Sameer Velankar, PDBe Team Leader
Structural biologist Sameer Velankar, Team Leader at EMBL-EBI, leads the Protein Data Bank in Europe. Here he answers some questions about his career, and his new role in the Worldwide Protein Data Bank (wwPDB).
Q&A with Sameer Velankar
Q: What is the worldwide Protein Data Bank (wwPDB)?
A: Proteins do all the work in a cell, so it’s important to have a clear picture of what each protein does, and how. This is essential for discovering how a protein’s function can be altered by another molecule, such as a drug. The wwPDB is a global partnership that collects, organises and shares data on biological macromolecular structures to help scientists understand how proteins work.
The Protein Data Bank (PDB) is the oldest data archive in life sciences. It was set up in 1971 as the single repository of information about the 3D structures of proteins, nucleic acids and complex assemblies and is managed by the wwPDB. The wwPDB comprises four major partners in Europe, the US and Japan. It is used by more than a million people every year, and continues to grow at an impressive rate.
Q: What does your team do?
A: My team runs the Protein Data Bank in Europe (PDBe) – the European partner of the wwPDB collaboration. We handle atomic-resolution and high-res structures, adding value and building tools to help people analyse structural data. We work very closely with the Cellular Structure and 3D Bioimaging team, which focuses on lower-resolution cellular imaging and is just across the hall.
We are always improving PDBe’s web interface so that users can access our data easily and employ our tools and services in their research. We also design new tools that improve the integrity, quality and dissemination of structural data. This makes a big difference – it can save a lot of time and frustration, and avoids people repeating the same costly experiments.
wwPDB is more than a repository of beautiful images – although some of them are very impressive to look at. It’s an essential resource for the world’s biomedical community, with 1.5 million downloads every day. For PDBe alone, usage increases by about 15% every year.
Q: What impact would you like your work in the PDBe to have?
A: I want us to make structural data accessible and interesting for non-specialists –people who are not necessarily structural biologists, but are fascinated by how life works at the atomic level.
We are currently expanding our connections with different digital tools to give scientists a broader view on proteins. In 2002, I started linking PDB and UniProt, a resource for protein sequence and annotation data. This brought us one step closer to integrating protein data from a range of resources, which gives a better sense of the bigger picture. I’d like to see the PDBe continue to work in this direction.
Q: How did you first get involved with wwPDB?
A: I was doing my post doc research at Oxford when I came across a data annotation job at EMBL-EBI. I liked the idea of making structural data accessible to the wider scientific community, and facilitating research. When I started there were only five of us in the team, so I did a little bit of everything, including database and software design and development.
Q: Where do you come from?
A: I did my PhD in the best-known structural biology department in India, at the Indian Institute of Science Bangalore. That’s where I got into crystallography. After a while, I decided to continue my postdoc research at Oxford.
Q: What got you interested in science in the first place?
A: I was lucky enough to go to a school that had its labs open at any time – day or night. I guess I really enjoyed being in that environment, designing experiments and learning new things.
Q: What is your philosophy for running your team?
A: I encourage everyone to be creative, look beyond their day-to-day role and think about how they can make a difference to the bigger picture. PDBe is not a building site where instructions come from the lead engineer and everyone else just follows blindly. My focus is on empowering everyone in the team to contribute and improve the work we do.
Q: What challenges do you face in your work?
A: Making our data meaningful to non-specialists can be a bit of a challenge. We want to make structures easy to understand, and convey why they’re so interesting. It takes a huge amount of patience to get the details right, show the wider biological context and inspire new hypotheses.