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Versatile ligand preparation tool for structure-based workflows



LigPrep is a tool to robustly and rapidly prepare high-quality small molecule ligand structures for structure-based virtual screening and other computational workflows. LigPrep works by expanding tautomeric and ionization states, ring conformations, and stereoisomers consistent with the input information to fully capture the relevant states of the molecule in 3D.

Key Capabilities

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Easily translate molecular structures from 1D, 2D to 3D while carefully enumerating structural and chemical possibilities to ensure the accuracy of subsequent modeling predictions
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Build a completely customized ligand library through automatic elimination of compounds that do not meet user-specified criteria
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Optimize output structures to meet the requirements of the downstream simulation workflows
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Efficiently process an entire database at once at a rate of one ligand per second on a single CPU in calculations that can be distributed across many processors in a cluster
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Browse the list of peer-reviewed publications using Schrödinger technology in related application areas.

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Investigation of drug-polymer miscibility and design of ternary solid dispersions for oral bioavailability enhancement by Hot Melt Extrusion
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Comprehensive evaluation of chiral sedaxane with four stereoisomers for risk reduction: Bioactivity, toxicity, and stereoselective dissipation in crop planting systems
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Computational prodrug design methodology for liposome formulability enhancement of small-molecule APIs
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Antibacterial, Antioxidant, and in silico NADPH Oxidase Inhibition Studies of Essential Oils of Lavandula dentata against Foodborne Pathogens
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Construction of Bio-conjugated nano-vesicles using non-ionic surfactants for targeted drug delivery: A computational supported experimental study
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Drug-Carrier Miscibility in Solid Dispersions of Glibenclamide and a Novel Approach to Enhance Its Solubility Using an Effervescent Agent
Materials Science
Structural basis for strychnine activation of human bitter taste receptor TAS2R46
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Toward in vivo-relevant hERG safety assessment and mitigation strategies based on relationships between non-equilibrium blocker binding, three-dimensional channel-blocker interactions, dynamic occupancy, dynamic exposure, and cellular arrhythmia
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Novel, Self-Assembling Dimeric Inhibitors of Human ‘ Tryptase
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Toward the Rational Design of Sustainable Hair Dyes Using Cheminformatics Approaches: Step 2. Identification of Hair Dye Substance Database Analogs in the Max Weaver Dye Library

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.