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Cheminformatics Microservice: unifying access to open cheminformatics toolkits
In recent years, cheminformatics has experienced significant advancements through the development of new open-source software tools based on various...
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A survey on computational taste predictors
Taste is a sensory modality crucial for nutrition and survival, since it allows the discrimination between healthy foods and toxic substances thanks...
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Free and open-source QSAR-ready workflow for automated standardization of chemical structures in support of QSAR modeling
The rapid increase of publicly available chemical structures and associated experimental data presents a valuable opportunity to build robust QSAR...
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A ligand-based computational drug repurposing pipeline using KNIME and Programmatic Data Access: case studies for rare diseases and COVID-19
Biomedical information mining is increasingly recognized as a promising technique to accelerate drug discovery and development. Especially,...
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Rational Metabolic Pathway Prediction and Design: Computational Tools and Their Applications for Yeast Systems and Synthetic Biology
Continuous progress in metabolic engineering of microbial cell factories like yeast requires the support of computational tools for finding novel...
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Towards reproducible computational drug discovery
The reproducibility of experiments has been a long standing impediment for further scientific progress. Computational methods have been instrumental...
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IDSL_MINT: a deep learning framework to predict molecular fingerprints from mass spectra
AbstractThe majority of tandem mass spectrometry (MS/MS) spectra in untargeted metabolomics and exposomics studies lack any annotation. Our deep...
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Immunoprecipitation : Variations, Considerations, and Applications
Immunoprecipitation (IP) refers to methods of affinity chromatography that enrich and/or purify a specific protein from a complex mixture using a...
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Hybrid Genome Assembly of Short and Long Reads in Galaxy
Galaxy is a web browser-based data analysis platform that is widely used in biology. Public Galaxy instances allow the analysis of data and...
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Computational Methodology
The implementation described in the previous Chapter was interfaced with a development version of the Q-Chem program package[68] based on version...
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MAW: the reproducible
M etabolomeA nnotationW orkflow for untargeted tandem mass spectrometryMap** the chemical space of compounds to chemical structures remains a challenge in metabolomics. Despite the advancements in untargeted liquid...
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Handling of problematic ion chromatograms with the Automated Target Screening (ATS) workflow for unsupervised analysis of high-resolution mass spectrometry data
Liquid chromatography (LC) or gas chromatography (GC) coupled to high-resolution mass spectrometry (HRMS) is a versatile analytical method for the...
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Automated relative binding free energy calculations from SMILES to ΔΔG
In drug discovery, computational methods are a key part of making informed design decisions and prioritising experiments. In particular, optimizing...
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Human–Device Interaction in the Life Science Laboratory
The interaction of the human user with equipment and software is a central aspect of the work in the life science laboratory. The enhancement of the...
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Empowering large chemical knowledge bases for exposomics: PubChemLite meets MetFrag
Compound (or chemical) databases are an invaluable resource for many scientific disciplines. Exposomics researchers need to find and identify...
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Evaluation guidelines for machine learning tools in the chemical sciences
Machine learning (ML) promises to tackle the grand challenges in chemistry and speed up the generation, improvement and/or ordering of research...
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Rethinking the applicability domain analysis in QSAR models
Notwithstanding the wide adoption of the OECD principles (or best practices) for QSAR modeling, disparities between in silico predictions and...
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Novel Bioinformatics Strategies Driving Dynamic Metaproteomic Studies
Constant improvements in mass spectrometry technologies and laboratory workflows have enabled the proteomics investigation of biological samples of...
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Autonomous Reaction Network Exploration in Homogeneous and Heterogeneous Catalysis
Autonomous computations that rely on automated reaction network elucidation algorithms may pave the way to make computational catalysis on a par with...
