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A Grid-Enabled Meta-Server for Protein Threading

Title
A Grid-Enabled Meta-Server for Protein Threading
Funding
ARC | Discovery Projects
Contract (GA) number
DP0667266
Start Date
2006/01/01
End Date
2008/12/31
Open Access mandate
no
Organizations
-
More information
http://purl.org/au-research/grants/arc/DP0667266

 

  • SiteSeek: Post-translational modification analysis using adaptive locality-effective kernel methods and new profiles

    Yoo, Paul D; Ho, Yung Shwen; Zhou, Bing Bing; Zomaya, Albert Y (2008)
    Projects: ARC | A Grid-Enabled Meta-Server for Protein Threading (DP0667266)
    Abstract Background Post-translational modifications have a substantial influence on the structure and functions of protein. Post-translational phosphorylation is one of the most common modification that occur in intracellular proteins. Accurate prediction of protein phosphorylation sites is of great importance for the understanding of diverse cellular signalling processes in both the human body and in animals. In this study, we propose a new machine learning based protein phosphorylation sit...

    Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index

    Zomaya Albert Y; Sikder Abdur R (2006)
    Projects: ARC | A Grid-Enabled Meta-Server for Protein Threading (DP0667266)
    Abstract Background Knowledge of protein domain boundaries is critical for the characterisation and understanding of protein function. The ability to identify domains without the knowledge of the structure – by using sequence information only – is an essential step in many types of protein analyses. In this present study, we demonstrate that the performance of DomainDiscovery is improved significantly by including the inter-domain linker index value for domain identification from sequence-bas...

    Improved general regression network for protein domain boundary prediction

    Yoo, Paul D; Sikder, Abdur R; Zhou, Bing Bing; Zomaya, Albert Y (2008)
    Projects: ARC | A Grid-Enabled Meta-Server for Protein Threading (DP0667266)
    Background Protein domains present some of the most useful information that can be used to understand protein structure and functions. Recent research on protein domain boundary prediction has been mainly based on widely known machine learning techniques, such as Artificial Neural Networks and Support Vector Machines. In this study, we propose a new machine learning model (IGRN) that can achieve accurate and reliable classification, with significantly reduced computations. The IGRN was traine...

    RBT-GA: a novel metaheuristic for solving the multiple sequence alignment problem

    Taheri, Javid; Zomaya, Albert Y (2009)
    Projects: ARC | A Grid-Enabled Meta-Server for Protein Threading (DP0667266)
    Background Multiple Sequence Alignment (MSA) has always been an active area of research in Bioinformatics. MSA is mainly focused on discovering biologically meaningful relationships among different sequences or proteins in order to investigate the underlying main characteristics/functions. This information is also used to generate phylogenetic trees. Results This paper presents a novel approach, namely RBT-GA, to solve the MSA problem using a hybrid solution methodology combining the Rubber B...

    A modular kernel approach for integrative analysis of protein domain boundaries

    Yoo, Paul D; Zhou, Bing; Zomaya, Albert Y (2009)
    Projects: ARC | A Grid-Enabled Meta-Server for Protein Threading (DP0667266)
    Background In this paper, we introduce a novel inter-range interaction integrated approach for protein domain boundary prediction. It involves (1) the design of modular kernel algorithm, which is able to effectively exploit the information of non-local interactions in amino acids, and (2) the development of a novel profile that can provide suitable information to the algorithm. One of the key features of this profiling technique is the use of multiple structural alignments of remote homologue...
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