Statistical Analysis of Docking Results and Scoring Functions 2.0.0 (SAnDReS 2.0.0)
SAnDReS 2.0.0 (de Azevedo Jr et al., 2024) brings together the most advanced tools for protein-ligand docking simulation and machine-learning modeling. We have the AutoDock Vina 1.2 (Eberhardt et al., 2021) as a docking engine. Also, SAnDReS 2.0.0 uses machine-learning methods available in the Scikit-Learn library (Pedregosa et al., 2011). It has 54 regression methods which allow us to explore the Scoring Function Space (SFS) (Ross et al., 2013). This exploration of the SFS permits us to have an adequate machine-learning (ML) model for a targeted protein system. SAnDReS predicts binding affinity for a specific protein system with superior performance compared against classical scoring functions. In summary, SAnDReS 2.0.0 makes it possible for you to design a scoring function adequate to the protein system of your interest.
You need Python 3 installed on your computer to run SAnDReS 2.0.0. In addition, you need Pandas, Matplotlib, NumPy, Scikit-Learn (Pedregosa et al., 2011), and SciPy. It is also necessary to have ADFRsuite version 1.0 (Ravindranath et al., 2015). You can make the installation of Python packages faster by installing Anaconda.
de Azevedo WF Jr, Quiroga R, Villarreal MA, da Silveira NJF, Bitencourt-Ferreira G, da Silva AD, Veit-Acosta M, Oliveira PR, Tutone M, Biziukova N, Poroikov V, Tarasova O, Baud S. SAnDReS 2.0: Development of machine-learning models to explore the scoring function space. J Comput Chem. 2024; 45(27): 2333–2346. PubMed
de Azevedo WF Jr, editor. Docking screens for drug discovery. 2nd ed. New York, NY: Springer; 2026. DOI: 10.1007/978-1-0716-4949-7
You should type all commands shown here in a Linux terminal. The easiest way to open a Linux terminal is to use the Ctrl+Alt+T key combination.
Step 1. Download Anaconda Installer for Linux (Anaconda3-2021.11-Linux-x86_64.sh).
Do not install newer versions of Anaconda, you may have dependency version issues.
Go to the directory where you have the installer file and type the following commands:
chmod u+x Anaconda3-2021.11-Linux-x86_64.sh
./Anaconda3-2021.11-Linux-x86_64.sh
Follow the instructions of the installer.
Step 2. Download ADFRsuite version 1.0 (ADFRsuite 1.0 Linux 64 installer app).
Type the following commands:
cd ~
cp Downloads/ADFRsuite_Linux-x86_64_1.0_install .
chmod a+x ADFRsuite_Linux-x86_64_1.0_install
./ADFRsuite_Linux-x86_64_1.0_install
Follow the instructions of the installer. You need to add the path of ADFRsuite to your .bashrc (e.g.,PATH="/home/walter/ADFRsuite-1.0/bin:$PATH"). You need to change to your user.
Step 3. To run SAnDReS 2.0 properly, you need Scikit-Learn 1.5.2. To be sure you have version 1.5.2, open a terminal and type the following commands:
python3 -m pip uninstall scikit-learn
python3 -m pip install scikit-learn==1.5.2
Step 4. Download SAnDReS 2.0.0 here. Copy the sandres2 zipped directory (sandres2.zip) to wherever you want it and unzip the zipped directory.
Type the following command:
unzip sandres2.zip
cd to sandres2 directory then, type:
python3 sandres2.py
Now you have the GUI window for SAnDReS 2.0.0. That´s it, good SAnDReS session!
My scientific interests are interdisciplinary, with three main emphases: computational structural biology, artificial intelligence, and complex systems. In my studies, I developed several free software programs to explore the concept of Scoring Function Space.
As a result of my research, I published over 200 scientific works about protein structures, computer models of complex systems, and simulations of protein systems. These publications have generated over 12,000 citations on Google Scholar (h-index of 63) and more than 10,000 citations and an h-index of 58 in Scopus.
Due to the impact of my work, I have been ranked among the most influential researchers in the world (Fields: Biophysics, Biochemistry & Molecular Biology, and Biomedical Research) according to a database created by Journal Plos Biology (see news here). The application of the same set of metrics recognized the influence of my work in the following years ( Baas et al., 2021; Ioannidis, 2022; Ioannidis, 2023; Ioannidis, 2024; Ioannidis, 2025). Not bad for a poor guy who was a shoe seller at a store in the city of São Paulo and had the gold opportunity to study at the University of São Paulo with a scholarship for food and housing. I was 23 when I initiated my undergraduate studies and the first in my family to have access to higher education.
Regarding scientific impact (Peterson, 2005), Hirsch says that for a physicist, a value for the h index of 45 or higher could mean membership in the National Academy of Sciences of the USA. So far, there have been no invitations. No hard feelings because I am in good company. Carl Sagan was never allowed into the National Academy of Sciences. According to Google Scholar, his work accumulates more than 1,000 citations per year. Indeed, his current citation rate exceeds that of many members of the National Academy of Sciences.
I will continue working in science with low-budget and interdisciplinary projects, combating denialism and fascism with science and technology. The fight against denialism and fascism is a continuing work, and scientists should not forget their role in a complex society where social media gave the right to speak to legions of imbeciles.
“Social media gives the right to speak to legions of imbeciles who previously only spoke at the bar after a glass of wine, without damaging the community. They were immediately silenced, but now they have the same right to speak as a Nobel Prize winner. It’s the invasion of imbeciles.”
Umberto Eco. Source: Quote Investigator
"Let the light of science end the darkness of denialism." My quote (DOI:10.2174/092986732838211207154549).