ASSAM
Find other structures with a similar arrangement of amino-acid side chains.
- Input
- A PDB query containing up to 12 residues.
- Output
- Matching local arrangements in a structure database.
Tools & databases
Find the right starting point.
Research software for exploring local three-dimensional arrangements in proteins and RNA, together with resources from our genomics and applied data work.
GrAfSS
A shared entry point to the laboratory’s graph-based structure-searching programs. Choose a tool below according to your input and research question.
SPRITE
Search a protein structure for arrangements resembling known sites or motifs.
- Input
- A protein structure in PDB format.
- Output
- Candidate site and motif annotations.
IMAAAGINE
Search for a theoretical spatial arrangement without requiring an existing coordinate model of the complete motif.
- Input
- Residue types and distance constraints.
- Output
- Structures containing compatible arrangements.
NASSAM
Annotate RNA structures by matching known tertiary base arrangements.
- Input
- An RNA structure in PDB format.
- Output
- Related base arrangements and RNA motifs.
COGNAC
Identify clusters of RNA bases connected by hydrogen bonds.
- Input
- An RNA structure and interaction criteria.
- Output
- Base-interaction networks for motif analysis.
Drug ReposER
Compare amino-acid arrangements with known drug-binding interfaces to explore candidate targets for repositioning.
- Input
- A structure, PDB identifier, ligand or drug query.
- Output
- Similar binding-site arrangements for further evaluation.
These links open the existing research services. Structural similarity supports hypothesis generation; it does not by itself establish a shared function or drug-binding activity.
Research collections
Databases and related resources
Specialist collections developed from the laboratory’s research.
InterRNA
A database of computationally and manually curated base–base interactions and arrangements in RNA structures.
GlacIER
An integrated resource for genome sequence, functional genomics and structural genomics data from Glaciozyma antarctica.
ICBMs
A collection of three-dimensional residue motifs at inter-chain and intermolecular interfaces of protein oligomers.
Legacy databases are hosted separately; their availability may vary. Contact the lab for access enquiries.
Applied data resources
Beyond molecular structures
Software outputs supporting the laboratory’s collaboration on narcotics data and public reporting.
SARAN
A resource for anti-narcotics data and analytics.
SEDAR
A platform for citizen-submitted reports to support anti-narcotics information gathering.