From: Theresa H (theresahsu8_at_live.com)
Date: Mon Aug 06 2012 - 12:41:18 CDT
I am a protein crystallographer with interest in MDS. Since we don't have any computational biologist in the department, I want to ask a few basic questions.
I have the structures of two membrane proteins (protein C and D) and one soluble protein (protein B). Protein A can interact with protein C or D through protein B. The protein D also has a domain similar to protein B. Therefore I am interested in knowing why the protein A can't interact directly with protein D.
1. Is NAMD the right tool to answer this question?
2. If so, do I need anything else apart from the crystal structures?
3. How much computational resource is needed?
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