Visual Clustering Approach for Docking Results from Vina and AutoDock

AutoDock Tools allows the analysis of docking files and is used to represent clustering conformations, yet it analyses only one docking file at a time and the method applied to represent the clustering complicates the visualization of clustering conformations. The creation of a plugin called PyDRA for the molecular visualizer PyMOL resolves that problem and allows to simultaneously process more than one docking file for the two types of file format from AutoDock 4.2 and Vina 1.1 (dlg and pdbqt). Moreover, this plugin facilitates the visualization of conformations through two clustering methods. The first method is a K-RMSD algorithm, which is based on the clustering through RMSD and enables the interactive visualization groups through a treemap. And the other one is based on a hierarchical clustering algorithm, using an algorithm of average distances which generates a dendrogram that offers the possibility to explore sequentially the groups that illustrate best the docking. The results obtained with the visualization methods implemented showed that the treemap, due to the implemented colour bar, facilitates to identify the clusters that have a greater affinity to the protein at a glance, and to determine which of the clusters hold a greater number of elements, on the other hand, the dendrogram shows a detailed analyses of the hierarchical clustering, which also enables the user to distinguish the clustering regardless the size of the window, as well as to differentiate each cluster and conformation in order to gain insight of docking results of Autdock and Vina. The fact that both visualizations are connected to PyMOL increases its ability of discernment.

[1]  Mark McGann,et al.  FRED Pose Prediction and Virtual Screening Accuracy , 2011, J. Chem. Inf. Model..

[2]  A Bogdanchikov,et al.  Python to learn programming , 2013 .

[3]  Roberto Therón,et al.  JADOPPT: java based AutoDock preparing and processing tool , 2016, Bioinform..

[4]  B. Seifert,et al.  Application of Exploratory Data Analyses opens a new perspective in morphology-based alpha-taxonomy of eusocial organisms , 2014 .

[5]  Todd J. A. Ewing,et al.  DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases , 2001, J. Comput. Aided Mol. Des..

[6]  Sumra Wajid Abbasi,et al.  Molecular docking studies for the identification of novel melatoninergic inhibitors for acetylserotonin-O-methyltransferase using different docking routines , 2013, Theoretical Biology and Medical Modelling.

[7]  Federico Milano,et al.  A python-based software tool for power system analysis , 2013, 2013 IEEE Power & Energy Society General Meeting.

[8]  Kwong-Sak Leung,et al.  Improving AutoDock Vina Using Random Forest: The Growing Accuracy of Binding Affinity Prediction by the Effective Exploitation of Larger Data Sets , 2015, Molecular informatics.

[9]  Arthur J. Olson,et al.  AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading , 2009, J. Comput. Chem..

[10]  Jiancheng Shi,et al.  Molecular docking and molecular dynamics simulation approaches for identifying new lead compounds as potential AChE inhibitors , 2017 .

[11]  David S. Goodsell,et al.  AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility , 2009, J. Comput. Chem..

[12]  Charles K. Gatebe,et al.  PolarBRDF: A general purpose Python package for visualization and quantitative analysis of multi-angular remote sensing measurements , 2016, Comput. Geosci..

[13]  Richard D. Taylor,et al.  Improved protein–ligand docking using GOLD , 2003, Proteins.

[14]  Gunes Ercal,et al.  A comparative analysis of progressive multiple sequence alignment approaches using UPGMA and neighbor joining based guide trees , 2015, ArXiv.

[15]  Mahipal Jadeja,et al.  Tree-Map: A Visualization Tool for Large Data , 2015, GSB@SIGIR.

[16]  Ben Shneiderman,et al.  Tree-maps: a space-filling approach to the visualization of hierarchical information structures , 1991, Proceeding Visualization '91.

[17]  Thomas Lengauer,et al.  Evaluation of the FLEXX incremental construction algorithm for protein–ligand docking , 1999, Proteins.