Macromolecular Modeling Blog ™

In a recent post, Derek Lowe, from “In The Pipeline”, asks his readership “If we could just walk right up and calculate the free energies of binding events reliably, what would you most want such calculations to be able to do for you? What would convince you that they’re actually believable? And how close to you think that we actually are to that?” We tried to briefly answer some of these questions. How close are we to predict small molecules binding free energy?

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How do enzymes catalyze reactions? There are countless answers of course, but one answer that has gained much attention and popularity in recent years is – through intrinsic dynamics. Is that so? PNAS recently published a paper by Arieh Warshel entitled: “Enzyme millisecond conformational dynamics do not catalyze the chemical step”. Warshel, an avid assailant of the coupling between dynamics and catalysis was met by Martin Karplus, devoted advocate for catalytic dynamics, to engage in a public dispute over the letters section of PNAS. Who do you find more convincing?

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The latest crop of interesting literature in our field. There are a bunch of papers about protein dynamics (and its conservation) and another bunch on protein design. And if you search carefully there is also one paper by us on peptide docking with a new Rosetta protocol.

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