Easy-to-use pharmacophore modeling solution for ligand- and structure-based drug design

Create and validate pharmacophore hypotheses

Identify novel hits with pharmacophore screening

Phase is an intuitive pharmacophore modeling tool that allows assessment of compounds based on the steric and electronic features of molecules known to have biological activity. Phase employs a unique common pharmacophore perception algorithm designed for use in both lead optimization and virtual screening, and helps create understanding of an unknown binding site in the absence of a protein structure.

Key Capabilities

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Easily setup, execute, and analyze pharmacophore screening with an intuitive user interface
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Screen and determine the spatial arrangement of chemical features that interact with a receptor and use the binding information to better identify novel compounds and chemotypes that are likely to bind to the target receptor
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Create hypotheses from protein-ligand complexes, apo proteins, or from ligands and selectively merge hypotheses features to create hybrid models 
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Exercise precise control over pharmacophore creation, generation and screening
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Rapidly and thoroughly sample conformational, ionization, and tautomeric states, with optional minimization using the best-in-class OPLS4 force field to create a phase database 
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Benefit from fully prepared databases of purchasable compounds from Enamine, MilliporeSigma, MolPort and Mcule for out-of-the-box screening

Save compute time and effort using prepared commercial libraries for Phase

Schrödinger has partnered with leading providers to help you access commercial databases of fragments, lead-like, near drug-like, and drug-like compounds ranging from millions to billions of compounds encompassing a vast chemical space.

Case StudyCase-study_Nimbus-ACC

Discovery of a novel, potent ACC inhibitor driven by computationally-guided design and assessment of water energetics in the binding site

See how Nimbus identified potent, selective inhibitors using a virtual screening workflow guided by hydration energetics.

read the case study

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

Life Science
ePharmaLib: A Versatile Library of e-Pharmacophores to Address Small-Molecule (Poly-)Pharmacology
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A Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein-Ligand Binding
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A Comprehensive Ligand Based Mapping of the ‘2 Receptor Binding Pocket
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Identification of Novel Fluorescent Probes Preventing PrPSc Replication in Prion Diseases
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Discovery and Structure Activity Relationships of a Highly Selective Butyrylcholinesterase Inhibitor by Structure-Based Virtual Screening
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IDSite: An Accurate Approach to Predict P450-Mediated Drug Metabolism
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Discovery of Thienoquinolone Derivatives as Selective and ATP Non-Competitive CDK5/p25 Inhibitors by Structure-Based Virtual Screening
Life Science
Optimization, Pharmacophore Modeling and 3D-QSAR Studies of Sipholanes as Breast Cancer Migration and Proliferation Inhibitors
Life Science
Multiple e-pharmacophore modeling combined with high-throughput virtual screening and docking to identify potential inhibitors of ‘-Secretase(BACE1)
Life Science
PHASE: A Novel Approach to Pharmacophore Modeling and 3D Database Searching

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.