P212121 » Scientific Publication and Presentation

Customize Your RCSB PDB Homepage

Sean — Fri, 05 Mar 2010 06:13:42 +0000

RCSB PDB adds customized widgets to their homepage.

(if you are having trouble seeing this video try the full screen option)

Neutron Crystallography Data Collection

Sean — Mon, 01 Mar 2010 01:42:15 +0000

Neutron crystallography can be used to gain insight into hydrogen positions. This is extremely beneficial when trying to determine a mechanism. This was the case for endothiapepsin. If one is able to substitute hydrogen for deuterium, the scattering is significantly increased (see slide 14 of Roger Pynn’s presentation on Neutron Crystallography Theory). Deuterons scatter neutrons in a manner similar to that of carbon. In X-ray crystallography, however, we see that they are quite different.

Two methods are used to exchange hydrogens:
1) The crystal can be soaked in deuterated buffer or by placing deuterated water at the ends of the capillary to allow for vapor exchange.
2) The protein can be expressed by using perdueterated media, in which the carbon source for E. coli contains deuterium. Check with your favorite neutron beam line to find out if they offer perdeuteration services. Perdeuteration is the ideal method because nearly all hydrogens can be exchanged. The only downside here is that you may not be able to use the exact same crystallization conditions as the native protein.

If you are considering using neutron crystallography, I would suggest using these two general criteria based on previous published neutron structures.
1) Crystal size ~1 mm^3 or larger
2) Crystal has been solved to ~1 A or better with X-rays

Recently, a nice summary figure and table have been published. They show the current parameters of neutron structures that have been published up to 2007.

Data collection time can be greatly reduced if your crystal is in a high symmetry. High symmetry is a significant benefit in neutron crystallography since it may take 12 hours to collect a frame (mileage will vary depending on beam line).

Finally, it has been proposed that Oak Ridge be able to reduce crystal size to 0.1 mm^3 (pdf). If this is made possible, we may see neutron crystallography becoming a more routine crystallographic technique.

BRENDA the Enzyme Database

Sean — Sat, 27 Feb 2010 22:16:32 +0000

BRENDA is a gold mine for those studying enzymes! The database proclaims to be the comprehensive enzyme information system and with 5010 enzymes it looks to be the case. Here is a screenshot of the navigation bar. As you can see BRENDA brings together many different categories such as IC50 values, pH stability range and crystallization.

My only suggestion so far is to change ‘Recommended Name’ to ‘Enzyme name’. I think it would save some confusion in the search entry.

I have never seen another database bring together this much information about a class of proteins. If you have a colleague working in enzymology this is site is definitely worth passing along.

SEO: Titles and Keywords in Scientific Publications

Sean — Thu, 25 Feb 2010 00:46:02 +0000

The way in which scientific publications appear online is going to become increasingly important. How literacy research is conducted is changing rapidly. People are turning to online resources rather than utilizing libraries. Publications that haven’t been made available on the internet may be overlooked. This could result in your paper not being referenced as often, or worse, your research may be repeated.

The number of citations a paper receives helps to determine the impact of the research within that paper. Even if your research is excellent, if no one finds the paper it won’t be cited.

The probability of your paper being read increases the closer it is to the number one search result.

So how do you become the #1 publication in search results?

SEO (search engine optimization) is a field that studies how search engines are influenced by content. The basis for this work is that it is believed that search engines are not perfectly efficient. Therefore with a little tweaking, you may be able to give your publication the boost it needs to be noticed and deemed an appropriate match by search engines. Just to be clear, papers should not be poorly written in an attempt to gain search ranking and in the end content will have a much great impact than SEO.

There are many factors a search engine considers when assembling a results page. The scientist in me cringes a bit at presenting this information since the search algorithms are kept secret making it very difficult to know exactly how search results can be influenced.

Today, we are going to focus on the two items that you can control.
1) Paper Title
2) Keyword Density

Paper Title:
The basics of SEO of titles is that your keywords (the search terms that you people may use to find your paper) should be contained within your title. Although opinions are mixed it is also thought that keywords placed near the beginning have a higher influence than those at the end.

Here’s a great example of how a title should be written for SEO from Acta D:
‘Eukaryotic expression: developments for structural proteomics’

An example of a disadvantageous title would be:
‘The 1.6 Å resolution crystal structure of a mutant plastocyanin bearing a 21-25 engineered disulfide bridge’

The problem here is the resolution of the structure is listed first in the title. More than likely, this paper is going to rank higher for the term ‘1.6 Å’ rather than, for example, ‘mutant plastocyanin’.
If you were the author of this paper and thought each word in that title was critical, it would be more beneficial to arrange the words as follows:

‘Mutant plastocyanin a 1.6 Angstrom crystal structure bearing a 21-25 engineered disulfide bridge’

This tweaked title would be ideal if you were looking to rank for ‘mutant plastocyanin’.

Keywords:
Of course, your paper should be written for humans, but it may help to keep search engines in mind. Although not as influential as in the past increasing the keyword percentage in your document should also help. For example, if you wanted to keyword for ‘protein crystallization’ think about if you can increase the number of times the term is being used.

Again, I don’t have direct proof of how much influence these changes make, but many top brands have excellent top keyword density (percent that term is used on their site) and my feeling is that it wasn’t by accident:
Zappos: shoe (8.33%), shoes (7.78%), zappos (5.00%)
Visa: visa (25.00%), card (10.61%), cards (4.55%), credit (3.03%)
JCrew: crew (6.77%), clothing (3.59%), dresses (3.19%)

Take some time and really think about the title of your paper and what keywords are important. You may find that the one thing standing between you and the first page of Google scholar……is a little tweaking.

P212121.com 1st Birthday

Sean — Mon, 22 Feb 2010 23:28:04 +0000

A year ago today this site was created.

P212121 has been more successful than I would have ever imagined. My primary goal has been to help someone in the field of macromolecular crystallography. I hoped that by bring together resources, creating tutorials and answering questions that this website would be helpful.

I also need to say thank you. I have had many readers contribute so much time and effort answering my questions and sharing their experiences. My friends that have share with me more than I given with a comment here, thank you.

If you like numbers, the current RSS count here considering only Google is at 140 as a (probably bad) reference point Acta Crystallographica Section D is at 93.

The blogging community has been wonderful and for fear of leaving someone off of a list, I hope a general thanks will suffice.

A number of crystallographic companies have shown their link love:
Emerald Biosystems
Hampton Research
Microlytic
Rigaku

This site was also recently included in the science Alltop, which is cool resource for finding science information.

What’s next? I have a lot in the pipeline, but before we get there I would love to hear from you. Have an idea or suggestion to make this site better? If we have spent the last couple of months together and haven’t met just a Hi or Happy Birthday would be great.

Thanks again.

15 Carbohydate Databases

Sean — Mon, 22 Feb 2010 03:26:56 +0000

Carbohydrates (glycans) are a major class of biological macromolecules along with proteins and DNA molecules. The array of possible combination of carbohydrates is astounding. Here is an extensive list of carbohydrate databases that offer a number of different searching methods as well as entries, enjoy.

1) GlycomeDB is a carbohydrate structure metadatabase that has combined all free databases (CFG, KEGG (right panel), GLYCOSCIENCES.de (no $), BCSDB, GlycoBase (Dublin, Lille) and Carbbank) including both their structures and annotations.

2) Glycoconjugate Data Bank has a really cool search GUI (see ‘Search glycan structures’)

3) O-GlycBase contains 242 glycoprotein entries of both O- and C-glycosylated proteins.

4) Glycan Binding Proteins seems heavily dependent on knowing the CFG ID of your glycan of interest.

5) GLYCO3D breaks down glycans into seperate databases such as monosaccharides, di, oligo, poly, lectins, glycosyltranserases and Gag binding proteins. The search is organized by a series of drop down menus, which is really helpful if you are taking a top down approach (animal to glycan). On the downside, the website has not been updated since May of 2007.

6) Lectins contains lectins from plant, algae, virus, animal, bacteria, yeast and fungus.

7) Carbohydrate-Active enZYmes Database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.

Glyco Enzymes is good if you have a monosaccharide and want to find out the glyco-enzymes involved. This database is not for finding structural information such as what is found in the PDB.

9) Bacterial Polysaccharide Gene Database doesn’t seem to be working anymore

MajorGroove.org Q&A for the CCP4bb

Sean — Sat, 20 Feb 2010 19:06:00 +0000

At the beginning of the year, we discussed whether the CCP4bb should become a forum. Initially, BioKlatch.com was created by Matt Harrington – the site is now being redirected to MajorGroove.org.

The site is based on StackExchange, which is a new website designed around a simple question and answer format. It will be interesting to see if the pricing changes once the site is out of beta. The site includes a number of community features. On example: the ability to earn badges by performing various activities, from filling out your profile to posing a good question.

The discussions are still kept on the CCP4bb, but the answers/responses are then posted on MajorGroove.org. If the system works well, it should provide an extensive selection of Q&A that have previously been addressed on the CCP4bb.

Are you excited about this new resource? Is this just one more place to visit? I have joined, will you?

MeRNA Database: RNA and Metals

Sean — Thu, 18 Feb 2010 22:33:25 +0000

For structural information concerning metals and RNA then you may find MeRNA quite helpful (pdf ref). Metals have been shown to play an important role in RNA folding. The MeRNA database currently contains 398 PDB entries which include 22 different metals.
Note: The MESPEUS database is excellent resource for metals and proteins.

The simple periodic table display works well. The results page would be easier to read if the titles were not all in italics.

The advance search offers a number of function with my favorite being the ability to search through 8 different binding motifs. The advanced search also allows for search by reference and/or author.

Tattoos

Sean — Mon, 01 Feb 2010 13:00:06 +0000

Just found out some scientists like tattoos.

Our contribution:

1) hkl (on the appropriate knuckles)

2) Bragg’s Law (arm)
3) Diffraction pattern (full back)

Send in pictures of your crystallography tattoos for bonus points.

Anonymous Feedback

Sean — Sat, 30 Jan 2010 19:51:13 +0000

At our university we are required to give a literature presentation. The presentation is 1 hour including time for questions. The goal of this exercise is to help students develop various skills that are valuable in a scientific career such as presenting, evaluating literature and answering questions. Good stuff.

I did my presentation and it really well except to one professor. According to my evaluation, I had confidently fabricated an answer and misled an entire audience. Fair enough, I make mistakes, but in this case I was right and had the literature to back it up. My scores were fine despite this one professor, but I wanted to discuss the issue. I was curious if the book and papers that supported my view were wrong. I wanted to learn.

I went to the head of session and asked who gave this evaluation. I was then told that the feedback was anonymous and they were not allowed to tell me. I then asked if he could ask the professor to contact me so that I could visit their office and discuss the evaluation. The head of session said that would be fine and sent out an email, but the professor never got in touch.

From this experience, I have also decided to no longer give anonymous feedback. I don’t want to hide. If the person who is getting my feedback disagrees, wants clarification, suggestions then great, let’s talk.

Scientific dialogue is invaluable and is reflected in our numerous publications and conferences.

I asked a faculty member of nearly 30 years why the policy existed and was told ‘this is the way we have always done it.’

Does your department give anonymous feedback? Do you find it helpful? Do you know why they keep that policy?