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Rapid pKa and protonation state prediction tool

Prioritize the right protonation states for your drug discovery or materials science research

Epik is a tool for accurately and rapidly predicting the aqueous phase pKa values and protonation state distributions of complex, drug-like molecules. Leveraging the power of Schrödinger’s machine learning technology, the Epik model employs an ensemble of atomic graph convolutional neural networks, trained across a broad range of chemical space.

Key Capabilities

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Query the microscopic and macroscopic pKa values of a small molecule
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Enumerate and score protonation states to obtain the lowest energy states at a specified pH
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Generate an easy-to-read report that includes the macroscopic pKa values of a small molecule, its different constituent protonation states and their populations, and a speciation diagram for the major species in solution
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Make reliable predictions across an extremely broad range of chemistry supported by ML technology
FeaturedSchrödinger solutions for small molecule protonation state enumeration and pKa prediction

Schrödinger solutions for small molecule protonation state enumeration and pKa prediction

Schrödinger provides several solutions for predicting pKa values, protonation state distribution, and derived properties that can be applied across a range of drug discovery stages – from screening through lead optimization.

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Browse the list of peer-reviewed publications using Schrödinger technology in related application areas.

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FEP augmentation as a means to solve data paucity problems for machine learning in chemical biology
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Adverse Drug Reactions Triggered by’the Common HLA-B*57:01 Variant: A Molecular Docking Study
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Epik: a software program for pKa prediction and protonation state generation for drug-like molecules
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Structure-based design of potent aromatase inhibitors by high-throughput docking
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Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution
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Estimating binding affinities by docking/scoring methods using variable protonation states
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Testing physical models of passive membrane permeation
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Predicting and improving the membrane permeability of peptidic small molecules
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Discovery of Thienoquinolone Derivatives as Selective and ATP Non-Competitive CDK5/p25 Inhibitors by Structure-Based Virtual Screening
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Boosting virtual screening enrichments with data fusion: Coalescing hits from two-dimensional fingerprints, shape, and docking

Training & Resources

Online certification courses

Level up your skill set with hands-on, online molecular modeling courses. These self-paced courses cover a range of scientific topics and include access to Schrödinger software and support.


Learn how to deploy the technology and best practices of Schrödinger software for your project success. Find training resources, tutorials, quick start guides, videos, and more.