A comprehensive cheminformatics computing environment
The Advantages of Cheminformatics
The discovery of novel therapeutic agents requires exploring increasingly expanded and complex chemical space, resulting in rapidly growing data proliferation. Computational techniques that scale favorably with the expanding chemical space and provide efficient insights have become critical to any lead discovery and lead optimization effort.
Cheminformatics techniques such as fingerprint-based similarity searching and substructure matching can screen millions of compounds in seconds; clustering and diversity selection can analyze and improve the content of real and virtual compound libraries; principal components analysis and self-organizing maps reduce complex, high dimensional information into easily visualized relationships in a small number of dimensions; and supervised learning techniques offer quantitative models that elucidate structure-activity relationships and provide insights into new compounds' activities.
Cross-platform, cutting edge user interface:
Built from the ground up, the Canvas graphical interface was designed with scalability in mind, and features a chemical spreadsheet with smooth, instantaneous access to millions of structures and thousand of properties, all of which are stored in an infinitely expandable relational database.
Users can save a snapshot of any particular set of rows and columns, which can be recalled and modified at any later time and combined with other custom views using various logical operations.
Unparalleled fingerprinting capabilities:
Canvas offers seven types of hashed fingerprints, MACCS keys, and customizable SMARTS-base structural keys. All popular fingerprinting methods are represented, and a sparse storage scheme allows each chemical feature to be mapped to a unique bit.
Ultra-fast substructure searching:
As structures are imported into a Canvas project, a 2D index is automatically built in the background, which allows the user to search millions of compounds in mere seconds.
Explore activity of a congeneric series based on R-group composition.
Classify and explore a set of structures based on the scaffolds they contain.
Users can create custom rules to prohibit or require the presence of any number of different chemical features, or use the built-in REOS filter.
Data analysis and visualization:
Univariate and bivariate statistics, scatter plots, histograms, pie charts, and heat maps allow the user to spot trends and rapidly drill down to critical pieces of information.
Maximum common substructure:
A unique, innovative methodology rigorously identifies maximum common substructures matching any number of compounds at a speed that is orders of magnitude faster than conventional algorithms.
Extensive access to tools for property calculations, clustering, diversity, classification, QSAR, and data reduction.
The core Canvas engine is exposed through a Python API (application programming interface), which provides a comprehensive, object-oriented library that allows users to develop custom applications.
Citations and Acknowledgements
Schrödinger Release 2016-4: Canvas, Schrödinger, LLC, New York, NY, 2016.
ö Duan, J.; Dixon, S.L.; Lowrie, J.F.; Sherman, W., "Analysis and Comparison of 2D Fingerprints: Insights into Database Screening Performance Using Eight Fingerprint Methods," J. Molec. Graph. Model., 2010, 29, 157-170
ö Sastry, M.; Lowrie, J.F.; Dixon, S.L.; Sherman, W., "Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments," J. Chem. Inf. Model., 2010, 50, 771-784