23466253
The CATH Database provides insights into protein structure/function relationships
We report the latest release (version 1.4) of the CATH protein domains database (http://www.biochem.ucl.ac.uk/bsm/cath). This is a hierarchical classification of 13 359 protein domain structures into evolutionary families and structural groupings. We currently identify 827 homologous families in which the proteins have both structual similarity and sequence and/or functional similarity. These can be further clustered into 593 fold groups and 32 distinct architectures. Using our structural classification and associated data on protein functions, stored in the database (EC identifiers, SWISS-PROT keywords and information from the Enzyme database and literature) we have been able to analyse the correlation between the 3D structure and function. More than 96% of folds in the PDB are associated with a single homologous family. However, within the superfolds, three or more different functions are observed. Considering enzyme functions, more than 95% of clearly homologous families exhibit either single or closely related functions, as demonstrated by the EC identifiers of their relatives. Our analysis supports the view that determining structures, for example as part of a 'structural genomics' initiative, will make a major contribution to interpreting genome data.
33375279
Mapping PDB chains to UniProtKB entries
MOTIVATION
UniProtKB/SwissProt is the main resource for detailed annotations of protein sequences. This database provides a jumping-off point to many other resources through the links it provides. Among others, these include other primary databases, secondary databases, the Gene Ontology and OMIM. While a large number of links are provided to Protein Data Bank (PDB) files, obtaining a regularly updated mapping between UniProtKB entries and PDB entries at the chain or residue level is not straightforward. In particular, there is no regularly updated resource which allows a UniProtKB/SwissProt entry to be identified for a given residue of a PDB file.


RESULTS
We have created a completely automatically maintained database which maps PDB residues to residues in UniProtKB/SwissProt and UniProtKB/trEMBL entries. The protocol uses links from PDB to UniProtKB, from UniProtKB to PDB and a brute-force sequence scan to resolve PDB chains for which no annotated link is available. Finally the sequences from PDB and UniProtKB are aligned to obtain a residue-level mapping.


AVAILABILITY
The resource may be queried interactively or downloaded from http://www.bioinf.org.uk/pdbsws/.
2188414
Agents in bioinformatics, computational and systems biology
The adoption of agent technologies and multi-agent systems constitutes an emerging area in bioinformatics. In this article, we report on the activity of the Working Group on Agents in Bioinformatics (BIOAGENTS) founded during the first AgentLink III Technical Forum meeting on the 2nd of July, 2004, in Rome. The meeting provided an opportunity for seeding collaborations between the agent and bioinformatics communities to develop a different (agent-based) approach of computational frameworks both for data analysis and management in bioinformatics and for systems modelling and simulation in computational and systems biology. The collaborations gave rise to applications and integrated tools that we summarize and discuss in context of the state of the art in this area. We investigate on future challenges and argue that the field should still be explored from many perspectives ranging from bio-conceptual languages for agent-based simulation, to the definition of bio-ontology-based declarative languages to be used by information agents, and to the adoption of agents for computational grids.
16348358
Agent Chameleons: Virtual Agents Real Intelligence
Agent Chameleons provides virtual agents powered by real intelligence, delivering next generation autonomic entities that can seamlessly migrate, mutate and evolve on their journey between and within physical and digital information spaces.
10076896
Agent Assistance for 3D World Navigation
This paper presents mechanisms and approaches to assist user navigation and exploration within 3-dimensional worlds. Specifically, we advocate the deployment of an agent based approach for dynamic system assistance and intervention. An algorithm has been developed, that produces a performance measure, which is employed by the intelligent agent to activate system interventions. We outline the importance of providing discrete navigational cues to users in order to increase their sense of immersion and their overall satisfaction while working within the 3D world. We present HADES - the Home of the Adaptive Environmental System, which is a 3-dimensional world within which the intelligent agent is immersed. The agent therefore has the ability to transform this 3D world into an intelligent environment. HADES reacts proactively to users' movements and offers navigational help indirectly. Indirect navigational support increases the user's satisfaction with his own performance and therefore endorses the user's sense of immersion.
34718551
Encoding W: A Logic for Z in 2OBJ
A prototype proof system for “\(\mathcal{W}\): A Logic for Z” has been produced using the 2OBJ metalogical theorem-prover. 2OBJ permits an encoding which is very similar in structure to that of \(\mathcal{W}\), and the details are presented here. Like \(\mathcal{W}\)the encoding assumes that all its inputs are well-typed. The structure of the encoding is enhanced by a meta-rule on the lifting of proof rules and tactics. There is some discussion of how tactics can make \(\mathcal{W}\)more easily usable.
26464031
A Taxonomy of Web Services Using CSP
Terms such as conversational and stateless are widely used in the taxonomy of web services. We give formal definitions of these terms using the CSP process algebra. Within this framework we also define the notion of Service-Oriented Architecture. These definitions are then used to prove important scalability properties of stateless services. The use of formalism should allow recent debates, concerning how and whether web services provide standardized access to state, to progress more rigorously.
145836
Packing Steiner trees: polyhedral investigations
LetG=(V, E) be a graph andT⊆V be a node set. We call an edge setS a Steiner tree forT ifS connects all pairs of nodes inT. In this paper we address the following problem, which we call the weighted Steiner tree packing problem. Given a graphG=(V, E) with edge weightswe, edge capacitiesce,e∈E, and node setT1,…,TN, find edge setsS1,…,SN such that eachSk is a Steiner tree forTk, at mostce of these edge sets use edgee for eache∈E, and the sum of the weights of the edge sets is minimal. Our motivation for studying this problem arises from a routing problem in VLSI-design, where given sets of points have to be connected by wires. We consider the Steiner tree packing problem from a polyhedral point of view and define an associated polyhedron, called the Steiner tree packing polyhedron. The goal of this paper is to (partially) describe this polyhedron by means of inequalities. It turns out that, under mild assumptions, each inequality that defines a facet for the (single) Steiner tree polyhedron can be lifted to a facet-defining inequality for the Steiner tree packing polyhedron. The main emphasis of this paper lies on the presentation of so-called joint inequalities that are valid and facet-defining for this polyhedron. Inequalities of this kind involve at least two Steiner trees. The classes of inequalities we have found form the basis of a branch & cut algorithm. This algorithm is described in our companion paper (in this issue).