About · The Jorgensen Foundation

The Science Behind
the Foundation

Decades of computational chemistry research from Yale University, now accessible to researchers and industry worldwide.

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Our Story

From New Haven
to the world.

The Jorgensen Foundation grew from decades of pioneering research at Yale University. Over more than forty years, the Jorgensen research group developed a suite of computational chemistry programs that became foundational tools for researchers in academia and industry around the world. These programs — BOSS, MCPRO, BOMB, and the OPLS force fields — were written to answer fundamental questions about the behaviour of molecules in solution, and in doing so, changed how scientists approach drug discovery and materials design.

The Foundation was established to carry this legacy forward. Rather than leaving these tools accessible only to those with the technical expertise to compile and run legacy software, we built modern cloud infrastructure and graphical interfaces on top of the proven scientific core. The result is a platform that any researcher, anywhere, can access through a browser — no installation, no command line, no barriers.

The Science

What is computational
chemistry?

Computational chemistry uses mathematical models and algorithms to simulate the behaviour of atoms and molecules. Rather than running experiments at a bench, computational chemists can predict how a drug molecule will bind to a protein, how a material will respond to heat or pressure, or how a reaction will proceed — all from a computer.

These predictions are grounded in physics: quantum mechanics for electronic structure, statistical mechanics for ensemble behaviour, and molecular mechanics for large systems. When the underlying models are good, the predictions are remarkably accurate. When the models are fast enough to screen thousands of compounds, they become transformative.

In drug discovery, computational chemistry shortens the path from target to lead compound. Rather than synthesising and testing thousands of molecules in the lab, researchers can computationally screen vast libraries, rank candidates by predicted binding affinity, and focus experimental resources on the most promising leads. The Jorgensen group's free energy perturbation methods are among the most accurate approaches available for this task.

In materials science, the same principles apply to predicting the properties of polymers, solvents, electrolytes, and solid-state materials. The OPLS force fields, developed and refined over decades, are the industry standard for organic and biomolecular systems.

The Yale Legacy

Programs developed at
Yale University.

These tools were developed over forty years within the Jorgensen research group at Yale. Each represents a landmark contribution to the field — widely cited, widely used, and now accessible through the Foundation's cloud platform.

01

BOSS — Biochemical and Organic Simulation System

The cornerstone of the Jorgensen group's software. Molecular mechanics, Monte Carlo statistical mechanics, and semi-empirical quantum mechanics. Used in thousands of published studies for computing conformational energies, solvation free energies, and chemical equilibria.

Since 1983View Program →
02

MCPRO — Monte Carlo for Proteins

An extension of BOSS for biomolecular systems — peptides, proteins, and nucleic acids in explicit solvent. The primary tool for computing protein-ligand binding free energies using statistical perturbation theory.

Since 1995View Program →
03

BOMB — Biochemical and Organic Model Builder

A virtual screening and lead discovery platform. Grows and scores combinatorial libraries inside protein binding sites, then ranks candidates for synthesis and experimental testing. The front end of the Jorgensen group's drug discovery pipeline.

Since 2002View Program →
04

OPLS Force Fields

Optimised Potentials for Liquid Simulations. Developed to reproduce thermodynamic and structural properties of liquids, and extended to cover the full range of organic molecules, proteins, nucleic acids, and lipids. The OPLS-AA and OPLS3 force fields are among the most widely used in the field.

Since 1984View Program →
05

Free Energy Perturbation (FEP)

Statistical perturbation theory applied to computing free energies of binding, hydration, and reaction. FEP calculations using BOSS and MCPRO have been used to guide lead optimisation programs at pharmaceutical companies worldwide, and remain among the most accurate methods for ranking drug candidates.

Since 1985View Program →
Our Mission

Open science.
Sustainable access.

The Jorgensen Foundation was established on a simple principle: world-class computational chemistry tools should be accessible to any researcher, regardless of institution or resources. Academic users receive full access at prices that reflect the reality of research budgets.

The Model

Funded by industry.
Given to academia.

Revenue from industry partnerships — pharmaceutical companies, biotechnology firms, and materials science organisations — directly funds academic access. This model ensures that the tools remain financially sustainable without placing the burden on academic budgets.

The Team

The people behind
the Foundation.

WLJ
William L. Jorgensen
Founder & Scientific Director
Sterling Professor of Chemistry, Yale
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Position Open
Executive Director
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Position Open
Lead Platform Engineer
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Position Open
Computational Chemistry Scientist
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Position Open
Head of Academic Partnerships
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Position Open
Head of Industry Relations
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simulation?

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