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Title |
A protein short motif search tool using amino acid sequence and their secondary structure assignment |
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Authors |
Arun Venkataraman1, Teong Han Chew1, Zeti Azura Mohamed Hussein2, Mohd Shahir Shamsir1* |
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Affiliation |
1Bioinformatics Research Laboratory, Faculty of Biosciences and Bioengineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia; 2School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia.
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shahir@utm.my, shahir@fbb.utm.my; *Corresponding author
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Article Type |
Web server
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Date |
Received October 27, 2011; Accepted October 31, 2011; Published November 20, 2011
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Abstract |
We present the development of a web server, a protein short motif search tool that allows users to simultaneously search for a protein sequence motif and its secondary structure assignments. The web server is able to query very short motifs searches against PDB structural data from the RCSB Protein Databank, with the users defining the type of secondary structures of the amino acids in the sequence motif. The output utilises 3D visualisation ability that highlights the position of the motif in the structure and on the corresponding sequence. Researchers can easily observe the locations and conformation of multiple motifs among the results. Protein short motif search also has an application programming interface (API) for interfacing with other bioinformatics tools.
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Keywords |
Protein short motif search, protein secondary structure, visualization, application programming interface (API)
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Citation |
Venkataraman et al.
Bioinformation 7(6): 304-306 (2011) |
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Edited by |
P Kangueane
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ISSN |
0973-2063
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Publisher |
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License |
This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License. |