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Updated: May 24, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
A protein short motif search tool using amino acid sequence and their secondary structure assignment
Unlabelled:
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.
Availability:
The database is available for free at http://birg3.fbb.utm.my/proteinsms.
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