17288038
The PSIPRED protein structure prediction server
SUMMARY
The PSIPRED protein structure prediction server allows users to submit a protein sequence, perform a prediction of their choice and receive the results of the prediction both textually via e-mail and graphically via the web. The user may select one of three prediction methods to apply to their sequence: PSIPRED, a highly accurate secondary structure prediction method; MEMSAT 2, a new version of a widely used transmembrane topology prediction method; or GenTHREADER, a sequence profile based fold recognition method.


AVAILABILITY
Freely available to non-commercial users at http://globin.bio.warwick.ac.uk/psipred/
11334584
The rapid generation of mutation data matrices from protein sequences
An efficient means for generating mutation data matrices from large numbers of protein sequences is presented here. By means of an approximate peptide-based sequence comparison algorithm, the set sequences are clustered at the 85% identity level. The closest relating pairs of sequences are aligned, and observed amino acid exchanges tallied in a matrix. The raw mutation frequency matrix is processed in a similar way to that described by Dayhoff et al. (1978), and so the resulting matrices may be easily used in current sequence analysis applications, in place of the standard mutation data matrices, which have not been updated for 13 years. The method is fast enough to process the entire SWISS-PROT databank in 20 h on a Sun SPARCstation 1, and is fast enough to generate a matrix from a specific family or class of proteins in minutes. Differences observed between our 250 PAM mutation data matrix and the matrix calculated by Dayhoff et al. are briefly discussed.
31768671
Protein fold recognition
SummaryAn important, yet seemingly unattainable, goal in structural molecular biology is to be able to predict the native three-dimensional structure of a protein entirely from its amino acid sequence. Prediction methods based on rigorous energy calculations have not yet been successful, and best results have been obtained from homology modelling and statistical secondary structure prediction. Homology modelling is limited to cases where significant sequence similarity is shared between a protein of known structure and the unknown. Secondary structure prediction methods are not only unreliable, but also do not offer any obvious route to the full tertiary structure. Recently, methods have been developed whereby entire protein folds are recognized from sequence, even where little or no sequence similarity is shared between the proteins under consideration. In this paper we review the current methods, including our own, and in particular offer a historical background to their development. In addition, we also discuss the future of these methods and outline the developments under investigation in our laboratory.
9402109
Toward a Scoring Function for Quality-Driven Machine Translation
We describe how we constructed an automatic scoring function for machine translation quality; this function makes use of arbitrarily many pieces of natural language processing software that has been designed to process English language text. By machine-learning values of functions available inside the software and by constructing functions that yield values based upon the software output, we are able to achieve preliminary, positive results in machine-learning the difference between human-produced English and machine-translation English. We suggest how the scoring function may be used for MT system development.
44981587
A Tool for Inference Detection and Knowledge Discovery in Databases
Latent dependencies and relationships between groups of attributes in databases can produce inference channels that pose serious security threats. This paper uses a powerful knowledge discovery formalism for modeling and identifying latent inference channels in relational databases. The inference discovery methodology supports the analysis of precise and imprecise inference in database schemes and extensions. An interactive graphical tool for aiding inference discovery in Oracle databases is described. This tool is useful for identifying compromising inference channels in databases with many hidden dependencies.
14144660
Systematic protection mechanism design
This work describes an attempt to systematically design a hardware resource protection mechanism when given the requirements of a particular language as a target. The design process is formalized as a structured walk through the multidimensional computer design space towards a hypothetical class of optimal machines. Each step in this walk involves a change in the distribution of work between the compiler and run-time system but no change in the source language semantics. The starting point for this walk is the result of a semantic analysis of the language to be implemented; typically, this produces a very high level machine where the compiler, if any, is trivial. The walk ends when no changes result in a net improvement. This does not guarantee that the result is even locally optimal, since the changes tried depend on the ingenuity and persistence of the designer.
 This design approach has been used to arrive at a practical, general purpose protection mechanism oriented towards the needs of the Ada language (preliminary version). This architecture was evaluated by comparing it with the PDP-11/45. For the purpose of this comparison, the protection mechanism was incorporated into a partially specified PDP-11 like instruction set. The number of bits making up the processor state and the number of operations involved in address computation were evaluated. On this basis, the result appears to be competitive and worth further investigation.
7107822
Minimax disappointment criterion for video broadcasting
Users of media broadcasting services generally experience different grades of overall performance because of the non-uniform quality of their channel conditions. In order to provide all users equally satisfactory performance, we propose a new performance criterion named "minimax disappointment", based on layered service levels and the basic principle of joint source-channel coding. This criterion minimizes for all users the maximum value of performance degradation between the received performance and the expected optimal performance, given each user's individual channel situation. In support of this criterion, we develop two broadcasting systems and a gradient-based optimization scheme. Our systems achieve universally near-maximal performance for multiple user classes by providing layered service.
17269099
Edge detection in ultrasound speckle noise
Presents a statistical approach to edge detection in ultrasound speckle, and uses actual noise statistics to derive an expression for an optimal detection rule. The authors compute the optimal detector for the special case of uncorrelated speckle, and an approximation to the optimal detector for the case when signal-to-noise ratio (SNR) is high. They also discuss a simple sub-optimal detection scheme, and show that its performance is close to that of the optimal uncorrelated speckle detection rule, and surpasses that of the high-SNR approximation except in the case of extremely high SNR, in which case they both perform equally well.<<ETX>>