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The properties of fragrance molecules in the public databases SuperScent and Flavornet were analyzed to define a “fragrance-like” (FL) property range (Heavy Atom Count ≤ 21, only C, H, O, S, (O + S) ≤ 3, Hydro...
Acute toxicity means the ability of a substance to cause adverse effects within a short period following dosing or exposure, which is usually the first step in the toxicological investigations of unknown subst...
Research efforts in the field of descriptive and predictive Quantitative Structure-Activity Relationships or Quantitative Structure–Property Relationships produce around one thousand scientific publications an...
In many experimental pipelines, clustering of multidimensional biological datasets is used to detect hidden structures in unlabelled input data. Taverna is a popular workflow management system that is used to ...
Measures of similarity for chemical molecules have been developed since the dawn of chemoinformatics. Molecular similarity has been measured by a variety of methods including molecular descriptor based similar...
A challenge for drug of abuse testing is presented by ‘designer drugs’, compounds typically discovered by modifications of existing clinical drug classes such as amphetamines and cannabinoids. Drug of abuse sc...
Combining different sources of knowledge to build improved structure activity relationship models is not easy owing to the variety of knowledge formats and the absence of a common framework to interoperate bet...
Chemical liabilities, such as adverse effects and toxicity, play a significant role in modern drug discovery process. In silico assessment of chemical liabilities is an important step aimed to reduce costs and an...
It is known that any individual similarity measure will not always give the best recall of active molecule structure for all types of activity classes. Recently, the effectiveness of ligand-based virtual scree...
The drug discovery process is now highly dependent on the management, curation and integration of large amounts of potentially useful data. Semantics are necessary in order to interpret the information and der...
The rapid increase in the flow rate of published digital information in all disciplines has resulted in a pressing need for techniques that can simplify the use of this information. The chemistry literature is...
Identification of ligand-protein binding interactions is a critical step in drug discovery. Experimental screening of large chemical libraries, in spite of their specific role and importance in drug discovery,...
There are many databases of small molecules focused on different aspects of research and its applications. Some tasks may require integration of information from various databases. However, determining which e...
Protein-based pharmacophore models are enriched with the information of potential interactions between ligands and the protein target. We have shown in a previous study that protein-based pharmacophore models ...
Modern medicine often clashes with traditional medicine such as Chinese herbal medicine because of the little understanding of the underlying mechanisms of action of the herbs. In an effort to promote integrat...
The calculation of hydrogen positions is a common preprocessing step when working with crystal structures of protein-ligand complexes. An explicit description of hydrogen atoms is generally needed in order to ...
Most work on the topic of activity landscapes has focused on their quantitative description and visual representation, with the aim of aiding navigation of SAR. Recent developments have addressed applications ...
We address the problem of selecting and assessing classification and regression models using cross-validation. Current state-of-the-art methods can yield models with high variance, rendering them unsuitable fo...
A methodology based on spectral similarity is presented that allows to compare NMR predictors without the recourse to assigned experimental spectra, thereby making the task of benchmarking NMR predictors less ...
A new algorithm has been developed to enable the interpretation of black box models. The developed algorithm is agnostic to learning algorithm and open to all structural based descriptors such as fragments, ke...
Chemical space is virtual space occupied by all chemically meaningful organic compounds. It is an important concept in contemporary chemoinformatics research, and its systematic exploration is vital to the dis...
Countless chemicals and mixtures are used in laboratories today, which all possess their own properties and dangers. Therefore, it is important to brief oneself about possible risks and hazards before doing an...
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
This article is part of a Supplement: Volume 6 Supplement 1
