David Gilbert

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We present the first computational kinetic model of polyamine metabolism in bloodstream-form Trypanosoma brucei, the causative agent of human African trypanosomiasis. We systematically extracted the polyamine pathway from the complete metabolic network while still maintaining the predictive capability of the pathway. The kinetic model is constructed on the(More)
Crucial to glucose homoeostasis in humans, the hPDC (human pyruvate dehydrogenase complex) is a massive molecular machine comprising multiple copies of three distinct enzymes (E1-E3) and an accessory subunit, E3BP (E3-binding protein). Its icosahedral E2/E3BP 60-meric 'core' provides the central structural and mechanistic framework ensuring favourable E1(More)
  • David Gilbert, David Westheady, Juris Viksnaz, Janet Thorntonx
  • 2000
Overview We describe the design and implementation of a fast topology{based method for protein structure comparison. The approach uses the TOPS topological representation of protein structure, aligning two structures using a common discovered pattern and generating measure of distance derived from an insert score. Heavy use is made of a constraint-based(More)
In this chapter we review techniques for sequence based pattern discovery and comparison, and show how these can be extended to RNA structures and abstract representations of protein structure at the fold level. We first define deterministic patterns over sequences and distinguish pattern matching from string comparison, reviewing the use of dynamic(More)
Concurrent constraint programming is classically based on asynchronous communication via a shared store. This paper presents new versions of the ask and tell primitives which features synchronicity. Our approach is based on the idea of telling new information just in the case that a concurrently running process is asking for it. The new primitives are shown(More)
In this paper we describe the timetabling problem and its solvability in a Constraint Logic Programming Language. A solution to the problem has been developed and implemented in ECL i PS e , since it deals with finite domains, it has well-defined interfaces between basic building blocks and supports good debugging facilities. The implemented timetable was(More)
This paper introduces the constructive logic speciication language SILCS (Speciication In Logic of Concurrent Systems). The operational semantics of SILCS encapsulates the computational rule required for the correct interpretation of`programs' derived from Horn clause characterisations of the behaviour of concurrent systems. SILCS is expressive enough to(More)
We describe an implementation in a nite domain constraint logic programming language of a web-based biosequence structure search program. We have used the clp(FD) language for the implementation of our search engine and have ported the PiLLoW libraries to clp(FD). Our program is based on CBSDL, a constraint based structure description language for(More)