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Dockomatic - automated ligand creation and docking.

Bullock CW, Jacob RB, McDougal OM, Hampikian G, Andersen T - BMC Res Notes (2010)

Bottom Line: In its current version, AutoDock requires significant amounts of user time to setup and run jobs, and collect results.DockoMatic allows the user to invoke and manage AutoDock jobs on a single computer or cluster, including jobs for evaluating secondary ligand interactions.It also automates the process of collecting, summarizing, and viewing results.

View Article: PubMed Central - HTML - PubMed

Affiliation: Computer Science Department, Boise State University, Boise, Idaho 83725, USA. tim@cs.boisestate.edu.

ABSTRACT

Background: The application of computational modeling to rationally design drugs and characterize macro biomolecular receptors has proven increasingly useful due to the accessibility of computing clusters and clouds. AutoDock is a well-known and powerful software program used to model ligand to receptor binding interactions. In its current version, AutoDock requires significant amounts of user time to setup and run jobs, and collect results. This paper presents DockoMatic, a user friendly Graphical User Interface (GUI) application that eases and automates the creation and management of AutoDock jobs for high throughput screening of ligand to receptor interactions.

Results: DockoMatic allows the user to invoke and manage AutoDock jobs on a single computer or cluster, including jobs for evaluating secondary ligand interactions. It also automates the process of collecting, summarizing, and viewing results. In addition, DockoMatic automates creation of peptide ligand .pdb files from strings of single-letter amino acid abbreviations.

Conclusions: DockoMatic significantly reduces the complexity of managing multiple AutoDock jobs by facilitating ligand and AutoDock job creation and management.

No MeSH data available.


DockoMatic output. DockoMatic result output .pdb file image showing the best ranked (lowest binding energy) binding conformation for CCMWF in complex with Ac-AChBP as calculated by AutoDock.
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Figure 3: DockoMatic output. DockoMatic result output .pdb file image showing the best ranked (lowest binding energy) binding conformation for CCMWF in complex with Ac-AChBP as calculated by AutoDock.

Mentions: For this test, the evaluation of DockoMatic made use of a 61 node Beowulf cluster at Boise State University. The files used for the testing process included: 1) the receptor .pdb file for the crystal structure of the Aplysia californica acetylcholine binding protein (Ac-AChBP) obtained from the Research Collaboratory for Structural Bioinformatics (RCSB) database at http://www.pdb.org, 2UZ6, and 2) five peptide ligands each comprised of five amino acids: CCMWF, CDCMW, CFWMW, CHMWW, and CHWWM. All five ligands were submitted as a simple text file. DockoMatic successfully created the corresponding .pdb files, viewable in Figure 2. These five .pdb files were then automatically directed and paired with the Ac-AChBP .pdb file and the matching .gpf file into submission ready AutoDock jobs by DockoMatic. Upon job completion, DockoMatic parsed the .dlg files into individual, ranked result .pdb files. These files were easily viewable by clicking on the PyMOL button. Figure 3 is an example of one of the created ligands docked with the Ac-AChBP receptor as viewed by PyMOL. In addition to individually ranked .pdb files, DockoMatic also provides a master list of ranked results for each job. This list appears as a simple text file consisting of the detailed results for each rank, such as the estimated binding energy and inhibition constant as calculated by AutoDock.


Dockomatic - automated ligand creation and docking.

Bullock CW, Jacob RB, McDougal OM, Hampikian G, Andersen T - BMC Res Notes (2010)

DockoMatic output. DockoMatic result output .pdb file image showing the best ranked (lowest binding energy) binding conformation for CCMWF in complex with Ac-AChBP as calculated by AutoDock.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2991342&req=5

Figure 3: DockoMatic output. DockoMatic result output .pdb file image showing the best ranked (lowest binding energy) binding conformation for CCMWF in complex with Ac-AChBP as calculated by AutoDock.
Mentions: For this test, the evaluation of DockoMatic made use of a 61 node Beowulf cluster at Boise State University. The files used for the testing process included: 1) the receptor .pdb file for the crystal structure of the Aplysia californica acetylcholine binding protein (Ac-AChBP) obtained from the Research Collaboratory for Structural Bioinformatics (RCSB) database at http://www.pdb.org, 2UZ6, and 2) five peptide ligands each comprised of five amino acids: CCMWF, CDCMW, CFWMW, CHMWW, and CHWWM. All five ligands were submitted as a simple text file. DockoMatic successfully created the corresponding .pdb files, viewable in Figure 2. These five .pdb files were then automatically directed and paired with the Ac-AChBP .pdb file and the matching .gpf file into submission ready AutoDock jobs by DockoMatic. Upon job completion, DockoMatic parsed the .dlg files into individual, ranked result .pdb files. These files were easily viewable by clicking on the PyMOL button. Figure 3 is an example of one of the created ligands docked with the Ac-AChBP receptor as viewed by PyMOL. In addition to individually ranked .pdb files, DockoMatic also provides a master list of ranked results for each job. This list appears as a simple text file consisting of the detailed results for each rank, such as the estimated binding energy and inhibition constant as calculated by AutoDock.

Bottom Line: In its current version, AutoDock requires significant amounts of user time to setup and run jobs, and collect results.DockoMatic allows the user to invoke and manage AutoDock jobs on a single computer or cluster, including jobs for evaluating secondary ligand interactions.It also automates the process of collecting, summarizing, and viewing results.

View Article: PubMed Central - HTML - PubMed

Affiliation: Computer Science Department, Boise State University, Boise, Idaho 83725, USA. tim@cs.boisestate.edu.

ABSTRACT

Background: The application of computational modeling to rationally design drugs and characterize macro biomolecular receptors has proven increasingly useful due to the accessibility of computing clusters and clouds. AutoDock is a well-known and powerful software program used to model ligand to receptor binding interactions. In its current version, AutoDock requires significant amounts of user time to setup and run jobs, and collect results. This paper presents DockoMatic, a user friendly Graphical User Interface (GUI) application that eases and automates the creation and management of AutoDock jobs for high throughput screening of ligand to receptor interactions.

Results: DockoMatic allows the user to invoke and manage AutoDock jobs on a single computer or cluster, including jobs for evaluating secondary ligand interactions. It also automates the process of collecting, summarizing, and viewing results. In addition, DockoMatic automates creation of peptide ligand .pdb files from strings of single-letter amino acid abbreviations.

Conclusions: DockoMatic significantly reduces the complexity of managing multiple AutoDock jobs by facilitating ligand and AutoDock job creation and management.

No MeSH data available.