Judith and David Coffey Seminar: Prof Shoba Ranganathan

Title: The 7TM family: are template-based models better than AlphaFold models? 

Speaker: Prof Shoba Ranganathan (Macquarie University) 

Abstract: Insect odorant and gustatory receptors (ORs/GRs) are 7-transmembrane-domain
(7TM) ion channels essential for the survival of insects.  ORs play a key role in many
insect behaviours, including foraging, pollination, social interactions, and recognizing
prey and enemies.  ORs are also the target of biocontrol of insect pests and disease
vectors.  Ors are therefore highly specialized and bear very little sequence similarity,
even within the same species.  These receptors are “upside-down” compared to
G-protein coupled receptors (GPCRs), and function without any accessory G proteins to
let calcium ions in upon ligand binding.  To design or identify novel volatile
attractant or repellent chemicals, a knowledge of the 3D structure of these inverted
topology 7TM receptors is essential.  With the rise of AlphaFold, currently in its third
avatar, we explored if detailed template-based modelling (TBM) using the few
experimental insect OR structures available is still required, instead of a quick
AI-generated AlphaFold3 (AF3) model.  Using all Ors from the genomes of two economically
important Australian fruit fly pest species, we show that 7TM receptors still need
step-by-step TBM rather than AF3 models.  

About the speaker: Shoba Ranganathan is an Honorary Professor of Bioinformatics in
Applied Biosciences, Macquarie University.  She was the first Chair of Bioinformatics in
Australia (2004-22).  She has held research and academic positions in India, USA,
Singapore and Australia as well as a consultancy in industry.  Shoba’s research
addresses several key areas of bioinformatics to understand biological systems using
computational approaches.  Her group has achieved both experience and expertise in
different aspects of computational biology, ranging from metabolites and small molecules
to biochemical networks, pathway analysis and computational systems biology.  She has
authored as well as edited several books in as well as contributed several articles to
the 1st edition of this Encyclopedia.  She was awarded the 2023 Outstanding
Contributions to the International Society for Computational Biology (ISCB) Award.  She
is an Honorary Senior Fellow of the Australian Society for Bioinformatics and
Computational Biology since 2018, an ISCB Fellow since 2023 and an Asia Association for
Artificial Intelligence Fellow since 2024.