The Jorgensen Foundation brings the computational chemistry programs developed over decades at Yale University to researchers and industry professionals worldwide — accessible by browser, powered by cloud, with modern graphical interfaces built on top of proven science. No installation. No barriers. Just results.
Explore Our ProgramsThe power of BOSS and MCPRO with a modern 3D interface. No command line required.
Explore ProgramsBOSS — Biochemical and Organic Simulation System
Molecular mechanics, Monte Carlo statistical mechanics, and semi-empirical QM calculations (AM1, PM3, PDDG/PM3). Energy minimisation, normal mode analysis, conformational searching with OPLS force fields.
MCPRO — Monte Carlo for Proteins
Monte Carlo simulations of peptides, proteins, and nucleic acids in solution. Derived from BOSS with extensive biomolecular extensions. Free energy perturbation calculations for protein-ligand systems.
BOMB — Biochemical and Organic Model Builder
Growing combinatorial libraries inside protein binding sites. Virtual high-throughput screening for drug lead discovery. Guided lead optimisation with Monte Carlo free-energy simulations.
OPLS Force Fields
Optimised Potentials for Liquid Simulations — the industry-standard force fields developed by the Jorgensen group. Covers organic molecules, proteins, nucleic acids, and lipids.
Free Energy Perturbation (FEP)
Statistical perturbation theory for computing free energies of hydration, binding, and chemical equilibria. Thermodynamic integration for lead optimisation in drug discovery.
Molecular Visualisation Suite
Browser-based 3D rendering of all simulation outputs. Interactive visualisation of trajectories, electron density surfaces, and binding modes. No external software required.
Submit your inputs. Run in the cloud. Visualise and export results instantly.
Request accessOur programs run securely in the cloud. Your data stays yours. The source code never leaves our servers — only your results do. Built for researchers who value both openness and scientific integrity.
Read our principlesRevenue from industry partners funds academic access — and student travel grants for international conferences and meetings.
Full access to all simulation programs with cloud computing, 3D visualisation, and results export. Verified through your institutional email address.
Priority access with unlimited computing, dedicated support, and custom integrations. Verified through your company email address.
Already have an account? Sign in here
BOSS has been a cornerstone of our group's research for years. The cloud platform removes every barrier we used to face with installation and configuration — our graduate students are running free energy calculations on day one now, rather than spending weeks wrestling with legacy software. The OPLS-AA implementation is impeccable.
Dr. Sarah Mitchell
We have been using MCPRO for protein-ligand binding affinity predictions throughout our lead optimisation campaigns. The accuracy of the FEP results is consistently excellent — comparable to what we see from far more expensive commercial platforms. The academic pricing makes it genuinely accessible for university groups working on drug discovery.
Prof. James Okafor
The browser-based interface for BOSS and BOMB has transformed how we teach computational chemistry at the undergraduate level. Students can set up Monte Carlo simulations and visualise results interactively without any of the traditional command-line overhead. This is what modern computational chemistry education should look like.
Dr. Elena Vasquez
When you submit a simulation job, it is queued on our cloud infrastructure and executed on dedicated compute nodes. You do not need to install any software — the programs run entirely on our servers and results are returned to your browser. Jobs are processed in the order they are received, with priority queue access available to industry subscribers. Most standard calculations complete within minutes; larger free energy perturbation runs may take several hours.
Yes. All data is transmitted over encrypted HTTPS connections and stored securely. Your input structures, simulation parameters, and results are private to your account and are never shared with other users. The underlying program source code never leaves our servers — you interact only with the results. We do not use your data for any purpose other than running your requested calculations.
The platform accepts standard molecular structure formats including PDB, MOL2, SDF, and SMILES strings for small molecules. Protein structures can be uploaded directly as PDB files. Output files are provided in the native program formats as well as common interchange formats (PDB, SDF) and CSV for numerical results. The built-in 3D visualisation suite renders all outputs directly in the browser without requiring any additional software.
Yes. The platform is designed to be accessible through a graphical interface — you do not need to write code, edit input files, or use a command line. All simulation parameters are configured through forms and menus, and results are presented as interactive visualisations and downloadable reports. That said, the underlying programs are also accessible to advanced users who wish to customise parameters in detail.
Academic pricing is available to researchers at universities, colleges, and non-profit research institutes. Your account type is determined automatically from your email domain — if you register with an institutional address (e.g. .edu, .ac.uk), you will be offered academic pricing. The academic subscription is $49 per month or $490 per year, and provides full access to all programs and cloud computing hours. If your institution does not have a standard academic domain, please contact us and we will verify your affiliation manually.
Both tiers provide full access to all simulation programs. Industry subscribers additionally receive priority queue access (your jobs run before standard-queue jobs), a dedicated technical support contact, API access for integration with internal pipelines, and custom integration assistance. Industry subscriptions are priced at $199 per month or $1,990 per year. Revenue from industry subscriptions directly funds academic access and student travel grants.
Yes. You can cancel your subscription at any time from your account settings. If you cancel a monthly subscription, access continues until the end of the current billing period. If you cancel an annual subscription, access continues until the end of the current annual term — we do not offer partial-year refunds. Your saved data and results remain accessible for 90 days after cancellation, after which they are permanently deleted.
The Jorgensen Foundation awards travel grants to graduate students and postdoctoral researchers presenting computational chemistry work at international conferences and symposia. Grants cover conference registration, travel, and accommodation up to a defined limit. Academic subscribers are eligible to apply. Applications open twice per year and are reviewed by the Foundation's scientific committee. Details on the current grant cycle are sent to eligible subscribers by email.