Janet Thornton retires: a pioneer in structural bioinformatics

In recognition of Janet Thornton’s retirement, we look back at some of her biggest accomplishments shaping the field of bioinformatics

Woman standing at podium
Professor Dame Janet Thornton. Credit: EMBL

Professor Dame Janet Thornton is one of the world’s pioneers in structural bioinformatics. Her incredible career and active voice on many topics, including science in Europe, open data and women in science, has inspired scientists the world over. 

As the Director of EMBL’s European Bioinformatics Institute (EMBL-EBI) between 2001 and 2015, Janet Thornton led the growth of the institute from 160 to over 600 people. She currently leads a research group at EMBL-EBI, studying the biology of proteins and ageing, and is a leading voice in the scientific community, having undertaken leadership and governance roles in the Royal Society, European Research Council, ELIXIR, and many more.  

A cake shaped like books with dates on running from 2001 to 2015
Janet’s celebration cake for her stepping down as Director of EMBL-EBI. Credit: Robert Slowley

As Janet retires in summer 2023, we reflect on some of her highlights and achievements during her time at EMBL. 

Structural biology and bioinformatics

Thornton has seen the field of structural biology change completely. When she started her career there were only about 20 known protein structures, and now there are over 200,000 structures in the Protein Data Bank (PDB), and over 200 million predictions made by AlphaFold. Her work at EMBL has been highly interdisciplinary, interfacing with structural biology, bioinformatics, biological chemistry and chemoinformatics.

Woman standing at a podium
Janet giving a speech at the EMBL-EBI 20th anniversary celebration. Credit: Robert Slowley

Janet started her career by trying to predict protein structures from sequence. She spent years characterising and analysing the new protein structures as they were determined and stored in the PDB. She is also well known for developing, with Roman Laskowski, the widely used ProCheck software for checking the quality of protein structures. Together with her colleague Christine Orengo, Thornton also introduced the CATH classification of protein structures, which provides information on the evolutionary relationships of protein domains. CATH now exists as an open access database and is part of the ELIXIR infrastructure. 

The recent predictions of structure using AlphaFold, developed by DeepMind based on deep learning approaches, have delighted Janet together with the fact that more than 200 million predicted structures are openly available at EMBL-EBI in the AlphaFold Database

Current research 

Janet’s research group at EMBL-EBI is developing robust search, comparison and annotation tools for enzymes,  which are available as open access algorithms and web tools for quantitative similarity searches between enzyme reactions. Recent work from the group has led to several exciting new knowledge-based approaches to investigate the evolution of enzymes, most recently at a mechanistic level.

“I’m very lucky to work with such brilliant minds every day,” said Janet. “My team at EMBL-EBI is truly an outstanding group of scientists. They’re passionate, driven, and never fail to inspire and surprise me.” 

Data sharing across Europe

Thornton led the establishment of ELIXIR, an intergovernmental organisation that brings together life science data resources from across Europe. Its goal is to ensure sustainable funding and harmonise data resources within the bioinformatics ecosystem, making it easier for scientists to find and share data, exchange expertise, and agree on best practices.

“The launch of ELIXIR was the first step towards building a distributed infrastructure for biological information throughout Europe,” said Janet. “By providing public access to the wealth of knowledge generated by the global research community, ELIXIR empowers researchers in academia and industry to solve some of society’s most pressing problems.”

Two people standing in front of a building
Janet Thornton and then UK Minister for Universities and Science David Willetts at the opening of the EMBL-EBI South Building and ELIXIR Hub. Credit: Robert Slowley

Inspiring the next generation

As an advocate for women in science, Thornton has spoken openly about what can be done to support all scientists throughout their career. One impact of this includes the establishment of the Janet Thornton Fellowship, which funds researchers after taking a career break. Throughout her career, Thornton has also supervised a multitude of PhD and postdoctoral researchers including Sarah Teichmann, Head of Cellular Genetics and Senior Group Leader at the Wellcome Sanger Institute and David Jones, Professor of Bioinformatics at University College London.

Woman holding a medal
Janet Thornton holding her medal after she was appointed Dame Commander of the Order of the British Empire (DBE) in the 2012 Birthday Honours for services to bioinformatics. Credit: EMBL

“I think every scientist, but perhaps especially women, need to decide how they will deal with their work–life balance. There is no “right” way to do this – different solutions suit different people,” said Janet. “A scientist has about 50 years to do their research; taking a short time out of that time to be at home for whatever reason should certainly be possible.”

Finally, Janet stood out as a fantastic public speaker and science communicator. Her regular appearances in the press, explaining complex concepts in an accessible and engaging way, shared her wonder for the molecular world beyond the many colleagues, collaborators and mentees who have had the privilege to meet and work with Janet in person. 

“I have much enjoyed my career as a scientist and would advocate it as one of the best jobs I can imagine,” said Janet. “I have met and worked with brilliant people at Oxford, Birkbeck, UCL and EMBL and enjoyed being part of a joint endeavour to discover the fabulous world of protein structures.”

Janet’s legacy will live on at EMBL-EBI as our new building named in her honour currently undergoes development. Construction work on the Thornton building began in autumn 2022 and the building is expected to open in summer 2024, providing a hub for collaboration and translation. 

This article originally featured in the EMBLetc issue 100.

Tags: alphafold, bioinformatics, elixir, embl-ebi, farewell, protein structure, structural biology, thornton


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