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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 GUI interface. The Graphical User Interface for DockoMatic with user input fields (left), current processing status (center), and results/analysis fields (right).
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Figure 1: DockoMatic GUI interface. The Graphical User Interface for DockoMatic with user input fields (left), current processing status (center), and results/analysis fields (right).

Mentions: See Figure 1 for details.


Dockomatic - automated ligand creation and docking.

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

DockoMatic GUI interface. The Graphical User Interface for DockoMatic with user input fields (left), current processing status (center), and results/analysis fields (right).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: DockoMatic GUI interface. The Graphical User Interface for DockoMatic with user input fields (left), current processing status (center), and results/analysis fields (right).
Mentions: See Figure 1 for details.

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.