Books

 

 

 

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Editorships

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Frontiers Section Editor (Bioinformatics and Biophysics) for the Current Drug Targets ISSN: 1873-5592

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Section Editor (Bioinformatics in Drug Design and Discovery) for the Current Medicinal Chemistry ISSN: 1875-533X

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Member of the Editorial Board for the PeerJ ISSN: 2167-8359

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Member of the Editorial Board for the Current Bioinformatics ISSN: 2212-392X (Online) ISSN: 1574-8936 (Print)

 

Research

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Protein-Ligand Interacions

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Molecular Docking

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Bioinspired Computing

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Computational Systems Biology

 

Recent Publications

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da Silva AD et al. J Comput Chem. 2020; 41(1): 69-73.

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Volkart PA et al. Curr Drug Targets. 2019;20(7):716-726

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Russo S, De Azevedo WF. Curr Med Chem 2019. 26(10):1908-1919

SAnDReS

Citation

Please cite the following reference (Xavier et al., 2016) if SAnDReS program was useful.  

Xavier MM, Heck GS, de Avila MB, Levin NM, Pintro VO, Carvalho NL, Azevedo WF Jr. SAnDReS a Computational Tool for Statistical Analysis of Docking Results and Development of Scoring Functions. Comb Chem High Throughput Screen. 2016; 19(10): 801–812.   Google Scholar    PubMed   Publons       

Chapter of a Springer Nature Book About SAnDReS 

Bitencourt-Ferreira G, de Azevedo WF Jr. SAnDReS: A Computational Tool for Docking.In: de Azevedo Jr. W. (eds) Docking Screens for Drug Discovery. Methods in Molecular Biology, 2019; 2053:51-65. Humana, New York, NY doi: 10.1007/978-1-4939-9752-7_4.   PubMed   Springer    




How to Install

You need to have Python 3 installed on your computer to run SAnDReS. Also, you need to install NumPyMatplotlibscikit-learn, and SciPy.  

You can make the installation process easier by installing Anaconda 32 bits (download here

Windows
  • Step 1. Download SAnDReS 1.1.0 from GitHub (here
  • Step 2. Unzip the zipped file (sandres.zip
  • Step 3. Copy sandres directory to c:\ 
  • Step 4. Open a command prompt window and type: cd c:\sandres
  • Step 5. Then type: python sandres1_GUI.py

This launches GUI window for SAnDReS. That´s it, good SAnDReS session. You can also start SAnDReS clicking on the sandres.bat file. You may also create a shortcut for SAnDReS right clicking on the sandres.bat file. 

Downloads   

   

Overview

SAnDReS draws inspiration from several protein-ligand projects that we have been working on in the last decades. These projects began in the 1990s with pioneering studies focused on intermolecular interactions between cyclin-dependent kinase and inhibitors (De Azevedo et al., 1996; 1997). SAnDReS is a free and open-source (GNU General Public License) computational environment for the development of machine-learning models for prediction of ligand-binding affinity. SAnDReS is also a tool for statistical analysis of docking simulations and evaluation of the predictive performance of computational models developed to calculate binding affinity. We have implemented machine learning techniques to generate regression models based on experimental binding affinity and scoring functions such as PLANTS and MolDock scores. The scikit-learn library has a wide spectrum of supervised machine learning techniques for regression, such as Ordinary Least Squares and Ridge Regression. SAnDReS was developed using Python programming language, and SciPy, NumPy, scikit-learn, and Matplotlib libraries. Data obtained from any protein-ligand docking program can be analyzed by SAnDReS, the only requisite is to have protein structures in Protein Data Bank (PDB) format, ligands in Structure Data File (SDF) format, docking and scoring function data in comma-separated values (CSV) format. This program has been applied to several datasets comprised of crystallographic structures for which there is information for the ligand-binding affinity, in order to generate scoring functions tailored to the biological system of interest (Xavier et al., 2016).  The flowchart below illustrates the main steps to integrate a molecular docking program and SAnDReS.

Flowchart for application of SAnDReS to analyze docking results and develop scoring functions. Grey boxes indicate tasks carried out by SAnDReS.

Gallery

 

Scatter plots and ROC Curve generated by SAnDReS  

GUI

SAnDReS has GUI that allows the user to directly execute all tasks available in the program.

SAnDReS 1.1.0 GUI window.

Biological Systems

Below you have a list of biological systems (datasets) that were analyzed using SAnDReS. Each zipped folder has the necessary files to reproduce the results reported for each dataset. 

  • Coagulation Factor Xa with Ki Information   ZIP   PubMed   
  • Cyclin-Dependent Kinases with IC50 Information   ZIP   PubMed   
  • Cyclin-Dependent Kinases with Ki Information   ZIP   (to be published)   
  • High-resolution Structures with Delta G Information   ZIP   PubMed
  • DeltaG   ZIP   
  • High-resolution Structures with IC50 Information   ZIP   PubMed     
  • HIV-1 Protease with Ki Information   ZIP   PubMed