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Editor for the Following Journals


Research

SAnDReS: Statistical Analysis of Docking Results and Scoring functions

SAnDReS code is available from theGitHub.

 

SAnDReS draws inspiration from several protein-ligand projects that we have been working on in the last two 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 Stochastic Gradient Descent and Support Vector. 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).  


Gallery of Plots Generated by the Program SAnDReS      


Scatter plots and ROC Curve generated by SAnDReS  


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.


Below you have a list of biological systems being investigated using Taba and  SAnDReS.

-3-enol-pyruvoylshikimate-5-phosphate synthase (EPSP synthase) (EC 2.5.1.19)   PubMed    IC50   Kd   Ki
-11-Beta-Hydroxysteroid Dehydrogenase (EC 1.1.1.146)   PubMed   IC50   Ki        

-Acetylcholinesterase (EC 3.1.1.7)   PubMed   MOTM   IC50   Kd   Ki   
-ADAM 17 Endopeptidase (EC 3.4.24.86)   PubMed   IC50   Kd   Ki    
-Adenosine A2a Receptor (EC 3.2.1.17)   PubMed   IC50   Kd   Ki           
-Adenosine Deaminase (EC 3.5.4.4)   PubMed   IC50   Ki    
-Adenosylhomocysteinase (EC 3.3.1.1)   PubMed    IC50   Ki   
-Aldehyde Reductase (EC 1.1.1.21)   PubMed   IC50   Kd   Ki    
-Angiotensin-Converting Enzyme (EC 3.4.15.1)   PubMed   IC50   Kd   Ki    

-Beta-2 Adrenergic Receptor (EC 3.2.1.17)   PubMed   IC50   Kd   Ki   
-Beta-Glucocerebrosidase  (EC 3.2.1.45)   PubMed   IC50   Ki   
-Beta-Lactamase (EC 3.5.2.6)   PubMed   MOTM   IC50   Kd   Ki   
-Beta-Secretase 1 (EC 3.4.23.46)   PubMed   MOTM    IC50   Kd   Ki   

-Carbonic Anhydrase II (EC 4.2.1.1)   PubMed   MOTM   IC50   Kd   Ki     
-Caspase-3 (or Apopain) (EC 3.4.22.56)   PubMed     MOTM   IC50   Kd   Ki    
-Catechol O-Methyltransferase (EC 2.1.1.6)   PubMed   IC50   Ki    
-Chorismate Synthase (EC 4.2.3.5)   PubMed   Kd   
-c-Jun N-Terminal Kinase 3 (EC 2.7.11.24)   PubMed   IC50   Kd   Ki   
-Coagulation Factor X (EC 3.4.21.6)   PubMed    IC50   Kd   Ki   
-Coagulation Factor VIIa (EC 3.4.21.21)   PubMed   IC50   Kd   Ki    
-C-X-C Chemokine Receptor Type 4 (EC 3.2.1.17)   PubMed   IC50   Kd   Ki    
-Cyclin-Dependent Kinase (EC 2.7.11.22)   PubMed   IC50   Kd   Ki    
-Cyclooxygenase-1 and 2 (EC 1.14.99.1)   PubMed   MOTM   IC50   Kd   Ki   
-Cytochrome P450 2C9 (EC 1.14.13.-)   PubMed   MOTM   IC50   Kd   Ki   

-Dihydrofolate Reductase (EC 1.5.1.3)   PubMed   MOTM   IC50   Kd   Ki
-Dihydroorotate Dehydrogenase (EC 1.3.5.2)   PubMed   IC50   Ki       
-Dipeptidyl Peptidase IV (EC 3.4.14.5)   PubMed   IC50   Kd   Ki       
-Dopamine D3 Receptor (EC 3.2.1.17)   PubMed   IC50   Kd   Ki    
-Dual Specificity Mitogen-Activated Protein Kinase Kinase 1 (EC 2.7.12.2)   PubMed   IC50   Kd   Ki           

-Enoyl-[Acyl-Carrier-Protein] Reductase (NADH) (EC 1.3.1.9)   PubMed   IC50   Kd   Ki       
-Epidermal Growth Factor Receptor ErbB1 (EC 2.7.10.1)   PubMed   MOTM   IC50   Kd   Ki  

-Farnesyl Diphosphate Synthase (EC 2.5.1.10)   PubMed   IC50   Kd   Ki             
-Fibroblast Growth Factor Receptor 1 (EC 2.7.10.1)   PubMed   IC50   Kd   Ki           
-FK506-Binding Protein 1 (EC 5.2.1.8)   PubMed   IC50   Kd   Ki           
-Focal Adhesion Kinase 1 (EC 2.7.10.2)   PubMed   IC50   Kd   Ki           

-GAR Transformylase (EC 2.1.2.2)   PubMed   Ki          
-Glucocorticoid Receptor (EC 2.3.1.48)   PubMed   IC50   Kd   Ki          

-Hepatocyte Growth Factor Receptor (EC 2.7.10.1)   PubMed   IC50   Kd   Ki              
-Hexokinase Type IV (EC 2.7.1.2)   PubMed   Kd   Ki           
-High-Resolution Crystallographic Structures   DeltaG   IC50   Kd   Ki     
-Histone Deacetylase (EC 3.5.1.98)   PubMed   IC50   Kd   Ki                  
-HMG-CoA Reductase (EC 1.1.1.34)   PubMed   IC50   Kd   Ki           
-Human Immunodeficiency Virus Type 1 Integrase (EC 2.7.7.-)   PubMed   MOTM   IC50   Kd   Ki   
-Human Immunodeficiency Virus Type 1 Protease (EC 3.4.23.16)   PubMed   MOTM   IC50   Kd   Ki              
-Human Immunodeficiency Virus Type 1 Reverse Transcriptase (EC 2.7.7.49)   PubMed  MOTM   IC50   Kd   Ki          
-Hydrolases (EC 3.-.-.-)   PubMed   IC50   Kd   Ki        

-Insulin-Like Growth Factor I Receptor (EC 2.7.10.1)   PubMed   IC50   Kd   Ki          
-Isomerases (EC 5.-.-.-)   PubMed   IC50   Kd   Ki          
 
-Kinases (EC 2.7.-.-)   PubMed   IC50   Kd   Ki         

-Leukotriene-A(4) Hydrolase (or LTA-4 Hydrolase) (EC 3.3.2.6)   PubMed   IC50   Kd   Ki        
-Ligases (EC 6.-.-.-)   PubMed   MOTM   IC50   Kd   Ki             
-Lyases (EC 4.-.-.-)   PubMed   IC50   Kd   Ki        
      
-Macrophage Colony Stimulating Factor Receptor (EC 2.7.10.1)   PubMed   IC50   Kd   Ki        
-MAP Kinase-Activated Protein Kinase 2 (EC 2.7.11.1)   PubMed   IC50   Kd   Ki       
-MAP Kinase (EC 2.7.11.24)   PubMed   IC50   Kd   Ki    
-Matrix Metalloproteinase 13 (EC 3.4.24.-)   PubMed   IC50   Kd   Ki       
-Monoamine Oxidase B (EC 1.4.3.4)   PubMed   IC50   Kd   Ki       
-Muscle Glycogen Phosphorylase (EC 2.4.1.1)   PubMed   MOTM   IC50   Kd   Ki         

-Nitric-Oxide Synthase (EC 1.14.13.39)   PubMed   MOTM   IC50   Kd   Ki         
-Neuraminidase (EC 3.2.1.18)   PubMed   MOTM   IC50   Kd   Ki   

-Oxidoreductases (EC 1.-.-.-)   PubMed   IC50   Kd   Ki            

-Peptide Deformylase (EC 3.5.1.88)   PubMed   IC50   Kd   Ki               
-Peroxisome Proliferator-Activated Receptor (EC 2.3.1.48)   PubMed   IC50   Kd   Ki     
-Phosphodiesterase 5A (EC 3.1.4.35)   PubMed   IC50   Kd   Ki           
-Phospholipase A(2) Group IIA (EC 3.1.1.4)   PubMed   IC50   Kd   Ki        
-Poly [ADP-ribose] Polymerase-1 (EC 2.4.2.30)   PubMed   IC50   Kd   Ki            
-Protein Farnesyltransferase/Geranylgeranyltransferase Type I Alpha Subunit (EC 2.5.1.58 or EC 2.5.1.59)   PubMed   IC50   Kd   Ki        
-Protein Kinase C Beta (EC 2.7.11.13)   PubMed   IC50   Kd   Ki            
-Purine Nucleoside Phophorylase (EC 2.4.2.1)   PubMed   IC50   Kd   Ki         

-Renin (EC 3.4.23.15)   PubMed   IC50   Kd   Ki    
-Rho-Associated Protein Kinase 1 (EC 2.7.11.1)   PubMed   IC50   Kd   Ki    
-Serine/Threonine-Protein Kinase AKT(EC 2.7.11.1)   PubMed   IC50   Kd   Ki     
-Serine/Threonine-Protein Kinase AKT2 (EC 2.7.11.1)   PubMed   IC50   Kd   Ki    
-Serine/Threonine-Protein Kinase B-raf (EC 2.7.11.1)   PubMed   MOTM   IC50   Kd   Ki       
-Serine/Threonine-Protein Kinase PLK1 (or Polo Kinase) (EC 2.7.11.21)   PubMed   IC50   Kd   Ki     
-Serine/Threonine-Protein Kinase WEE1 (EC 2.7.10.2)   PubMed   IC50   Kd   Ki     
-Shikimate Kinase (EC 2.7.1.71)   PubMed   Kd   Ki    
-Stem Cell Growth Factor Receptor (EC 2.7.10.1)   PubMed   IC50   Kd   Ki     

-TGF-Beta Receptor Type I (EC 2.7.11.30)   PubMed   IC50   Kd   Ki     
-Thymidine Kinase (EC 2.7.1.21)   PubMed   IC50   Kd   Ki    
-Thymidylate Synthase (EC 2.1.1.45)   PubMed   IC50   Kd   Ki    
-Thrombin (or Fibrinogenase) (EC 3.4.21.5)   PubMed   IC50   Kd   Ki    
-Transferases (EC 2.-.-.-)   PubMed   IC50   Kd   Ki     
-Trypsin I  (EC 3.4.21.4)   PubMed   IC50   Kd   Ki      
-Tryptase Beta-1 (EC 3.4.21.59)   PubMed   IC50   Ki        
-Tyrosine-Protein Kinase (EC 2.7.10.2)   PubMed   IC50   Kd   Ki       

-Urokinase-Type Plasminogen Activator (EC 3.4.21.73)   PubMed   IC50   Kd   Ki    

-Vascular Endothelial Growth Factor Receptor 2 (EC 2.7.10.1)   PubMed   IC50   Kd   Ki  


Last updated on December 4th 2017 by Ms. Gabriela Bitencourt-Ferreira.

Related Links  

     -A Database of Useful Decoys: Enhanced (DUDE)     
     -Enzyme Nomenclature Database (Expasy)     
     -Scikit-learn Machine Learning Techniques for Regression   
     -Matplotlib     
     -NumPy     
     -Protein Data Bank (PDB)     
     -Python      
     -SAnDReS       
     -SciPy      
     -UCI Machine Learning Repository   
     -Wolfram Demonstration Projects for Machine Learning   
     -Wolfram Demonstration Projects for Regression     
     -Wolfram Demonstration Projects for Stochastic Gradient Descent