0 0 0 0 0 0 0 Other Revenue 2331 2331 2331 5422298 1760684 271 X 937591 937591 0 70090 70090 0 102098 102098 0 1382179 1344262 37917 54330 53244 1086 48717 44301 4416 114057 110944 3113 0 51801 38767 13034 25500 25500 0 0 0 1551555 1348278 203277 7294 7294 0 118421 118421 0 172 30 142 385844 385844 0 354539 354539 0 0 0 9796 6 9790 Supplies 26415 26415 Payroll Processing 17640 15857 1783 Training 5000 5000 Bank Fees 4810 4810 4676 4553 123 5272525 4972344 300181 0 1790942 1078545 1267468 0 744924 1144515 0 0 0 0 37915 19367 0 0 0 0 0 0 2573781 3509895 7776 173284 1546134 2166967 1553910 2340251 X 1019871 517481 652163 1019871 1169644 2573781 3509895 149773 X false false false X 674623 1455202 1966947 3661343 7758115 0 0 674623 1455202 1966947 3661343 7758115 0 7758115 271 271 0 2331 2331 7760717 X 0.00000 RESTRICTED RESTRICTED RESTRICTED RESTRICTED RESTRICTED RESTRICTED RESTRICTED RESTRICTED true Europe 0 0 Grantmaking Grantmaking for Research 70090 70090 70090 Europe Research 68090 EFT FMV Europe Sponsorship 2000 EFT FMV 2 false false false false false false true Arizona State University 1151 S Forest Ave Tempe CA 85287 860196696 501(c)(3) 7069 0 Open Source Ecosystem Development Johns Hopkins University 3400 North Charles Street Baltimore MD 21218 520595110 501(c)(3) 32522 0 Research Rosetta Commons Foundation 3400 North Charles Street Baltimore MD 21218 520595110 501(c)(3) 863000 0 Software Platform Development UC Irvine 1111 California Ave Irvine CA 92697 952226406 501(c)(3) 35000 0 Research 4 0 Grantmaker's Description of How Grants are Used The consortium governing board approves the scope of work and funding amount for recipient. OMSF enters into an agreement with the recipient's institution specifying the amount of funding, allowable expenses, and reporting requirements. true X X X X X false false false false false false false false false Julia Koehler Project Director 176313 10365 186678 Marcus Wieder ML Scientist 208101 208101 X Cloud Compute 1 80000 FMV false false false Form 990, Part VI, Section A, Line 6 THEORGANIZATIONHASONECLASSOFMEMBERSHIP.THEPRIMARYRIGHTANDOBLIGATIONOF THE MEMBERSISTO ELECTANEFFECTIVEBOARDOFDIRECTORS. Form 990, Part VI, Section B, Line 11b THE FORM 990 AND RELATED STATE FILINGS ARE PREPARED BY AN INDEPENDANT CPA. THE FORMS ARE REVIEWED AND APPROVED BY THE ORGANIZATION AND MADE AVAILABLE TO BOARD MEMEBRS FOR REVIEW. Form 990, Part VI, Section B, Line 12c The Conflict of Interest Policy is adopted by the Board of Directors of the Open Molecular Software Foundation to protect the interests of the Foundation when it is contemplating entering into a transaction or arrangement that might benefit the private interest of an officer, member of the Board, or any other member of a committee with powers delegated by the Board or which might result in a possible excess benefit transaction. Form 990, Part VI, Section C, Line 19 No documents available to the public. Part III Line 4a (Continued) In 2024, the Open Rosetta project received an NSF POSE grant to build sustainable open source practices around their community and newly developed ML tools. They have grown the team at OMSF and organized several successful events: Winter RosettaCon in Boston (Feb 2024), Summer RosettaCon in Seattle (Aug 2024), and a user workshop in Nashville in Jul 2024. The RosettaCommons community is committed to responsible development of or the responsible development of AI tools for the life sciences, and as a part of those efforts, they introduced the Biosecurity Fellow role to bridge the gap between scientists and policymakers. Open Rosetta is funded by the Rosetta Commons, University of Washington. More information about Rosetta can be found on the Rosetta Commons website: https://rosettacommons.orgBoston Protein Design and Modeling ClubThe Boston Protein Design and Modeling Club (BPDMC) unites computational protein engineers and modelers from academia and industry. Founded in 2017, its 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. OMSF provides administrative support to the project. The full list of speakers in 2024 can be found here: https://www.bpdmc.org/archive/2024. Program ServicesASAP AViDD (MSKCC)AI-driven Structure-enabled Antiviral Platform (ASAP) Consortium used artificial intelligence and computational chemistry to accelerate structure-based open science antiviral drug discovery and deliver oral antivirals for pandemics with the goal of global, equitable, and affordable access. ASAP Consortium was an NIH-funded project via the Antiviral Drug Discovery (AViDD) U19 Centers and a part of the Antiviral Program for Pandemics. This project was administered by MSKCC, but spans a number of international institutions, from universities to biotech startups and large infrastructure facilities for determining protein structure, such as Diamond Light Source in the UK. MSKCC continued to work with OMSF on integration of open source tools developed under the OMSF umbrella (OpenFF, OpenFE) into their computational pipeline with a very specific application discovering new antivirals in silico and bringing them all the way to clinical trials. Accurate force fields for small molecules and free energy calculations are an integral part of the computational work in drug discovery. The resulting jointly developed infrastructure and data was released under open licenses for easier reuse. In Dec 2024, OpenADMET and ASAP teams jointly launched a blind challenge for predictive modeling in collaboration with Polaris based on the experimental datasets collected during the ASAP AViDD project (see here for more details: https://polarishub.io/blog/antiviral-competition). Community-oriented programsAlchemistryThe goal of this project is to bring together experts in free energy calculations and related methods to share their scientific advancements and achievements, and encourage an open dialogue for challenges in the field between practitioners in industry and academia by organizing annual gatherings with the location alternating between the US and Europe. The Free Energy Workshop in May 2024 was held in Leiden (Netherlands) and OMSF Symposium was leaning against this event, as many of our industry stakeholders were in attendance of the Free Energy Workshop. Please find more details about this initiative at their website: https://alchemistry.org/. Virtual School of Computational ChemistryVirutal School of Computational Chemistry is an educational initiative with the mission to support scientists worldwide through accessible education and facilitation of communication with international experts in computational chemistry and their peers. They organize one virtual workshop in January every year and make content available to attendants and other users of their platform. More details about their activities can be found at https://winterschool.cc/. Chan Zuckerberg Initiative Essential Open Source Software ProgramOMSF received a CZI EOSS 5 grant awarded in 2022 for supporting community development at OMSF, and improving communication across different projects internally and with external stakeholders and broader community. The grant supported the OMSFs community manager role and our second annual symposium in Leiden (May 2024). We continued to strengthen our internal knowledge sharing infrastructure, improved engagement on social media and started releasing regular newsletter and blog posts. NSF Pathways to Open Source Ecosystems (POSE)Building open source ecosystems in molecular sciences through collaboration and technology awarded in Oct 2023 to PI Condic-Jurkic. The aims of the grant include: 1) creating resources to better support open source molecular software projects and their communities, such as legal and training materials; 2) building technical solutions to improve software quality and security; and 3) strengthening OMSFs position as the key partner for multi-institutional collaborative open source projects pushing the scientific frontier in chemistry and biology. This project further aims to build and support strong and diverse open source communities with transparent governance and development practices, helping ensure responsible and sustainable creation and stewardship of future technologies in molecular sciences.As a part of the POSE grant, the organization conducted comprehensive surveys of both internal staff and external partners to guide strategic development. We hired two ecosystem engineers, David Swenson and Ethan Holz, to provide technical support by creating standardized development practices, implement self-hosted GitHub Action runners for specialized hardware testing, scope cookiecutter requirements, and manage developer relationships. We also started developing six playbooks as living documents covering developer best practices, contributor management, project structure, benchmarking, academic collaboration, and internal operations. Additionally, OMSF started working on establishing a new legal framework including an updated IP policy, fellowship templates for students and postdocs, fiscal sponsorship agreements for community-led initiatives, and a redesigned membership model aimed at reducing bureaucracy for multi-project support and improving community representation in governance structures.Transitioning Rosetta Commons to a self-sustainable Open Source Ecosystem awarded in Jul 2024 to PI Koehler. The overall goal of this project is to transition the Rosetta Commons to an Open-Source Environment. Specifically, the team will (1) drive collaborative development, governance and adoption of new artificial intelligence (AI) technologies in molecular modeling through open licenses; (2) develop standardized application programming interfaces (APIs), workflows, documentation standards, and tutorials to fuel the growth of the Open-Source Ecosystem (OSE), while maintaining desirable levels of software quality, security and accessibility; (3) provide support and maintenance for key infrastructure, (4) develop a new governance model to empower leaders in the community to ensure long-term sustainability and broad impact of the projects. This work expands the Open Rosetta Ecosystem beyond the traditional Rosetta codebase, and it allows the community to create scientific breakthroughs through complex workflows with or without traditional Rosetta.