SUMMARY: The PROTORP server analyses protein-protein associations in 3D structures. The server calculates a series of physical and chemical parameters of the protein interaction sites that contribute to the binding energy of the association. These parameters include, size and shape, intermolecular bonding, residue and atom composition and secondary structure contributions. The server is flexible, in that it allows users to analyse individual protein associations or large datasets of associations deposited in the PDB, or upload and analyse proprietary files. The properties calculated can be compared with parameter distributions for non-homologous datasets of different classes of protein associations provided on the server website. The server provides an efficient way of characterizing protein-protein associations of new or existing proteins, and a means of putting these values in the context of previously observed associations. AVAILABILITY: http://www.bioinformatics.sussex.ac.uk/protorp

MOTIVATION: All eukaryotic proteomes are characterized by a significant percentage of proteins of unknown function. Comp-utational function prediction methods are therefore essential as initial steps in the function annotation process. This article describes an annotation method (PiRaNhA) for the prediction of RNA-binding residues (RBRs) from protein sequence information. A series of sequence properties (position specific scoring matrices, interface propensities, predicted accessibility and hydrophobicity) are used to train a support vector machine. This method is then evaluated for its potential to be applied to RNA-binding function prediction at the level of the complete protein. RESULTS: The 5-fold cross-validation of PiRaNhA on a dataset of 81 RNA-binding proteins achieves a Matthews Correlation Coefficient (MCC) of 0.50 and accuracy of 87.2%. When used to predict RBRs in 42 proteins not used in training, PiRaNhA achieves an MCC of 0.41 and accuracy of 84.5%. Decision values from the PiRaNhA predictions were used in a second SVM to make predictions of RNA-binding function at the protein level, achieving an MCC of 0.53 and accuracy of 76.1%. The PiRaNhA RBR predictions allow experimentalists to perform more targeted experiments for function annotation; and the prediction of RNA-binding function at the protein level shows promise for proteome-wide annotations. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at www.bioinformatics.sussex.ac.uk/PIRANHA or http://piranha.protein.osaka-u.ac.jp. SUPPLEMENTARY INFORMATION: Supplementary data are available at the Bioinformatics online.

UNLABELLED: SHARP2 is a flexible web-based bioinformatics tool for predicting potential protein-protein interaction sites on protein structures. It implements a predictive algorithm that calculates multiple parameters for overlapping patches of residues on the surface of a protein. Six parameters are calculated: solvation potential, hydrophobicity, accessible surface area, residue interface propensity, planarity and protrusion (SHARP2). Parameter scores for each patch are combined, and the patch with the highest combined score is predicted as a potential interaction site. SHARP2 enables users to upload 3D protein structure files in PDB format, to obtain information on potential interaction sites as downloadable HTML tables and to view the location of the sites on the 3D structure using Jmol. The server allows for the input of multiple structures and multiple combinations of parameters. Therefore predictions can be made for complete datasets, as well as individual structures. AVAILABILITY: http://www.bioinformatics.sussex.ac.uk/SHARP2.

SUMMARY: HTHquery is a web-based service to determine if a protein structure has a helix-turn-helix structural motif which could bind to DNA. It is based on a similarity with a set of structural templates, the accessibility of a putative structural motif and a positive electrostatic potential in the neighbourhood of the putative motif. A set of scores are computed, based on each template, using a linear predictor. From the training set used, the predictor has a true positive rate of 83.5% and a false positive rate of 0.8%. The emphasis for the website is on providing a straightforward interface which can be easily used by a bench-based scientist. AVAILABILITY: HTHquery is implemented using a set of Perl scripts and C program and can be accessed freely on the website http://www.ebi.ac.uk/thornton-srv/databases/HTHquery.

Current multimedia design guidelines support the development of effective multisensory interfaces but pay scant attention to the broader context in which educational multimedia is deployed. Here a multimodal approach was used to encourage senior managers to learn a complex management topic. Through co-design of multimedia with a learning context, otherwise inaccessible content was shown to have wide appeal. The aim of this short paper is to show that to confidently design effective multimedia learning experiences, it is necessary to co-design multimedia with a broader learning context.

We explore some interface design issues raised by the development and evaluation of a highly interactive information retrieval (IR) system based on a probabilistic retrieval model with relevance feedback. The Okapi system uses term frequency weighting functions to display retrieved items in a best match ranked order; it can also find additional items similar to those marked as relevant by the searcher. Its query expansion mechanism has been implemented in several different ways, and subjected to a number of evaluative studies. The object has been to compare the effectiveness of automatic and interactive query expansion in different user interface environments. In automatic query expansion, the system extracts terms from items judged relevant by the searcher and immediately creates a new query to search for more items. In the interactive versions the extracted terms are displayed, and the searcher may intervene in the construction of a modified query for the next phase of the search. These contrasting approaches serve to illustrate the interplay between different principles of human computer interaction and the information retrieval task. The discussion focuses on the nature of interaction in IR and the interrelationship between functional visibility, the user's cognitive loading, and the balance of control between user and system.

We discuss whether it is feasible to build intelligence rule- or weight-based algorithms into general-purpose software for interactive thesaurus navigation. We survey some approaches to the problem reported in the literature, particularly those involving the assignment of “link weights” in a thesaurus network, and point out some problems of both principle and practice. We then describe investigations which entailed logging the behavior of thesaurus users and testing the effect of thesaurus-based query enhancement in an IR system using term weighting, in an attempt to identify successful strategies to incorporate into automatic procedures. The results cause us to question many of the assumptions made by previous researchers in this area. © 1995 John Wiley & Sons, Inc.

This paper gives an account of the development and use of software to manipulate and display networks. The work was done as part of the LSE LEGOL Project in Information Systems Analysis and Design, but the programs were written to be generally applicable; so that they might be equally suitable for displaying the results of statistical processes like single-linkage cluster analysis and path analysis, or producing structure diagrams for program or system components.