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The Bioinformatics (computational biology and system biology) division of NRL is actively engaged in generating specialized multi-facet data bases using knowledge in drug discovery, chemistry and biochemistry of molecules, applied mathematics, informatics, statistics, computer science and artificial intelligence to understand more towards novel drug discovery of several molecular targets. NRL is currently developing its own software to dissect NRL’s data bases of over 100,000 compounds for predicting molecular functional activities, defining core pharmacophores and eliminating possible side-effects and toxicities applying computationally intensive techniques such as data mining and algorithms. NRL is utilizing three specific areas to generate predictable novel drugs for various chronic diseases.
In the last two decades, tens of thousands of protein three-dimensional structures have been determined by X-ray crystallography and protein nuclear magnetic resonance spectroscopy (protein-NMR). NRL-drug discovery effort would like to utilize such data base to predict possible Protein-Protein Interactions, Protein-Peptide Interactions and Protein-Drug Interactions based on these 3D structures without doing actual experiments. A variety of methods that have been developed and are readily accesible to tackle such understanding of Target-Drug interactions are being applied for better predictions and precise understandings of novel structures.
Software tools for NRL-bioinformatics range from simple command-line tools, to more complex graphical programs. Standalone web-services available from various bioinformatics companies or public institutions is being used for predictable structures from natural sources. The computational biology tool best-known is probably BLAST, an algorithm for determining the similarity of arbitrary sequences against other sequences, possibly from curated databases of protein or DNA sequences can be intigrated. The NCBI provides a popular web-based implementation that searches their databases, and can be utilized in further predictive structures. Since no specific data base and software are currnetly available for Target-Drug interactions, development of such softwares at NRL will be the primary focus under the bioinformatics division.
SOAP and REST-based interfaces have been developed for a wide variety of bioinformatics applications allowing an application running on one computer in one part of the world to use algorithms, data and computing resources on servers in other parts of the world. The main advantages lay in the end user not having to deal with software and database maintenance overheads. Basic bioinformatics services are classified by the EBI into three categories: SSS (Sequence Search Services), MSA (Multiple Sequence Alignment) and BSA (Biological Sequence Analysis). The availability of these service-oriented bioinformatics resources are intigrated in generating bioinformatics at NRL.
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