Macromolecular Modeling Blog ™

A virtual docking screen discovers a small molecule activator of the pro-apoptotic protein BAX. This novel approach could lead to a ‘new generation’ of apoptotic modulators that directly activate BCL-2 killer proteins. Moreover – it’s cool!

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Instead of our regular Bi-weekly digest, Lets take a pause and dissect the trends in computational structural biology. As you may noticed, we added to the sidebar a “Structural Bioinformatics” titles feed. This feed is maintained by ~ 30 people at CiteULike, grouped by their liking to: “topics ranging from sequence-structure relationships to molecular simulations of biomolecules”. We used wordle to present popular items on that feed (around 1350 titles) and the results are striking.

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Incorporation of flexibility into docking simulations and accounting for backbone conformational changes during association is probably the toughest problem protein-protein dockers are facing today. Normal Mode Analysis is lately the answer of many groups to this problem. We hereby review two approaches of incorporating NMA into docking simulations, reflecting the induced fit vs. conformational sampling association mechanisms. 

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