Dataset Information

Introduction to the BioChemical Library (BCL): An Application-Based Open-Source Toolkit for Integrated Cheminformatics and Machine Learning in Computer-Aided Drug Discovery.

ABSTRACT: The BioChemical Library (BCL) cheminformatics toolkit is an application-based academic open-source software package designed to integrate traditional small molecule cheminformatics tools with machine learning-based quantitative structure-activity/property relationship (QSAR/QSPR) modeling. In this pedagogical article we provide a detailed introduction to core BCL cheminformatics functionality, showing how traditional tasks (e.g., computing chemical properties, estimating druglikeness) can be readily combined with machine learning. In addition, we have included multiple examples covering areas of advanced use, such as reaction-based library design. We anticipate that this manuscript will be a valuable resource for researchers in computer-aided drug discovery looking to integrate modular cheminformatics and machine learning tools into their pipelines.

SUBMITTER: Brown BP

PROVIDER: S-EPMC8899505 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Introduction to the BioChemical Library (BCL): An Application-Based Open-Source Toolkit for Integrated Cheminformatics and Machine Learning in Computer-Aided Drug Discovery.

Brown Benjamin P BP Vu Oanh O Geanes Alexander R AR Kothiwale Sandeepkumar S Butkiewicz Mariusz M Lowe Edward W EW Mueller Ralf R Pape Richard R Mendenhall Jeffrey J Meiler Jens J

Frontiers in pharmacology 20220221

The BioChemical Library (BCL) cheminformatics toolkit is an application-based academic open-source software package designed to integrate traditional small molecule cheminformatics tools with machine learning-based quantitative structure-activity/property relationship (QSAR/QSPR) modeling. In this pedagogical article we provide a detailed introduction to core BCL cheminformatics functionality, showing how traditional tasks (e.g., computing chemical properties, estimating druglikeness) can be rea ...[more]

PMID: 35264967

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Project description:PurposeVESCL (pronounced 'vessel') is a novel vessel contouring library for computer-assisted 2D vessel contouring and segmentation. VESCL facilitates manual vessel segmentation in 2D medical images to generate gold-standard datasets for training, testing, and validating automatic vessel segmentation.MethodsVESCL is an open-source C++ library designed for easy integration into medical image processing systems. VESCL provides an intuitive interface for drawing variable-width parametric curves along vessels in 2D images. It includes highly optimized localized filtering to automatically fit drawn curves to the nearest vessel centerline and automatically determine the varying vessel width along each curve. To support a variety of segmentation paradigms, VESCL can export multiple segmentation representations including binary segmentations, occupancy maps, and distance fields.ResultsVESCL provides sub-pixel resolution for vessel centerlines and vessel widths. It is optimized to segment small vessels with single- or sub-pixel widths that are visible to the human eye but hard to segment automatically via conventional filters. When tested on neurovascular digital subtraction angiography (DSA), VESCL's intuitive hand-drawn input with automatic curve fitting increased the speed of fully manual segmentation by 22× over conventional methods and by 3× over the best publicly available computer-assisted manual segmentation method. Accuracy was shown to be within the range of inter-operator variability of gold standard manually segmented data from a publicly available dataset of neurovascular DSA images as measured using Dice scores. Preliminary tests showed similar improvements for segmenting DSA of coronary arteries and RGB images of retinal arteries.ConclusionVESCL is an open-source C++ library for contouring vessels in 2D images which can be used to reduce the tedious, labor-intensive process of manually generating gold-standard segmentations for training, testing, and comparing automatic segmentation methods.

Dataset Information

Introduction to the BioChemical Library (BCL): An Application-Based Open-Source Toolkit for Integrated Cheminformatics and Machine Learning in Computer-Aided Drug Discovery.

Publications

Introduction to the BioChemical Library (BCL): An Application-Based Open-Source Toolkit for Integrated Cheminformatics and Machine Learning in Computer-Aided Drug Discovery.

Similar Datasets

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