Exploring the potential of 3D Zernike descriptors and SVM for protein\u2013protein interface prediction

Abstract Background The correct determination of protein–protein interaction interfaces is important for understanding disease mechanisms and for rational drug design. To date, several computational methods for the prediction of protein interfaces have been developed, but the interface prediction problem is still not fully understood. Experimental evidence suggests that the location of binding sites is imprinted in the protein structure, but there are major differences among the interfaces of the various protein types: the characterising properties can vary a lot depending on the interaction type and function. The selection of an optimal set of features characterising the protein interface and the development of an effective method to represent and capture the complex protein recognition patterns are of paramount importance for this task. Results In this work we investigate the potential of a novel local surface descriptor based on 3D Zernike moments for the interface prediction task. Descriptors invariant to roto-translations are extracted from circular patches of the protein surface enriched with physico-chemical properties from the HQI8 amino acid index set, and are used as samples for a binary classification problem. Support Vector Machines are used as a classifier to distinguish interface local surface patches from non-interface ones. The proposed method was validated on 16 classes of proteins extracted from the Protein–Protein Docking Benchmark 5.0 and compared to other state-of-the-art protein interface predictors (SPPIDER, PrISE and NPS-HomPPI). Conclusions The 3D Zernike descriptors are able to capture the similarity among patterns of physico-chemical and biochemical properties mapped on the protein surface arising from the various spatial arrangements of the underlying residues, and their usage can be easily extended to other sets of amino acid properties. The results suggest that the choice of a proper set of features characterising the protein interface is crucial for the interface prediction task, and that optimality strongly depends on the class of proteins whose interface we want to characterise. We postulate that different protein classes should be treated separately and that it is necessary to identify an optimal set of features for each protein class

PACMAS: A Personalized, Adaptive, and Cooperative MultiAgent System Architecture

In this paper, a generic architecture, designed to support the implementation of applications aimed at managing information among different and heterogeneous sources, is presented. Information is filtered and organized according to personal interests explicitly stated by the user. User pro- files are improved and refined throughout time by suitable adaptation techniques. The overall architecture has been called PACMAS, being a support for implementing Personalized, Adaptive, and Cooperative MultiAgent Systems. PACMAS agents are autonomous and flexible, and can be made personal, adaptive and cooperative, depending on the given application. The peculiarities of the architecture are highlighted by illustrating three relevant case studies focused on giving a support to undergraduate and graduate students, on predicting protein secondary structure, and on classifying newspaper articles, respectively

Enhancing Web-Based Configuration with Recommendations and Cluster-Based Help

In a collaborative project with Tacton AB, we have investigated new ways of assisting the user in the process of on-line product configuration. A web-based prototype, RIND, was built for ephemeral users in the domain of PC configuration

Movie Popularity Classification based on Inherent Movie Attributes using C4.5,PART and Correlation Coefficient

Abundance of movie data across the internet makes it an obvious candidate for machine learning and knowledge discovery. But most researches are directed towards bi-polar classification of movie or generation of a movie recommendation system based on reviews given by viewers on various internet sites. Classification of movie popularity based solely on attributes of a movie i.e. actor, actress, director rating, language, country and budget etc. has been less highlighted due to large number of attributes that are associated with each movie and their differences in dimensions. In this paper, we propose classification scheme of pre-release movie popularity based on inherent attributes using C4.5 and PART classifier algorithm and define the relation between attributes of post release movies using correlation coefficient.Comment: 6 page

A Survey of Prediction and Classification Techniques in Multicore Processor Systems

In multicore processor systems, being able to accurately predict the future provides new optimization opportunities, which otherwise could not be exploited. For example, an oracle able to predict a certain application\u27s behavior running on a smart phone could direct the power manager to switch to appropriate dynamic voltage and frequency scaling modes that would guarantee minimum levels of desired performance while saving energy consumption and thereby prolonging battery life. Using predictions enables systems to become proactive rather than continue to operate in a reactive manner. This prediction-based proactive approach has become increasingly popular in the design and optimization of integrated circuits and of multicore processor systems. Prediction transforms from simple forecasting to sophisticated machine learning based prediction and classification that learns from existing data, employs data mining, and predicts future behavior. This can be exploited by novel optimization techniques that can span across all layers of the computing stack. In this survey paper, we present a discussion of the most popular techniques on prediction and classification in the general context of computing systems with emphasis on multicore processors. The paper is far from comprehensive, but, it will help the reader interested in employing prediction in optimization of multicore processor systems