Macromolecular Modeling Blog ™

We have recently conducted a poll amongst people interested in learning more about the Rosetta software (as a preliminary step to the Rosetta Academic Training Workshop). One of the questions in that poll was: “Which Rosetta related topics is of the most interest to you?” The results (from ~200 participants) are summarized in the graph below.

Interest trends amongst Rosetta users

Protein-protein docking was chosen as the topic with the highest interest level, with a slight gap from ab-initio structure prediction and protein-ligand docking. This correlates well with another superficial analysis we made a while back (What’s trendy in structural bioinformatics) in which we showed qualitatively that docking receives the most interest from ‘Cite U Like‘ structural bioinformaticians. It is worth noting that Molecular Dynamics was not included, since Rosetta is not intended for MD simulations.

What is your field in structural bioinformatics? Anyone has more evidence for the increase in interest in protein-protein docking?

One of the main tools of the structural biologist (computational or experimental) if not, THE main tool, is the molecular viewer he uses. There are various viewers available, but usually each of us, at a certain point at his career, chooses a specific one and specializes in it. It becomes a way of self expression, to the point that using a “non-native” viewer is like talking in a foreign language. (How do I select only the polar atoms within 4.5A of chain B and color them CPK in this awkward viewer ?!?!?! On MY viewer it would take me a second!)

We want to hear what is YOUR molecular viewer of choice. Each viewer is optimized for a different set of tasks. E.g. VMD is designed for molecular dynamics, UCSF Chimera integrates many molecular analysis tools, Rasmol is a quick and dirty command line operated little fellow, not producing the nicest figures though, PyMOL creates good looking figures and is highly scriptable (as we demonstrated before in PyMOL scripts), while Jmol is web oriented and easy to embed in web pages.

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There are other software available, please tell us in the comments what’s your favorite viewer advantages and what are the disadvantages of the other “lesser” viewers.