Design Documentation for JaWE2Openflow Project

Mehta, Nikhil; Barter, Robert H.

doi:10.2172/15014762

Cited by 2 publications

(9 citation statements)

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“…Process design and definition are prepared with JAWE2.0-2 [35]. Enhydra Shark1.1-2 [36] is employed to instantiate and executes a process.…”

Section: Methodsmentioning

confidence: 99%

“…We adapted the WfMC [ 29 ] generic structure for a workflow to describe FReDoWS (Figure 1 ). Process design and definition are prepared with JAWE2.0-2 [ 35 ]. Enhydra Shark1.1-2 [ 36 ] is employed to instantiate and executes a process.…”

Section: Methodsmentioning

confidence: 99%

“…During process design and definition we use the JAWE2.0-2 [ 35 ] (Figure 1 ). JAWE2.0-2 is a visual tool for creating, managing, and reviewing process definitions in a straightforward and simple manner.…”

Section: Methodsmentioning

confidence: 99%

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FReDoWS: a method to automate molecular docking simulations with explicit receptor flexibility and snapshots selection

et al. 2011

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BackgroundIn silico molecular docking is an essential step in modern drug discovery when driven by a well defined macromolecular target. Hence, the process is called structure-based or rational drug design (RDD). In the docking step of RDD the macromolecule or receptor is usually considered a rigid body. However, we know from biology that macromolecules such as enzymes and membrane receptors are inherently flexible. Accounting for this flexibility in molecular docking experiments is not trivial. One possibility, which we call a fully-flexible receptor model, is to use a molecular dynamics simulation trajectory of the receptor to simulate its explicit flexibility. To benefit from this concept, which has been known since 2000, it is essential to develop and improve new tools that enable molecular docking simulations of fully-flexible receptor models.ResultsWe have developed a Flexible-Receptor Docking Workflow System (FReDoWS) to automate molecular docking simulations using a fully-flexible receptor model. In addition, it includes a snapshot selection feature to facilitate acceleration the virtual screening of ligands for well defined disease targets. FReDoWS usefulness is demonstrated by investigating the docking of four different ligands to flexible models of Mycobacterium tuberculosis’ wild type InhA enzyme and mutants I21V and I16T. We find that all four ligands bind effectively to this receptor as expected from the literature on similar, but wet experiments.ConclusionsA work that would usually need the manual execution of many computer programs, and the manipulation of thousands of files, was efficiently and automatically performed by FReDoWS. Its friendly interface allows the user to change the docking and execution parameters. Besides, the snapshot selection feature allowed the acceleration of docking simulations. We expect FReDoWS to help us explore more of the role flexibility plays in receptor-ligand interactions. FReDoWS can be made available upon request to the authors.

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“…Process design and definition are prepared with JAWE2.0-2 [35]. Enhydra Shark1.1-2 [36] is employed to instantiate and executes a process.…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

FReDoWS: a method to automate molecular docking simulations with explicit receptor flexibility and snapshots selection

et al. 2011

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“…The activities in dashed lines correspond to those executed by the user, whilst the ones in solid lines are executed by the system without user intervention. The JAWE [6] and Shark [7] software tools were used to model and execute the workflow, respectively. These software tools are free, and can be used in the Linux environment (as well as AMBER6.0 and AutoDock3.05).…”

Section: The Molecular Docking Workflow Modelmentioning

confidence: 99%

“…To accomplish that, we developed a scientific workflow, modeled using the JAWE design tool [6] executed by the Shark workflow engine [7]. The docking software AutoDock3.05 [4] and the PTRAJ module of the AMBER6.0 package [8], herein called PTRAJ only, are executed by scripts and computer programs written to perform each one of the activities described in the workflow.…”

Section: Introductionmentioning

confidence: 99%

Automating Molecular Docking with Explicit Receptor Flexibility Using Scientific Workflows

Machado

Schroeder

Ruiz

et al. 2007

Advances in Bioinformatics and Computational Biology

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Abstract. 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.

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Design Documentation for JaWE2Openflow Project

Cited by 2 publications

References 0 publications

FReDoWS: a method to automate molecular docking simulations with explicit receptor flexibility and snapshots selection

FReDoWS: a method to automate molecular docking simulations with explicit receptor flexibility and snapshots selection

Automating Molecular Docking with Explicit Receptor Flexibility Using Scientific Workflows

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