2nd International Conference on Chemo and Bioinformatics ICCBIKG 2023 (51-52)
АУТОР(И) / AUTHOR(S): Rino Ragno, Alessio Ragno
Е-АДРЕСА / E-MAIL: rino.ragno@uniroma1.it
DOI: 10.46793/ICCBI23.051R
САЖЕТАК / ABSTRACT:
Field-Based Three-Dimensiona Quantitative Strucutere-Activity Relationships (FB 3D QSAR) comprise computational approaches used in drug design and molecular modeling to analyze the relationship between the three-dimensional structure of a list of molecules (described by molecular interaction fields) and their associated biological activities (BAs). It aims to understand how different structural features of the molecules contribute to enhancing or lowering the biological potency. The process of FB 3D QSAR involves several steps. First, a dataset of structurally diverse molecules with known BAs is selected. Then, their three-dimensional structures are generated using computational methods. Next, in the classical form of Cramer [1], sterical and electrostatic molecular interaction fields (MIFs) are calculated and as a final step a mathematical model is built through the correlation of BAs with MIFs by means of projection of latent structures (PLS) algorithm. With our interest in making 3D QSAR accessible to all as done with the www.3d-qsar.com [2] db.3d-qsar.com, the first publicly available database of 3D QSAR models, is presented in which the user can insert or draw a molecule and predict its potency against an available target. All the models available on db.3d-qsar.com have been heavily optimized in prediction power through a semi-systematic pretreatment and parameter selection procedure by initially dividing the datasets into training (80%) and prediction (20%) sets. Each published model was and will be prepared by a selection among thousands of alignment trials. The selected models were finally characterized using a validation set compiled with molecules taken from the ChEMBL database. At the time of writing more than 40 models associated to more than 30 different pharmacological targets have been prepared and are ready to be used. At the time of the presentation db.3d-qsar.com will be accessible to the public and during the presentation its features will be shown.
КЉУЧНЕ РЕЧИ / KEYWORDS:
3D QSAR, Prediction of activity, db.3d-qsar.com, www.3d-qsar.com
ЛИТЕРАТУРА / REFERENCES:
- Cramer, R.D.; Patterson, D.E.; Bunce, J.D.; Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc. 1988, 110, 5959-67
- Ragno, R. www.3d-qsar.com: a web portal that brings 3-D QSAR to all electronic devices-the Py-CoMFA web application as tool to build models from pre-aligned datasets. J. Comput., Aided Mol. Des. 2019, 33, 855-864.