Fathom Therapeutics

Atommap, established in 2023 and headquartered in New York City, is a computational drug discovery company operating at the intersection of quantum physics, artificial intelligence, and computation-driven design. The company was founded by CEO Huafeng Xu, Chief Computational Scientist Jesus Izaguirre, and Chief Technology Officer Yujie Wu. The leadership team brings a wealth of experience from previous roles at companies like Silicon Therapeutics, Roivant Discovery, D.E. Shaw Research, and Schrodinger, where they were instrumental in developing widely used software for molecular dynamics simulations (Desmond) and protein-ligand affinity prediction (FEP+). Dr. Xu, a PhD graduate from Columbia University, previously served as CTO of Silicon Therapeutics and Roivant Discovery, leading the development of computational platforms for drug discovery.

The firm's core business revolves around its computational molecular design platform, which is engineered to accelerate the discovery of new therapeutic molecules. This platform integrates physics-based simulations, machine learning models, and high-performance computing to generate and assess molecular designs at an atomic level. By modeling biomolecular motion, the system aims to uncover novel therapeutic approaches and expand the design space for new drugs. Atommap's technology has demonstrated the ability to significantly reduce both the time and cost associated with molecular discovery, in some cases by more than half and by 80%, respectively. The platform's capabilities include predicting binding affinities, simulating protein-protein interactions, and optimizing therapeutic degraders, which are molecules designed to break down specific target proteins. This has enabled the company to identify potent inhibitors for challenging oncology targets and deliver a clinical-stage STING agonist.

Atommap serves pharmaceutical researchers and biotech companies, offering its services through two primary business models: Computation as a Service (CaaS) and Molecular Discovery as a Service (MDaaS). The CaaS model provides pay-as-you-go access to their computational tools, allowing clients to test the platform on a smaller scale without a large upfront investment. The MDaaS model offers an end-to-end partnership where Atommap manages the entire molecular discovery project, from initial hits to development candidates, freeing partners to concentrate on biological and clinical validation. In November 2023, the company secured $7.08 million in a seed funding round led by Sutter Hill Ventures.

Keywords: computational drug discovery, quantum physics in drug design, AI in pharmaceuticals, molecular design, therapeutic molecule invention, physics-based simulations, machine learning models, high-performance computing, protein-protein interactions, binding affinity prediction, therapeutic degraders, STING agonist, oncology targets, Computation as a Service (CaaS), Molecular Discovery as a Service (MDaaS), Huafeng Xu, Jesus Izaguirre, Yujie Wu, atomistic simulation, molecular dynamics, drug development, biotech, life sciences, FEP+, Desmond, generative design, computational assay