AMBIT-SMARTS

We present new developments in the AMBIT open source software package for
efficient searching of chemical structures and structural fragments. AMBIT-SMARTS
is a Java based software built on top of The Chemistry Development Kit. The
AMBIT-SMARTS parser implements the entire SMARTS language specification with
several syntax extensions that enable support for custom modifications introduced
by third party software packages such as OpenEye, MOE and OpenBabel. The goal of
yet another open-source SMARTS parser implementation is to achieve better
performance and compatibility with multiple existing flavours of the SMARTS
language, as well as to provide utilities for running efficient SMARTS queries in
large structural databases. We describe a combination of approaches towards
lowering the computational cost and improving the response time of substructure
queries. An exhaustive comparison of the AMBIT algorithm with several subgraph
isomorphism implementations is performed. To demonstrate the performance of the
entire system from an end-user point of view, response time statistics for Web
service substructure search queries against a database of 4.5 M structures are
also reported. The package has wide applicability in the implementation of
various chemoinformatics tasks. It has already been used in several projects
dealing with descriptor calculation and predictive algorithms, database queries,
web applications and web services.

AMBIT-SMARTS: Efficient Searching of Chemical Structures and Fragments.

AMBIT-SMARTS is a parser that includes a complete SMARTS language specification and extensions for support MOE, OpenEye, and OpenBabel. The AMBIT-SMARTS algorithm used The Chemistry Development Kit. See  <a href="https://bioinformaticshome.com/db/tool/AMBIT" target="_blank">AMBIT</a>.

AMBIT-SMARTS

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