Rethinking the 'best method' paradigm: The effectiveness of hybrid and multidisciplinary approaches in chemoinformatics
In Chemoinformatics, as in many other computational-related disciplines, it is a common practice to identify the “single best” approach or methodology, for instance, identify the best fingerprint representation, the best single virtual screening approach or protocol, the optimal representation of th...
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| Language: | English |
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Elsevier
2024-12-01
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| Series: | Artificial Intelligence in the Life Sciences |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2667318524000242 |
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| author | José L. Medina-Franco Johny R. Rodríguez-Pérez Héctor F. Cortés-Hernández Edgar López-López |
| author_facet | José L. Medina-Franco Johny R. Rodríguez-Pérez Héctor F. Cortés-Hernández Edgar López-López |
| author_sort | José L. Medina-Franco |
| collection | DOAJ |
| description | In Chemoinformatics, as in many other computational-related disciplines, it is a common practice to identify the “single best” approach or methodology, for instance, identify the best fingerprint representation, the best single virtual screening approach or protocol, the optimal representation of the chemical space, the best predictive model, to name a few. In molecular modeling, a typical example is finding the best docking program. However, it is also known that each approach has its advantages and limitations. There are examples of benchmark studies comparing different approaches to find the most appropriate solution, and it is common to find that there are no single best programs in such studies. Yet, searching for the “best” methods is still common. The main goal of this work is to survey hybrid methodologies recently developed in Chemoinformatics. The list of approaches is not exhaustive, but it aims to cover several representative applications. One of the major outcomes of the survey is that, for various purposes, individual methods do not perform as well as the combination of approaches because single methods have inherent limitations with advantages and disadvantages. |
| format | Article |
| id | doaj-art-9fa6ce4f9603481aa53448085c9cd258 |
| institution | OA Journals |
| issn | 2667-3185 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Artificial Intelligence in the Life Sciences |
| spelling | doaj-art-9fa6ce4f9603481aa53448085c9cd2582025-08-20T01:56:17ZengElsevierArtificial Intelligence in the Life Sciences2667-31852024-12-01610011710.1016/j.ailsci.2024.100117Rethinking the 'best method' paradigm: The effectiveness of hybrid and multidisciplinary approaches in chemoinformaticsJosé L. Medina-Franco0Johny R. Rodríguez-Pérez1Héctor F. Cortés-Hernández2Edgar López-López3DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, México City 04510, Mexico; Corresponding authors.GIFAMol Research Group, School of Chemistry Technology, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; GIFAMol Research Group, School of Basic Sciences, Technology and Engineering, Universidad Nacional Abierta y a Distancia, Dosquebradas 661001, ColombiaDepartment of Chemistry and Graduate Program in Pharmacology, Center for Research and Advanced Studies of the National Polytechnic Institute, Section 14-740, Mexico City 07000, MexicoDIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, México City 04510, Mexico; Department of Chemistry and Graduate Program in Pharmacology, Center for Research and Advanced Studies of the National Polytechnic Institute, Section 14-740, Mexico City 07000, Mexico; Corresponding authors.In Chemoinformatics, as in many other computational-related disciplines, it is a common practice to identify the “single best” approach or methodology, for instance, identify the best fingerprint representation, the best single virtual screening approach or protocol, the optimal representation of the chemical space, the best predictive model, to name a few. In molecular modeling, a typical example is finding the best docking program. However, it is also known that each approach has its advantages and limitations. There are examples of benchmark studies comparing different approaches to find the most appropriate solution, and it is common to find that there are no single best programs in such studies. Yet, searching for the “best” methods is still common. The main goal of this work is to survey hybrid methodologies recently developed in Chemoinformatics. The list of approaches is not exhaustive, but it aims to cover several representative applications. One of the major outcomes of the survey is that, for various purposes, individual methods do not perform as well as the combination of approaches because single methods have inherent limitations with advantages and disadvantages.http://www.sciencedirect.com/science/article/pii/S2667318524000242ConsensusData fusionEducationHybrid methodMachine learningMultidisciplinary |
| spellingShingle | José L. Medina-Franco Johny R. Rodríguez-Pérez Héctor F. Cortés-Hernández Edgar López-López Rethinking the 'best method' paradigm: The effectiveness of hybrid and multidisciplinary approaches in chemoinformatics Artificial Intelligence in the Life Sciences Consensus Data fusion Education Hybrid method Machine learning Multidisciplinary |
| title | Rethinking the 'best method' paradigm: The effectiveness of hybrid and multidisciplinary approaches in chemoinformatics |
| title_full | Rethinking the 'best method' paradigm: The effectiveness of hybrid and multidisciplinary approaches in chemoinformatics |
| title_fullStr | Rethinking the 'best method' paradigm: The effectiveness of hybrid and multidisciplinary approaches in chemoinformatics |
| title_full_unstemmed | Rethinking the 'best method' paradigm: The effectiveness of hybrid and multidisciplinary approaches in chemoinformatics |
| title_short | Rethinking the 'best method' paradigm: The effectiveness of hybrid and multidisciplinary approaches in chemoinformatics |
| title_sort | rethinking the best method paradigm the effectiveness of hybrid and multidisciplinary approaches in chemoinformatics |
| topic | Consensus Data fusion Education Hybrid method Machine learning Multidisciplinary |
| url | http://www.sciencedirect.com/science/article/pii/S2667318524000242 |
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