Thursday, June 16, 2016

Planned papers (update 2)

Overall progress on my planned manuscripts:
  • the reactivity of P450 compound I towards 1,2-dihydroazaborines: in review
  • electron-transfer to oxygen vs. singlet-triplet crossings in a cofactor-free dioxygenase  submitted to PeerJ on June 16th
  • the influence of solute-solvent dispersion/repulsion interactions on the behavior of molecular torsion balances.  No progress since last update. I doubt this could ever become publishable :-(
  • the binding of rubromycin derivatives to telomerase and DNA polymerase. Analysis of the last 100 ns MD mostly complete
  • analysis of molecular determinants of inhibitor binding to monoamine oxidases A and B Analysis of the MD simulations almost complete
  • the reaction mechanism of copper-catalyzed addition of azides to iodoalkynes. No progress since last update
  • the reaction mechanism of copper-catalyzed aldol synthesis described by Marek No progress since last update
  • reactivity of MerB towards p-block organometallic compounds No progress since last update
  • computational develoment of lead compunds for inhibition of plasmid-borne DHFR No progress since last update 
  • computational development of inhibitors of anthrax protective antigen cleavage by furin.  No progress since last update
     
     

Thursday, April 28, 2016

New scientific biographies wanted....

Biographies fulfill several different roles: they may simply satisfy one's curiosity over the lives/achievements of the biographees, provide tasty morsels of gossip or interesting stories, or play an "educational" role. Traditionally, the "educational role" of biographies has focused on their presentation of "role models" - whether moral, political or social - or the conditions/life experiences which led to the special significance of the biographee. Scientific biographies follow the same pattern. Like traditional biographies, they are usually limited to people of special significance: trailblazers, mavericks, geniuses, and people who left a mark on their scientific discipline or on the public perception of the worth of their subject.

I wish there were also another kind of biography, devoted to the intelectual careers of "normal" researchers: people who simply follow their intelectual curiosity, who are constrained by the amount of funding they can get and who pass away in obscurity after adding their small contributions to our colective knowledge. I do not want "human interest stories" played by researchers: I rather long for a description of their intelectual journeys, why they decided to study a specific problem, what kinds of mental connections they made (and why), in what measure their interpretation of their results was "commonplace" or (in contrast) specifically triggered by insights coming from seemingly unrelated work they had performed earlier, etc.

I want to read stories that show how each of these normal people, in their own way, made work which seems ordinary but is, in contrast, highly personal: work that would not have been done, or which would not have yielded the same insights, if that scientific question had been tackled by someone with a different research history. I am reasonably confident that most rank-and-file scientists would be fitting subjects for this style of biography, and that the study of these stories would teach us a lot about the roles that creativity, personality, luck and culture play in the fostering of a thriving research environment. 

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




Friday, January 1, 2016

Planned papers for 2016

Last year, Jan Jensen published his publication plans for 2015. I will do the same this year, mostly as a way to force myself to stop procrastinating, as I have a large backlog of research which is ready for publication  (except fo the pesky little detail that I have not started to write the papers).
So here it goes.... This year, I plan to submit my research on :
  • the reactivity of P450 compound I towards 1,2-dihydroazaborines
  • computational develoment of lead compunds for inhibition of plasmid-borne DHFR
  • computational development of inhibitors of anthrax protective antigen cleavage by furin
  • the influence of solute-solvent dispersion/repulsion interactions on the behavior of molecular torsion balances
  • the binding of rubromycin derivatives to telomerase and DNA polymerase
  • the reaction mechanism of copper-catalyzed addition of azides to iodoalkynes
  • the reaction mechanism of copper-catalyzed aldol synthesis described by Marek
  • analysis of molecular determinants of inhibitor binding to monoamine oxidases A and B
  • reactivity of MerB towards p-block organometallic compounds 
  • electron-transfer to oxygen vs. singlet-triplet crossings in a cofactor-free dioxygenase 

I will force myself to update this list with a progress report every month. Let's see if I can "shame myself" into getting  my thoughts in paper :-)