I amrunning DMD modelling to model possible conformations of my proteins. However when I submit my proteins for DMD modelling, it came back to me reporting that it had steric clashes.. How do I check for steric clashes?On the other hand, I will be running DMD with 5000 models of my protein. How will I filter the models that clash into each other? Does anyone know any program that I could use to filter the models?
Is it protein only or does your model include non-protein ligands? I personally would use the rosetta "score" application to rank the models, you can also use rosetta fixbb to see whether the clashes can be relieved by optimizing the side chain rotamers
Thank you Annemarie and Philippe. I found a feature on the latest version of us-somo that allows the filter of models that has steric clashes.
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