How to deal with rejection in science in two easy steps

Step 1: make a list your recent rejections

Proposals
Update: Nov 20: Danish Council for Strategic Research (NABIIT, second-round):

The program committee found that this was an interesting, relevant and support-worthy application associated with an important and fundamental issue. 

Unfortunately, however, when prioritizing support-worthy applications yours was not not given sufficiently high priority to receive support. 

Nov 12: European Research Area – Industrial Biotechnology framework (second-round):

We would like to inform you that your proposal EIB.12.031 DZYME was evaluated positively by the ERA-IB Expert Panel in its meeting on the 16th October. Unfortunately, not all positively evaluated proposals can be granted due to a limited budget of some of the national and/or regional funding organisations.

Oct 10: The Danish Council for Independent Research | Technology and Production Sciences (FTP; translated from Danish):

The council finds your application worthy of support.  However, the councils funds are insufficient to fund all qualified applications.  The council has in this round funded 29 applications out of 280.

Oct 3: The Danish Council for Independent Research | Natural Sciences (FNU; translated from Danish):

Your application was found very worthy of support.  This means that your professional qualifications, your CV, and your project was of such quality and character that it would have been funded had there been sufficient funds.

Papers (see this post)

Nov 1: Physical Chemistry Chemical Physics: 

All manuscripts submitted to Physical Chemistry Chemical Physics are initially evaluated by the Editors to ensure they meet the essential criteria for publication in the journal. I’m sorry to say that on this occasion your paper will not be considered further because it is not of sufficient novelty and impact to appeal to our readership.

Sep 29: Journal of Chemical Information and Modeling

"In my judgment, your submission is inappropriate for JCIM; it would be rejected upon full review."

Step 2: well ... uhm ... 
D'oh!


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Writing grant proposals versus working in industry

It seems like I am always working on a grant proposal - or a pre-proposal, which is a proposal that gives the successful applicant permission to write and submit an even longer proposal.

Recently, one call to the European Science Foundation required you to submit both the pre-proposal and the full proposal simultaneously! That call got over 700 applicants and 4% went on to the second round.  Mine wasn't one of then.

It is times like this when the grass looks greener in industry, but as the following documentary reenactment comedy sketch seems to indicate it's not all milk and honey there either.

Here are my funded grant proposals

I recently came across this interesting blog post by mathematician Doron Zeilberger entitled Opinion 117: People Should Learn to Share their Ideas, and Make their Funded Grant Proposals Public (and an Efficient Algorithm for convincing those that refuse).

There he writes:

Mathematics and Science is a communal enterprise, and it is very important that people share their ideas. Unfortunately, it is very hard to get the big picture. The number of good expository articles is, unfortunately, very small. (People who write them should be rewarded! A good expository article is worth one thousand mediocre (and even good) technical papers.)


People are at their expository best when they are begging for money, and in the case of mathematicians and scientists, this means writing a grant proposal. The scientific community would benefit a lot if people would publicly post their funded grants, and be generous with their ideas.

The man is right.  So, without further ado*, here are my (i.e. where I was PI) funded proposals:**


2010 Protein Design Using Quantum Mechanics (Danish Center for Supercomputing)

2008 Computational Design of Stable Enzymes (Danish National Science Foundation, DSF-NABIIT)

2006 Modeling pH-Dependence in Drug Design (EU Marie Curie Program)

2006 Computational Prediction and Validation of Protein Structure and Function in Protein Engineering and Rational Drug Design (Danish National Science Foundation, FNU)

2006 Prediction and Interpretation of Protein pKa’s Using QM/MM (US National Science Foundation - MCB; rescinded when I moved to Denmark)

2002 The Prediction and Interpretation of Protein pKa’s Using QM/MM (US National Science Foundation - MCB)

* Actually, just a bit more ado: This seems like a good occasion to publicly thank Lou Messerle at the University of Iowa.  Whatever success I have had in getting proposals funded is a direct result of Lou's fantastic help with the 2002 NSF proposal. 

** That still open correctly in Word 

The PROPKA proposal

It's hard to write a proposal, and I had made several false starts.  To get out of the rut I used a trick I've used before where I make a sort of outline/very condensed version where I focus exclusively on what I want to say rather than how I want to say it. 

Anyway, the trick worked once again, and the proposal was shipped off on Friday - three days before the deadline.  Only this time I wrote the document on blogger and, inspired by Rosie Redfields latest post, I am putting it up on the blog.


Title: Electrostatics in Protein/Nucleic Acid Complexes
Not a very sexy title, but what else?

Objective
Extend PROPKA to DNA and RNA and use it to ...?

Background and Significance
pKa Prediction. Proteins contains charged groups that are key to their stability and function.  Assigning correct charges is crucial for rationalizing and modeling protein chemistry.  It is hard to measure these charges, so they have to be computed.  PROPKA is arguably the most popular way of doing this: many users and citations, interface to popular programs such as PDB2PQR and VMD.

Thanks to these efforts protein charges can now be assigned with confidence.  However, picture is different for the other major biomolecules DNA and RNA, and protein-DNA/RNA complexes.

Most pKa prediction programs can only handle proteins. PROPKA is one of the few programs that have been extended to small molecule ligands.  No pKa prediction program has been extended to DNA and RNA (check if that's true?), and this is what is proposed here.

Protein-DNA/RNA complexes. Why are proteins-DNA/RNA complexes important? Why are charged groups important for these complexes?  What complexes will PROPKA be applied to and why these?

Who are involved?  Jan, Mats, PNNL, UIUC,

Research Plan and Methodology
How will PROPKA be modified to handle DNA and RNA? pKmodel values, hydrogen bond strengths,
How will it be validated? What experimental data is there?  Compute pKa values using EFMO.
What systems will it be applied to? What will be computed?

This work is licensed under a Creative Commons Attribution 3.0 Unported License.