Chemoinformatics and Bioinformatics Tools in Structure-Activity Modelling in Molecular Sciences: 3rd Edition
A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".
Deadline for manuscript submissions: closed (30 January 2026) | Viewed by 1646
Special Issue Editor
Interests: chemoinformatics; structural bioinformatics; structure–activity modeling; QSAR; QSPR; molecular modeling; computational chemistry; molecular structural biophysics; development of model validation algorithms; variable selection algorithms; classification modeling; chance accuracy estimation; development of accuracy parameters; computational research in bioprospecting research; protein structure analysis and prediction
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Special Issue Information
Dear Colleagues,
At a time of universal digitization of data in various fields of research, including molecular sciences, there are more and more studies modeling the continuous or classification endpoints (activities/properties) of molecules. In doing so, the endpoints of molecules are most often classified (digitized) into two classes—active or inactive, and the classification is often carried out by grouping data into three or more classes.
Quantitative structure–activity/property relationships (QSAR/QSPR) are the most common, but not the only, forms of structure–endpoint models in molecular sciences. The accuracy of these models is expressed through validation procedures, and many quality parameters are defined in the OECD document related to regulatory structure–activity models for the purpose of health and environmental protection [1]. In this document, the accuracy parameters of classification models are very sparsely presented. However, numerous accuracy parameters are used today, and those used for classification models are calculated from the confusion matrix elements [2]. There is also an increased need for a better definition of procedures for the validation of regulatory structure–activity models in the OECD document [1]. Their application in environmental and health protection (toxicity, bioavailability, sorption, biodegradability, etc.) has been defined by EU REACH regulations [3].
The development of the structure–activity modeling of different types of endpoints of molecules (usually various types of biological activities) is accelerated using chemoinformatics and bioinformatics tools, servers, algorithms, and databases developed for small molecules, macromolecules (RNA and DNA), and proteins.
The research activities in the development of novel chemoinformatics and bioinformatics tools are particularly important topics for this Special Issue, such as the following:
- Valuable databases, servers, and data mining tools;
- Drug or lead structure identification;
- Dereplication approaches used in bioprospecting research;
- Structure optimization tools;
- Molecular descriptors;
- Modeling and variable selection algorithms;
- Computational model validation methods;
- Multivariate linear and nonlinear methods;
- Machine learning and deep learning algorithms;
- Predictive or descriptive structure–activity models;
- Visualization tools in chemoinformatics and bioinformatics;
- Protein–ligand (target/small compound) interactions;
- Protein–protein interactions;
- Molecular docking;
- Macromolecule–macromolecule interactions;
- Macromolecule–ligand/drug interactions;
- RNA structure modeling;
- DNA structure modeling.
All these topics are of the highest importance for structure–activity modeling in molecular sciences.
This Special Issue aims to collect relevant contributions (papers) relating to one or more of the topics listed above (and those related to them), which are important for the acceleration of structure–activity research in molecular sciences. Applications aimed at modeling a broad spectrum of chemical, biological, pharmaceutical, biochemical, and environmentally relevant activities and properties of molecules are also welcome.
All forms of scientific articles covering the mentioned or related topics are welcome, i.e., original papers, reviews, and communications.
References
[1] Guidance Document on the Validation of (Quantitative) Structure-Activity Relationship [(Q)SAR] Models. Available online: https://www.oecd.org/env/guidance-document-on-the-validation-of-quantitative-structure-activity-relationship-q-sar-models-9789264085442-en.htm.
[2] D. M. W. Powers, Evaluation: from precision, recall and f-measure to roc, informedness, markedness & correlation. J. Machine Learning Techn. 2011, 2, 37–63.
[3] Regulation (EC) No 1907/2006: REACH—Registration, Evaluation, Authorisation and Restriction of Chemicals. Available online: http://ec.europa.eu/enterprise/sectors/chemicals/reach/index_en.htm.
Dr. Bono Lučić
Guest Editor
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Keywords
- chemoinformatics tools and models
- bioinformatics tools and models
- structure–activity modeling
- structure–property modeling
- QSAR
- QSPR
- drug/structure identification in bioprospecting research
- molecular docking
- molecular interactions
- protein–protein interactions
- development of algorithms
- databases and web servers
- data mining in chemoinformatics and bioinformatics
- structure representation and optimization
- molecular descriptors
- modeling of health and environmentally relevant endpoints (activities, properties)
- toxicity modeling and prediction
- carcinogenicity modeling and prediction
- computational methods in molecular sciences
- model validation approaches
- multivariate modeling
- predictive modeling
- descriptive modeling
- continuous data modeling
- classification data modeling
- machine learning in molecular sciences
- deep learning in molecular sciences
- structure visualization tools
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