Comprehensively Searching Ultra-Large Spaces for Ligand Analogues in 2D and 3D.

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Early-stage drug discovery depends on finding analogues of initial hits that mimic or approximate their 3D shape and pharmacophore configuration, with features carefully reweighted for bioisosteres. These analogues should offer novel scaffolds and distinct ADMET properties that resolve liabilities. The Alipheron platform combines physics- and ML-based methods to retrieve highly diverse active scaffolds by 2D and 3D search in commercial and custom trillion-scale spaces, enabling broad IP protection in the target domain.

Product · Pharos3D

What sets Pharos3D apart

Pharos3D, our 3D shape and pharmacophore search engine, has been put to the test by computational chemistry and CADD teams in pharma, biotech and academia on make-on-demand spaces of up to 100 trillion compounds. These are the differences that mattered most to them.

3D search of 100 trillion compounds, in hours

Comprehensive 3D shape and pharmacophore search used to stop at under 5 billion compounds. Pharos3D searches at least 100 trillion (10¹⁴), over four orders of magnitude more, in 5.5 hours per space on average on a single 80-core ARM CPU server. See the search times
Comprehensive search, not sampling

Unlike sampling methods such as Thompson Sampling, whose recall drops as spaces grow, Pharos3D finds anything findable, with close to 100% query recovery. That means far more diverse shape- and pharmacophore-aligned scaffolds, and dissimilar hits with different ADMET profiles. Read the benchmark
Multiple chemotypes, a stronger patent position

Each distinct, progressable chemotype can carry its own composition-of-matter patent family, more defensible than one oversized Markush genus and backed by the cross-chemotype data patent offices increasingly require. Claiming them first leaves competitors little room to scaffold-hop, and adds backup series that raise the program's value in licensing and M&A.
Curated vendor spaces

Direct access to nine regularly updated, highly diverse and well-maintained spaces from trusted chemical suppliers operating worldwide. Diversity, delivery times and synthetic feasibility are documented for each space. Compare the spaces
Fragment linking in trillion-sized spaces

Pharos3D can combine several distinct fragments into a single molecule that is synthesizable and orderable, solving the classic fragment-linking (“two-fragment”) problem directly in trillion-sized make-on-demand space. See how it works
Built for automated and agentic workflows

Alongside the interactive interface, Pharos3D and every other Alipheron tool can be driven through a REST API, so searches run unattended in automated pipelines, including agentic workflows in which an AI agent submits queries and processes the results.