Health AI Central
Peer-Reviewed Publication
J Chem Inf Model2026July 23, 2026Journal Article

Identifying Cryptic Binding Sites with Mixed Solvent MD Simulation and SiteMap.

Da Shi1, Dmitry Lupyan2, Steven Jerome3, Robert Abel3, Yuqi Zhang1
1Schrödinger Inc., 9868 Scranton Road, Suite 3200, San Diego, California 92121, United States.
2Schrödinger Inc., 1 Main Street, 11th Floor, Cambridge, Massachusetts 02142, United States.
3Schrödinger Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States.
PubMed DOI

Abstract

Identifying cryptic binding sites in proteins remains a challenge in structure-based drug discovery because these sites are often not apparent in apo structures. Here, we developed and validated a novel "induce-and-identify" workflow that integrates mixed solvent molecular dynamics (MxMD) simulations with SiteMap. This approach leverages MxMD to sample protein conformations to expose hidden pocket…

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