Scientific workflow management and the Kepler system: Research Articles
Concurrency and Computation: Practice & Experience - Workflow in Grid Systems
Extracting Information from Flexible Receptor-Flexible Ligand Docking Experiments
BSB '08 Proceedings of the 3rd Brazilian symposium on Bioinformatics: Advances in Bioinformatics and Computational Biology
FReDD: Supporting Mining Strategies through a Flexible-Receptor Docking Database
BSB '09 Proceedings of the 4th Brazilian Symposium on Bioinformatics: Advances in Bioinformatics and Computational Biology
Discretization of flexible-eceptor docking data
BSB'10 Proceedings of the Advances in bioinformatics and computational biology, and 5th Brazilian conference on Bioinformatics
BSB'11 Proceedings of the 6th Brazilian conference on Advances in bioinformatics and computational biology
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Computer assisted drug design (CADD) is a process involving the execution of many computer programs, ensuring that the ligand binds optimally to its receptor. This process is usually executed using shell scripts which input parameters assignments and result analyses are complex and time consuming. Moreover, receptors and ligands are naturally flexible molecules. In order to explicitly model the receptor flexibility during molecular docking experiments, we propose to use different receptor conformations derived from a molecular dynamics simulation trajectory. This work presents an integrated scientific workflow solution aiming at automating molecular docking with explicit inclusion of receptor flexibility. Enhydra JAWE and Shark software tools were used to model and execute workflows, respectively. To test our approach we performed docking experiments with the M. tuberculosis enzyme InhA (receptor) and three ligands: NADH, IPCF and TCL. The results illustrate the effectiveness of both the proposed workflow and the implementation of the docking processes.