Workshop on Sustainable Software for Science: Practice and Experiences

Interested in sustainability of scientific software?

First Workshop on Sustainable Software for Science: Practice and
Experiences (WSSSPE)
(to held in conjunction with SC13, Sunday, 17 November 2013, Denver, CO, USA)
http://wssspe.researchcomputing.org.uk/

Trendspotting in the Protein Data Bank

Our most recent article has become publicly available. It describes some of the trends that we can observe in the Protein Data Bank:

Trendspotting in the Protein Data Bank. FEBS Letters, (0). Berman, H. M., Coimbatore Narayanan, B., Costanzo, L. D., Dutta, S., Ghosh, S., Hudson, B. P., Lawson, C. L., et al. (n.d.). doi:http://dx.doi.org/10.1016/j.febslet.2012.12.029

http://www.sciencedirect.com/science/article/pii/S0014579313000240

Spring 2013 release of RCSB PDB

This week we released the spring 2013 release of the RCSB PDB's website. This release was a lot of work and we added a ton of new features and improvements. Here my wrap-up of some of our highlights. For a full listing see the What's New page for more features and examples.

Protein Symmetry and Stoichiometry

The calculation of protein symmetry and stoichiometry is one of the major features of this release. The goal is to better describe biological assemblies of proteins according to some of their characteristics.

Symmetry refers to the point group symmetry of a protein complex. Protein complexes with quaternary structure can have rotational symmetry belonging to the point groups: cyclic (Cn), dihedral (Dn), tetrahedral (T), octahedral (O), or icosahedral (I). 


The stoichiometry of a protein complex represents the composition of its subunits. For example, the biological assembly of hemoglobin has two alpha and two beta subunits, represented by the formula A2B2.

Here a few examples:



The Crystal structure of the Clostridium perfringens NetB toxin in the membrane inserted form
has a cyclic symmetry of C7 and is formed by a homo-7-mer (A7)



The Crystal structure of phosphoserine phosphatase from T. onnurineus has Dihedral - D4 symmetry and is formed by a homo-8-mer (A8)
The Plasmodium falciparum malaria aminopeptidase has Tetrahedral symmetry and is a homomer composed of 12 chains.

Ferritin has Octahedral symmetry and is a Homo 24-mer


The Foot-and Mouth Disease Virus has Icosahedral symmetry and is formed by a Hetero-240 mer with the a A60B60C60D60 stoichiometry.

Tip: Enable the Axes and Polyhedron options on the Jmol page to get a better understanding of the composition of the protein.

Biologically Interesting Molecules

Various biologically interesting molecules, such as peptide-like antibiotic and inhibitor molecules are being annotated by the PDB. The latest RCSB PDB website provides better access to these data. These molecules are now search-able in the top-bar search, and we provide better reports and visualisation.

Example: All structures that contain Vancomycin

Access to Drug Targets in the PDB 

For this release we integrated drug and drug target data from DrugBank (www.drugbank.ca). For example: look up Ibuprofen .

We also provide access to the Anatomical Therapeutic Chemical (ATC) Classification System, which is used for drug classification.

Better site navigation

We have re-designed our page header and given it a cleaner and simpler feel.

Uniprot Gene Names

We added a new search function for Gene names. Proteins that can be linked to PDB via Uniprot can now be identified by their associated gene annotations.

SCOP track in Protein Feature View

 The Protein Feature View now has a new track - domain annotations from SCOP. Example: Obelin

This was just a quick summary of some of the new features. For a complete list, take a look at the What's new page.

Protein Feature View goes open source

The source code for the Protein Feature View has been released at github. This allows you to incorporate the dynamic SVG graphics visualizing UniProt and PDB relationships into your own web sites. You can either use the public JSON services provided by RCSB PDB to populate the view, or display your own data (after setting up your own services).

RCSB PDB's NAR paper

The manuscript describing recent developments at the RCSB PDB has been released as part of the latest Nucleic Acid Research database issue.

View the manuscript at NAR

The Author Profile provides a graphical timeline on when a particular structure was released in the PDB.

Some of the highlights of this year are improvements in the following areas:

• Searching
• Better simple searches
• Auto suggest provides quick access to relevant results
• More advanced search options
• More and better tools
• Structure alignments now domain based
• Visualization
• Better ligand reporting and visualisation
• Visualisation of molecular surfaces
• Web services
• many new services
• customization of reports
• Mobile phone app
• New iPhone app
• PDB101 educational section
• Structural view of biology - browse through molecule of the month articles
• Author profiles

Our continuous efforts to provide a structural view of biology are also reflected by an increase in our user base.  The RCSB PDB web site currently hosts ∼240 000 unique visitors per month (based on the number of unique IP addresses), an increase from the 180 000 visitors last reported in 2011. 

Ten Simple Rules For The Open Development of Scientific Software

Jim Procter and I drafted a new manuscript for PLOS Computational Biology describing ten simple rules for the open development of scientific software. Our motivation for writing this was to make the development of open scientific software more rewarding and the experience of using software more positive.  The ten rules are intended to serve as a guide for any computational scientist:


Ten Simple Rules For the Open Development of Scientific Software (article)

RCSB PDB is hiring

The RCSB PDB is one of the leading biological databases with more than 240,000 unique visitors per month. We have an open position in our team for a Lead Web Architect. The position is located in beautiful San Diego at UCSD .

A detailed job description and online application form can be found at:
http://jobs.ucsd.edu/bulletin/job.aspx?cat=information&sortby=post&jobnum_in=64091

Qualifications:

* MS Degree in Computer Science or comparable combination of education and experience with considerable focus in JavaEE software development.

* Established demonstrated work experience in the role of an architect and developer on medium to large size database-driven web applications using Java EE technology and standards.

* Advanced experience developing the presentation layer of a dynamic, database-driven web application using HTML, CSS, JavaScript, JavaScript Toolkits, Ajax, JSP, XML, Java. Experience resolving browser and cross-platform compatibility issues. Advanced experience with Struts2, Tiles, jQuery.

* Advanced experience with database design, Structured Query Language and RDBMS's such as MySQL. Expertise in web application server administration and configuration such as Tomcat.

* Established expertise in software life cycle methodologies. Experience with build tools such as Maven and Ant, and continuous integration systems such as Cruise Control. Experience with project tracking tools such as Jira.