Members and collaborators
We apply techniques from computer science -- Data structures and Algorithms,
Information theory, Graph theory, Stringology, Combinatorial Optimisation,
Mathematics/Statistics -- to address computational problems that arise in biological data, predominantly in those involving protein 3D structures.
A command-line program and webserver to infer pairwise protein structural alignments and also identify closely-competing alternative alignments (when they exist). Uses statistical inference as the underlying framework, and employs improved I-value (information-based) measure of alignment quality.
Some programs and web utilities we developed for structural analyses
A web server to assign secondary structure to protein coordinate data using the Bayesian method of Minimum Message Length inference. Identifies helices, turns of various types, and strands of a sheet.
A command line program to align and superpose multiple three-dimensional structures of proteins.
A web server and a program to rapidly screen the entire (up-to-date) PDB and identify similar oligopeptide fragments. The method mathematically guarantees to find all superposable fragments for a given query that fits within a user-prescribed threshold of root-mean-squared deviation (RMSD).
A C++ library for least-squares superposition of 3D vector sets. This library implements sufficient statistics for this superposition problem, and allows updating existing superpositions (under vector set addition and symmetric difference) in constant time.
A web server to generate phase-search probes to support experimental solutions to protein crystal structures using crystallographic Molecular Replacement (MR).
A web server to assess the quality of any given protein structural alignment, or compare between competing alignments, using I-value (Information Content).