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Team:TU Darmstadt/Modeling Docking
From 2012.igem.org
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| - | =Docking= | + | ==Docking== |
| - | ==Theory== | + | ===Theory=== |
| - | == | + | ===Goal=== |
| + | Although PET.er is capable to degrade PET into its monomers various chemical compounds like polymer plasticizer are released. Moreover, PET is a waste material - it will never been in a pure state. Due to it is important to study possible interaction of plasticizer as well as PET with the degradation machinery. Hence an experimental design will give a deeper understanding into the interaction of our enzymes with additives. | ||
| + | ===Methods=== | ||
| + | Due to the absence of forcefield terms of plasticizer we choose a global docking approach to study the interaction. For the docking simulations we uses the Autodock plugin of Yasara structure. Autodock is one of the mreeost cized and scientific programs for Docking simulations. | ||
| - | ==Results== | + | ===Docking Protocol=== |
| + | For the docking approach we utilized the standard protocol dock_run.mcr and parallelized it up to six processors. Moreover, we choose three additives out of the literature acting as the ligand within the simulations. | ||
| + | *OET-dimeric | ||
| + | |||
| + | |||
| + | |||
| + | |||
| + | *S-120 | ||
| + | *AO-8 | ||
| + | *TPF | ||
| + | |||
| + | |||
| + | ====Parameter for the Docking Experiment==== | ||
| + | *Ligands = S120, AO-8, TPF, dimer OET | ||
| + | *Number of docking runs = 200 | ||
| + | *ForceField AMBER03 | ||
| + | *Flexible Ligand | ||
| + | ===Analytics=== | ||
| + | We extract binding energy from the atomic Bfactors and the binding constant from the Atomic property derived from all our calculations. In order to compare the palsticier as well as the PET substrat we computed scatter plots with the binding constant and the inhibition constant. | ||
| + | |||
| + | ===Results=== | ||
Revision as of 16:28, 15 September 2012
Contents |
Docking
Theory
Goal
Although PET.er is capable to degrade PET into its monomers various chemical compounds like polymer plasticizer are released. Moreover, PET is a waste material - it will never been in a pure state. Due to it is important to study possible interaction of plasticizer as well as PET with the degradation machinery. Hence an experimental design will give a deeper understanding into the interaction of our enzymes with additives.
Methods
Due to the absence of forcefield terms of plasticizer we choose a global docking approach to study the interaction. For the docking simulations we uses the Autodock plugin of Yasara structure. Autodock is one of the mreeost cized and scientific programs for Docking simulations.
Docking Protocol
For the docking approach we utilized the standard protocol dock_run.mcr and parallelized it up to six processors. Moreover, we choose three additives out of the literature acting as the ligand within the simulations.
- OET-dimeric
- S-120
- AO-8
- TPF
Parameter for the Docking Experiment
- Ligands = S120, AO-8, TPF, dimer OET
- Number of docking runs = 200
- ForceField AMBER03
- Flexible Ligand
Analytics
We extract binding energy from the atomic Bfactors and the binding constant from the Atomic property derived from all our calculations. In order to compare the palsticier as well as the PET substrat we computed scatter plots with the binding constant and the inhibition constant.
