____________________________________________________________

Please cite the following paper Xavier et al. 2016 when using SAnDReS

Tutorials for SAnDReS       

-Getting PDB Access Codes from Protein Data Bank    

-Cyclin-Dependent Kinases with Ki Information   

     -Introduction                    
     -Downloading Data from the PDB     
     -Pre-Docking Analysis   
     -Docking Hub   
     -Ensemble-Docking Analysis   
     -Structural Parameters   
     -Scoring Functions Analysis   
     -Machine Learning Box   
     -Analysis of Decoys         


Docking School 

-Re-dock of Roscovitine Against Human Cyclin-Dependent Kinase 2   PubMed   2A4L     

     -Using AutoDock 4    ZIP               
     -Using AutoDock Vina    ZIP   
     -Using GemDock   ZIP       
     -Using Molegro Virtual Docker   ZIP              
     -Using SwissDock   ZIP      

-Manuals        

     -AutoDock 4.2.6        
     -AutoDock Vina     
     -GemDock 2.1         
     -Molegro Data Modeller    
     -Molegro Virtual Docker 6               

-Webservers for Protein-ligand Docking Simulations          

     -DockBlast           
     -PatchDock       
     -SwissDock   

     

Homology Modeling 

-Homology Modeling of Human Cyclin-Dependent Kinase 3 with Multiple Templates   ZIP      

          Related Sites:     
                                  -Genbank       
                                  -Protein Data Bank         
                                  -MUSCLE       
                                  -MODELLER    

Molecular Dynamics  

-Molecular Dynamics Simulations of Protein-ligand Complexes Using GROMACS 4.0.5   ZIP   PubMed       


Python Programming Language for Bioinformatics  

-Docking Root Mean Square Deviation (RMSD) in Python   ZIP          

Crystallographic position and pose for docking simulation.


-B-factor Plot in Python   ZIP    

 

B-factor plot generated by bfactor_plot.py  .


Dihedral Angle in Python   ZIP        

Orthogonal system for calculation of torsion angle.   


- Ramachandran Plot in Python   ZIP     

Ramachandran plot for 1KXY