Friday, July 17, 2015

Planned papers for 2015 - six months in

In January I wrote about the papers I plan to publish and made this list:

Submitted
1. Søs Torpenholt, Leonardo De Maria, Mats H. M. Olsson, Lars H. Christensen, Michael Skjøt, Peter Westh, Jan H. Jensen and Leila Lo Leggio "Effect of mutations on the thermostability of Aspergillus aculeatus β-1,4-galactanase" Computational and Structural Biotechnology Journal, submitted
2. Lars A. Bratholm, Anders S. Christensen, Thomas Hamelryck, and Jan H. Jensen "Bayesian inference of protein structure from chemical shift data" PeerJ, submitted. Preprint

Probable
3. Automated prediction of the NMR structure of the protein CI-2.
4. Linear scaling HF-3c calculations by interface to FMO2 in GAMESS
5. Thermodynamics of binding. I plan to turn my recent blogposts (with 2 more to come) on this topic into a perspective article.
6. ProCS14. I need to turn this masters thesis into a paper (how will I find the time?).
7. NMR structure of the protein AKMT.
8. Benchmarking of PM6 and DFTB3 for barrier heights computed using enzyme active site models.
9. Predicting binding free energies for CB7
10. Probabilistic treatment of distance restraints in protein structure determination

Six months later this list is now:

Published
1. Søs Torpenholt, Leonardo De Maria, Mats H. M. Olsson, Lars H. Christensen, Michael Skjøt, Peter Westh, Jan H. Jensen and Leila Lo Leggio "Effect of mutations on the thermostability of Aspergillus aculeatus β-1,4-galactanase" Computational and Structural Biotechnology Journal 2015, 13, 256–264. DOI
2. Lars A. Bratholm, Anders S. Christensen, Thomas Hamelryck, and Jan H. Jensen "Bayesian inference of protein structure from chemical shift data" PeerJ 2015, 3:e861. DOI
5. Jan H. Jensen "Predicting accurate absolute binding energies in aqueous solution: thermodynamic considerations for electronic structure methods" PCCP 2015, 17, 12441-12451. DOI 

Actively being worked on
3. Automated prediction of the NMR structure of the protein CI-2.
We found a bug in the CamShift implementation.  This took a while to fix and to re-run a bunch of stuff, including the calculations in Paper 2.  The bug doesn't seem to affect the results much. Lars sent me the first rough draft of the paper this week.  There is still some calculations missing but it's coming together. My goal is a finished manuscript by the end of August.

6. ProCS15
As per usual, when writing up we found a bunch of small things that needed to be fixed/rerun/checked and since the MS student is now a PhD student in another group this, of course, takes time. I think we are at the point where we have all the data we need and know what to say, but enough has changed that it's a matter of writing the paper from scratch.  I'm working on this now. My goal is a finished manuscript by the end of August.

Very likely
8. Benchmarking of PM6 and DFTB3 for barrier heights computed using enzyme active site models.
Jimmy is now actively working on this and generating data at a rapid pace.  Current goal is to submit in early October at the latest, so that it will be published in 2015.  That means a first rough draft in early September, at the latest.

Probably next year
4. Linear scaling HF-3c calculations by interface to FMO2 in GAMESS
Jimmy basically needs to find a bug related to basis set normalization for heavier elements and run some benchmarks, once he is done with "paper 8".  I would like to submit this in December.

7. NMR structure of the protein AKMT//10. Probabilistic treatment of distance restraints in protein structure determination
These two papers are actually related and may be combined into 1.  However, there is some fundamental work with regard to "10" that still needs to be worked out and tested.

9. Predicting binding free energies for CB7
An undergraduate is now working on this, so there is a good chance we'll have something to publish in 2016.

New: 11. Protein structure refinement using ProCS15
We are getting some undergrads to work in this in September, so there is a good chance we'll have something to publish in 2016.



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