Friday, April 22, 2016

Planned papers (update 1)


It is said that "No battle plan ever survives contact with the enemy". In my case, the enemy is myself: a permanent inclination towards procrastination, often disguised as an urge to delve deeper into tangentially relevant (or even irrelevant) literature, or to run a new series of computations in yet another interesting system.

And so it came to pass that my plans to increase my manuscript production predictably advanced much more slowly than I had envisioned. In my defence, I can only say that the writing process showed that a few of my computations were not as complete as I expected: a few single-points had converged into an excited state, a couple of transition states had to be newly optimized, etc. But I finally managed to get one manuscript almost ready.

Overall progress on my planned manuscripts:
  • the reactivity of P450 compound I towards 1,2-dihydroazaborines: Available as a preprint here
  • computational develoment of lead compunds for inhibition of plasmid-borne DHFR Introduction/Methods section complete. Results tables and graphs ready
  • computational development of inhibitors of anthrax protective antigen cleavage by furin. No progress
  • the influence of solute-solvent dispersion/repulsion interactions on the behavior of molecular torsion balances.  Analysis of the results does not show any consistent improvement of the fit of computation with experiment upon inclusion of dispersion/repulsion interactions between implicit solvent and solutes
  • the binding of rubromycin derivatives to telomerase and DNA polymerase. Found serious shortcomings in my AutoDock computations. I have now repeated everything with AutoDock Vina, including flexibility of aminoacid sidechains. 100 ns MD now finishing for three ligands in three candidate binding poses.
  • the reaction mechanism of copper-catalyzed addition of azides to iodoalkynes. No progress
  • the reaction mechanism of copper-catalyzed aldol synthesis described by Marek No progress
  • analysis of molecular determinants of inhibitor binding to monoamine oxidases A and B No progress
  • reactivity of MerB towards p-block organometallic compounds No progress
  • electron-transfer to oxygen vs. singlet-triplet crossings in a cofactor-free dioxygenase  Introduction/Methods section complete. Results tables and graphs ready




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