Macromolecular structure comparison and docking: an algorithmic review

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DOIResolve DOI: http://doi.org/10.2174/1381612811319120006
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TypeArticle
Journal titleCurrent Pharmaceutical Design
ISSN1381-6128
Volume19
Issue12
Pages21832193; # of pages: 11
SubjectMacromolecular structures, docking, protein-protein interaction, alignment, algorithms, drug designers, comparison, Bayesian framework, kernel-based methods, projection-based techniques
AbstractThe comparison of macromolecular structures, in terms of functionalities, is a crucial step when aiming to identify potential docking sites. Drug designers require the identification of such docking sites for the binding of two proteins, in order to form a stable complex. This paper presents a review of current approaches to macromolecular structure comparison and docking, following an algorithmic approach. We describe techniques based on the Bayesian framework, kernel-based methods, projection-based techniques and spectral approaches. We introduce the use of quantum particle swarm optimization, in order to aid us to find the most appropriate docking sites. We discuss the importance of the heat and Schrödinger equations to address the non-rigid nature of proteins and highlight the strengths and limitations of the various methods.
Publication date
LanguageEnglish
AffiliationInformation and Communication Technologies; National Research Council Canada
Peer reviewedYes
NPARC number21270407
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Record identifier2581777b-164c-4529-a40d-ccf6df4af3c1
Record created2014-02-07
Record modified2016-05-09
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