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Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease
We present several workflows for protein-ligand docking and free energy calculation for use in the workflow management system Galaxy. The workflows...
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Bioinformatic Workflows for Metaproteomics
The strong influence of microbiomes on areas such as ecology and human health has become widely recognized in the past years. Accordingly, various...
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From desktop to benchtop with automated computational workflows for computer-aided design in asymmetric catalysis
The organic chemist’s toolbox is vast, with technologies to accelerate the synthesis of novel chemical matter. The field of asymmetric catalysis is...
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Revolution of Artificial Intelligence in Computational Chemistry Breakthroughs
The field of computational chemistry is one of many sectors that artificial intelligence (AI) has revolutionized in recent years. Chemists are now...
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CACHE (Critical Assessment of Computational Hit-finding Experiments): A public–private partnership benchmarking initiative to enable the development of computational methods for hit-finding
One aspirational goal of computational chemistry is to predict potent and drug-like binders for any protein, such that only those that bind are...
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SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction
A novel crystallographic fragment screening data set was generated and used in the SAMPL7 challenge for protein-ligands. The SAMPL challenges...
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Image Based Methodologies, Workflows, and Calculation Approaches for Tortuosity
In this chapter, modern methodologies for characterization of tortuosity are thoroughly reviewed. Thereby, 3D microstructure data is considered as...
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Bridging the complexity gap in computational heterogeneous catalysis with machine learning
Heterogeneous catalysis underpins a wide variety of industrial processes including energy conversion, chemical manufacturing and environmental...
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Molecular Dynamics Simulations for Computational Biology
Why it is important to know this material? Protein binding is implied in all biological mechanisms, and the definition of quantitative models and...
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Automated Identification of Ordered Phases for Simulation Studies of Block Copolymers
In unit cell simulations, identification of ordered phases in block copolymers (BCPs) is a tedious and time-consuming task, impeding the advancement...
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Non-targeted screening workflows for gas chromatography–high-resolution mass spectrometry analysis and identification of biomagnifying contaminants in biota samples
The health of key species in the Baltic region has been impaired by exposure to anthropogenic hazardous substances (AHSs), which accumulate in...
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Deconstructing allostery by computational assessment of the binding determinants of allosteric PTP1B modulators
Fragment-based drug discovery is an established methodology for finding hit molecules that can be elaborated into lead compounds. However it is...
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Non-target screening in water analysis: recent trends of data evaluation, quality assurance, and their future perspectives
This trend article provides an overview of recent advancements in Non-Target Screening (NTS) for water quality assessment, focusing on new methods in...
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Mass-Suite: a novel open-source python package for high-resolution mass spectrometry data analysis
Mass-Suite ( MSS ) is a Python-based, open-source software package designed to analyze high-resolution mass spectrometry (HRMS)-based non-targeted...
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Computational screening methodology identifies effective solvents for CO2 capture
Carbon capture and storage technologies are projected to increasingly contribute to cleaner energy transitions by significantly reducing CO 2 ...
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The Therapeutic Antibody Profiler for Computational Developability Assessment
The need to consider an antibody’s “developability” (immunogenicity, solubility, specificity, stability, manufacturability, and storability) is now...
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Chemical reaction network knowledge graphs: the OntoRXN ontology
AbstractThe organization and management of large amounts of data has become a major point in almost all areas of human knowledge. In this context,...
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Combinatorial synthesis for AI-driven materials discovery
Combinatorial synthesis of solid-state materials comprises the use of automation or parallelization to systematically vary synthesis parameters. This...
