The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform

SA Bray, X Lucas, A Kumar, BA Grüning - Journal of Cheminformatics, 2020 - Springer
Here, we introduce the ChemicalToolbox, a publicly available web server for performing
cheminformatics analysis. The ChemicalToolbox provides an intuitive, graphical interface for …

Open-source machine learning in computational chemistry

A Hagg, KN Kirschner - … of Chemical Information and Modeling, 2023 - ACS Publications
… To this end, we also include computational chemistry open-source software for generating
… machine learning work, open data, open source (code), and open models, we provide some …

[PDF][PDF] The ChemicalToolBox–Computational Chemistry in Galaxy

S Bray, A Khanteymoori, B Grüning - Developing a workflow management …, 2023 - d-nb.info
… Furthermore, apart from the features of the ChemicalToolbox itself, the inherent flexibility
of the Galaxy system allows combination of the ChemicalToolbox with existing platforms …

Cheminformatics Python Microservice (CPM): unifying access to open cheminformatics toolkits

V Chandrasekhar, N Sharma, J Schaub, C Steinbeck… - 2023 - chemrxiv.org
… code changes and toolkit versions. In the CPM container, RDKit and Open Babel
cheminformatics toolkits are accessed natively using Python, while the Chemistry Development Kit (…

Cheminformatics Microservice: unifying access to open cheminformatics toolkits

V Chandrasekhar, N Sharma, J Schaub… - Journal of …, 2023 - Springer
… Where a specific functionality provided by the microservice can be achieved in a similar
manner with RDKit, CDK, or Open Babel, the user has the option of employing the toolkit of their …

Free and open source software for computational chemistry education

S Lehtola, AJ Karttunen - Wiley Interdisciplinary Reviews …, 2022 - Wiley Online Library
… In the lack of a universal standard, the interconversion of various input and output file formats
between different programs can be carried out for example with the Open Babel 207 and …

An open source chemical structure curation pipeline using RDKit

AP Bento, A Hersey, E Félix, G Landrum… - Journal of …, 2020 - Springer
… A chemical curation pipeline has been developed using the open source toolkit RDKit. It
comprises three components: a Checker to test the validity of chemical structures and flag any …

AutoSolvate: A toolkit for automating quantum chemistry design and discovery of solvated molecules

E Hruska, A Gale, X Huang, F Liu - The Journal of Chemical Physics, 2022 - pubs.aip.org
… -solvent quantum chemistry (QC) calculations for arbitrary solutes and solvents in an
open-source framework are still lacking. We developed AutoSolvate, an open-source toolkit, to …

An open-source molecular builder and free energy preparation workflow

MK Bieniek, B Cree, R Pirie, JT Horton… - … chemistry, 2022 - nature.com
open science effort to crowd source design of SARS-CoV-2 main protease inhibitors 25 , the
Omega toolkit … In this study, we used the Open Babel software 33 for parsing input structure …

molli: A General-Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction.

AS Shved, BE Ocampo, ES Burlova, CL Olen… - 2024 - chemrxiv.org
… of modern chemistry. The adoption and success of data-oriented approaches to chemical
research is … Herein, we introduce the MOLecular LIibrary toolkit, “molli”, which is a Python 3 …