Mechanisms, patterns
and molecular origins.

Functional sites beyond sequence and fold.

A conserved local arrangement can preserve a chemical role even when surrounding structures differ. We develop and apply graph-theoretical methods to search for amino-acid side-chain arrangements across experimental and predicted structures.

• Functional annotation of uncharacterized proteins through substructural comparison.
• Conservation and variation of catalytic, ligand-binding and metal-binding sites.
• Evolution of functional sites in ancient protein families and molecular assemblies.

Representative work: GrAfSS (2022); four-carboxylate metal-binding motifs (2024); ATP-PPase diversity (2025).

The interactions that give RNA its shape.

RNA structure is built from networks of interactions between bases. We investigate how tertiary motifs recur, how they contribute to molecular function, and what their conservation reveals about the emergence of biological complexity.

• Graph-based discovery and annotation of hydrogen-bonded base arrangements.
• Ribosomal RNA motifs, riboswitches and RNA–ligand interactions.
• Bacterial small RNAs and their roles in stress responses and regulation.

Representative work: RNA motif search methods (2021); the Burkholderia glycine riboswitch (2021); InterRNA (2016).

From structural insight to testable hypotheses.

Comparing the geometry of known binding sites with other protein structures helps us propose new target relationships for existing compounds. Drug ReposER supports this exploration; a structural match is a hypothesis that requires further computational and experimental evaluation.

In molecular computing, our work with programmable DNA polyominoes connects algorithmic design with experimentally tested self-assembly. Current research directions include reinforcement learning for drug off-target identification and language-model-assisted identification of modular protein components.

Representative work: Drug ReposER (2019); drug repositioning and potential toxicity assessment (2020); DNA polyominoes (2016).

Understanding pathogen proteins.

Our long-running work on Burkholderia pseudomallei combines structural biology, computational analysis and genomics to investigate proteins and regulatory systems associated with bacterial survival and pathogenesis.

Collaborative studies identified Burkholderia Lethal Factor 1 (BLF1) and subsequently examined its specificity and deamidation of the host translation factor eIF4A. Related work characterizes hypothetical proteins and the BPSL1038 Cas-2/VapD nuclease subfamily.

Representative work: BLF1 toxin discovery (2011); BLF1–eIF4A recognition (2022); BPSL1038 (2023).

Adaptation across biological scales.

Collaborative genomics projects examine how organisms adapt to distinctive environments and lifestyles. These include the cold-adapted yeast Glaciozyma antarctica, parasitic Rafflesia plants and the evolution of Galápagos iguanas.

Our contributions connect genome and transcriptome data with protein function, molecular interactions and the history of biological systems.

Representative work: the G. antarctica genome (2018); Rafflesia biology (2023); Galápagos iguana genomics (2025).

Scientific tools for public-sector questions.

Beyond molecular biology, our collaboration with the Royal Malaysia Police brings scientific analysis and data-driven approaches to research on narcotics and new psychoactive substances.

The programme includes database development, analytical methods and training in the use of AI. SARAN and SEDAR are software outputs listed in the lab’s research portfolio.

Related publication: Imbalance in spatiotemporal analysis of narcotics-related activities (2025). See applied data resources.