Books
Docking Screens for Drug Discovery. Editor: de Azevedo Jr., Walter Filgueira (Ed.)
Projects
SAnDReS: Statistical Analysis of Docking Results and Scoring functions
Taba: A Tool to Analyze the Binding Affinity
Citation
Editorships
Frontiers Section Editor (Bioinformatics and Biophysics) for the Current Drug Targets ISSN: 1873-5592
Section Editor (Bioinformatics in Drug Design and Discovery) for the Current Medicinal Chemistry ISSN: 1875-533X
Member of the Editorial Board of the Journal of Molecular Structure ISSN: 0022-2860
Member of the Editorial Board of Molecular Diversity ISSN: 1381-1991 (Print) 1573-501X (Online)
Associate Editor for Exploration of Drug Science
Reviewer Editor for Frontiers in Chemistry ISSN: 2296-2646
Member of the Editorial Board for the Organic and Medicinal Chemistry International Journal ISSN: 2474-7610
Dr. Walter F. de Azevedo, Jr. has been ranked among the most influential researchers in the world according to a database created by Journal Plos Biology (see news here). Dr. Azevedo`s influential works can be found here. Citation metrics available here.
Updates
Exploring the Scoring Function Space [>>]
A view of the scoring function space as a way to develop a computational model to predict ligand-binding affinity.
We envisage protein-ligand interaction as a result of the relation between the protein space (Smith, 1970; Hou et al., 2005) and the chemical space (Bohacek et al., 1996; Dobson, 2004; Kirkpatrick & Ellis, 2004; Lipinski & Hopkins, 2004; Shoichet, 2004; Stockwell, 2004), and we propose to approach these sets as a unique complex system, where the application of computational methodologies could contribute to understand the structural basis for the specificity of ligands for proteins. Such approaches have the potential to create novel scoring functions to predict binding affinity with superior predictive power when compared with classical scoring functions available in docking programs (de Azevedo Jr., 2021). We propose to use the abstraction of a mathematical space composed of infinite computational models to predict ligand-binding affinity, named as scoring function space (Ross et al., 2013; Heck et al., 2017; Bitencourt-Ferreira & de Azevedo Jr., 2019; Veríssimo et al., 2022) . By the use of supervised machine learning techniques, we can explore this scoring function space (Bitencourt-Ferreira & de Azevedo Jr., 2019) to build a computational model targeted to a specific protein system (targeted-scoring funcion) (Seifert, 2009). For instance, we created targeted-scoring functions for cyclin-dependent kinases (EC 2.7.11.22) (de Ávila et al., 2017; Levin et al., 2018) and HIV-1 protease (EC 3.4.23.16) (Pintro & de Azevedo, 2017). We developed the programs SAnDReS (Xavier et al., 2016; Bitencourt-Ferreira & de Azevedo Jr., 2019), SFSXplorer, and Taba (da Silva et al., 2020; Bitencourt-Ferreira et al., 2021) to generate computational models to predict ligand-binding affinity. These programs are integrated computational tools to explore the scoring function space.