Sunday, June 26, 2016

Planned papers for 2016 - six months in

Pedro's post reminded me that mine was due

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

Submitted
None

Probable
1. Benchmarking of PM6 and DFTB3 for barrier heights computed using enzyme active site models.
2. pKa prediction using PM6 - part 1
3. Protein structure refinement using ProCS15 - starting from x-ray structure

Maybe
4. PM6 for all elements in GAMESS, including PCM interface
5. Protein structure refinement using ProCS15 - starting from 5 Å Cα RMSD
6. Vibrational effects on N amide chemical shifts
7. pKa prediction using PM6 - amines
8. Predicting binding free energies for CB7
9. Linear scaling HF-3c calculations by interface to FMO2 in GAMESS
10. Side chain chemical shift prediction with ProCS15
11. Rienstra-like chemical shift assignment in PHAISTOS

The status is

Published 

Submitted
Received "minor revision" verdict.  Sent back in last week.

Probable
3. Protein structure refinement using ProCS15 - starting from x-ray structure
Actively working on it. First draft about 2/3 done. It's a huge amount of work because I'm still new to the field and learning as I am writing. However, I am fairly confident that I'll get it published in 2016.

7. pKa prediction using PM6 - amines
The main issue here is whether we can automate all steps of the pKa calculation and based on what we have learned so far I am pretty sure we can. The main issue is the protonation. Once paper 3 is done I will start working on this.  The CPU requirements are not an issue so I am fairly confident that I'll get it published in 2016.

Maybe in 2016
*. Improved prediction of chemical shifts using machine learning
This wasn't even on the drawing board in January.  Lars spent a few months in Anatole von Lilienfelds lab working on increasing the accuracy of the ProCS15 data set  using machine learning. Calculations are still ongoing so I am a little hesitant to list it under "probable".
A companion paper in Scientific Data has also been discussed, 


Probably not in 2016
4. PM6 for all elements in GAMESS, including PCM interface
Jimmy is working on the first part.  The interface is there but debugging is really tough.  I think we will get it working in 2016 but getting a paper published this year is unlikely.

5. Protein structure refinement using ProCS15 - starting from 5 Å Cα RMSD
I think we will get most of the calculations done in 2016.

6. Vibrational effects on N amide chemical shifts
I had a visiting student working this. Bottom line: still no bug-free, black-box approach for computing vibrational that just works.  Much harder problem than I had anticipated.

8. Predicting binding free energies for CB7
Have some data but a long way to go yet.

9. Linear scaling HF-3c calculations by interface to FMO2 in GAMESS
This is actually working and being incorporated into the official version of GAMESS.  Not sure when we'll get around to generating data for a paper.

10. Side chain chemical shift prediction with ProCS15
Susanne is working on this but I doubt we will publish a paper on it in 2016. 

11. Rienstra-like chemical shift assignment in PHAISTOS
Still just an idea so far.



This work is licensed under a Creative Commons Attribution 4.0
Post a Comment