Limits...
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.


Competitive binding. Result for competitive binding simulation beginning with the docking of CCMWF to Ac-AChBP receptor. The best result of CCMWF with Ac-AChBP forms a new receptor-ligand complex, which is then allowed to bind to the secondary ligand, CDCMW. The lowest binding energy complex is displayed.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2991342&req=5

Figure 4: Competitive binding. Result for competitive binding simulation beginning with the docking of CCMWF to Ac-AChBP receptor. The best result of CCMWF with Ac-AChBP forms a new receptor-ligand complex, which is then allowed to bind to the secondary ligand, CDCMW. The lowest binding energy complex is displayed.

Mentions: Two of the created peptide ligands were selected to test in a sample competitive binding experiment. One ligand was selected in the ligand box, and the other was placed in the secondary ligand field. DockoMatic then prepared the necessary files for the competitive binding experiment (see Figure 4).


Dockomatic - automated ligand creation and docking.

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

Competitive binding. Result for competitive binding simulation beginning with the docking of CCMWF to Ac-AChBP receptor. The best result of CCMWF with Ac-AChBP forms a new receptor-ligand complex, which is then allowed to bind to the secondary ligand, CDCMW. The lowest binding energy complex is displayed.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Competitive binding. Result for competitive binding simulation beginning with the docking of CCMWF to Ac-AChBP receptor. The best result of CCMWF with Ac-AChBP forms a new receptor-ligand complex, which is then allowed to bind to the secondary ligand, CDCMW. The lowest binding energy complex is displayed.
Mentions: Two of the created peptide ligands were selected to test in a sample competitive binding experiment. One ligand was selected in the ligand box, and the other was placed in the secondary ligand field. DockoMatic then prepared the necessary files for the competitive binding experiment (see Figure 4).

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.