A novel method for comparing topological models of protein structures enhanced with ligand information

This article is available open access through the publisher’s website through the link below. Copyright @ 2008 The Authors.We introduce TOPS+ strings, a highly abstract string-based model of protein topology that permits efficient computation of structure comparison, and can optionally represent ligand information. In this model, we consider loops as secondary structure elements (SSEs) as well as helices and strands; in addition we represent ligands as first class objects. Interactions between SSEs and between SSEs and ligands are described by incoming/outgoing arcs and ligand arcs, respectively; and SSEs are annotated with arc interaction direction and type. We are able to abstract away from the ligands themselves, to give a model characterized by a regular grammar rather than the context sensitive grammar of the original TOPS model. Our TOPS+ strings model is sufficiently descriptive to obtain biologically meaningful results and has the advantage of permitting fast string-based structure matching and comparison as well as avoiding issues of Non-deterministic Polynomial time (NP)-completeness associated with graph problems. Our structure comparison method is computationally more efficient in identifying distantly related proteins than BLAST, CLUSTALW, SSAP and TOPS because of the compact and abstract string-based representation of protein structure which records both topological and biochemical information including the functionally important loop regions of the protein structures. The accuracy of our comparison method is comparable with that of TOPS. Also, we have demonstrated that our TOPS+ strings method out-performs the TOPS method for the ligand-dependent protein structures and provides biologically meaningful results. Availability: The TOPS+ strings comparison server is available from http://balabio.dcs.gla.ac.uk/mallika/WebTOPS/topsplus.html.University of Glasgo

Timetabling in constraint logic programming

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 ECLiPSe, since it deals with finite domains, it has well-defined interfaces between basic building blocks and supports good debugging facilities. The implemented timetable was based on the existing, currently used, timetables at the School of Informatics at out university. It integrates constraints concerning room and period availability

FURY: Fuzzy unification and resolution based on edit distance

We present a theoretically founded framework for fuzzy unification and resolution based on edit distance over trees. Our framework extends classical unification and resolution conservatively. We prove important properties of the framework and develop the FURY system, which implements the framework efficiently using dynamic programming. We evaluate the framework and system on a large problem in the bioinformatics domain, that of detecting typographical errors in an enzyme name databas

Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

Relations between extensional tectonics and magmatism within the Southern Oklahoma aulacogen

Variations in the geometry, distribution and thickness of Cambrian igneous and sedimentary units within southwest Oklahoma are related to a late Proterozoic - early Paleozoic rifting event which formed the Southern Oklahoma aulacogen. These rock units are exposed in the Wichita Mountains, southwest Olkahoma, located on the northern margin of a Proterozoic basin, identified in the subsurface by COCORP reflection data. Overprinting of the Cambrian extensional event by Pennyslvanian tectonism obsured the influence of pre-existing basement structures and contrasting basement lithologies upon the initial development of the aulacogen

A process algebra for synchronous concurrent constraint programming

Concurrent constraint programming is classically based on asynchronous communication via a shared store. This paper presents new version 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. An operational and an algebraic semantics are defined. The algebraic semantics is proved to be sound and complete with respect to a compositional operational semantics which is also presented in the paper

Transformations between HCLP and PCSP

We present a general methodology for transforming between HCLP and PCSP in both directions. HCLP and PCSP each have advantages when modelling problems, and each have advantages when implementing models and solving them. Using the work presented in this paper, the appropriate paradigm can be used for each of these steps, with a meaning-preserving transformation in between if necessary

Analysis of self-oscillating DC-DC resonant power converters using a hysteretic relay

The paper presents a technique for exciting resonant DC-DC converters in a self-oscillating manner. The analysis necessary to predict the behaviour of such converters is also given. The oscillation is based on the behaviour of a hysteretic relay with a negative hysteresis transition. Self-oscillating converters benefit from higher efficiency/higher power density than their non-self-oscillating counterparts as they can be operated closer to the tank resonant frequency. The self-oscillating mechanism presented here is also simple and cost effective to implement. A prototype converter is presented in order to verify the theoretical claims

Interactive visualisation and exploration of biological data

International audienceno abstrac

Design of an LCC current-output resonant converter for use as a constant current source

A methodology for the design of LCC resonant current-source converters, is presented. Unlike previous techniques, the resulting converter provides near constant steady-state output current over an extended load range when excited at the resonant frequency, through use of a self-oscillating controlle