| URL: | http://cluster.physics.iisc.ernet.in/sms |
| Full name: | Sequence, Motif and Structure |
| Description: | Sequence, Motif and Structure (SMS) is a database of structurally rigid peptide fragments, by combining amino acid sequences and the corresponding 3D atomic coordinates of non-redundant (25%) and redundant (90%) protein chains available in the Protein Data Bank (PDB). |
| Year founded: | 2006 |
| Last update: | 2014 |
| Version: | |
| Accessibility: |
Accessible
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| Country/Region: | India |
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| University/Institution: | Indian Institute of Science |
| Address: | Department of Computational and Data Sciences Room No: 341, 2nd Floor, Old CES Building Indian Institute of Science Bangalore - 560 012 India |
| City: | Bangalore |
| Province/State: | |
| Country/Region: | India |
| Contact name (PI/Team): | Kanagaraj Sekar |
| Contact email (PI/Helpdesk): | sekar@physics.iisc.ernet.in |
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SMS 2.0: an updated database to study the structural plasticity of short peptide fragments in non-redundant proteins. [PMID: 22449400]
The function of a protein molecule is greatly influenced by its three-dimensional (3D) structure and therefore structure prediction will help identify its biological function. We have updated Sequence, Motif and Structure (SMS), the database of structurally rigid peptide fragments, by combining amino acid sequences and the corresponding 3D atomic coordinates of non-redundant (25%) and redundant (90%) protein chains available in the Protein Data Bank (PDB). SMS 2.0 provides information pertaining to the peptide fragments of length 5-14 residues. The entire dataset is divided into three categories, namely, same sequence motifs having similar, intermediate or dissimilar 3D structures. Further, options are provided to facilitate structural superposition using the program structural alignment of multiple proteins (STAMP) and the popular JAVA plug-in (Jmol) is deployed for visualization. In addition, functionalities are provided to search for the occurrences of the sequence motifs in other structural and sequence databases like PDB, Genome Database (GDB), Protein Information Resource (PIR) and Swiss-Prot. The updated database along with the search engine is available over the World Wide Web through the following URL http://cluster.physics.iisc.ernet.in/sms/. |
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SMS: sequence, motif and structure--a database on the structural rigidity of peptide fragments in non-redundant proteins. [PMID: 16922686]
Structure prediction methods aim to identify the relationship between the amino acid sequence of an unknown protein and information comprised in databases of known protein structures. Towards this end, we created a database by combining the amino acid sequences and the corresponding three-dimensional atomic coordinates for all the 25% non-redundant protein chains available in the Protein Data Bank. It contains information about the peptide fragments that are 5 to 10 residues long. In addition, options are provided for the users to visualize the individual motifs and the superposed fragments in the client machine. Further, useful functionalities areprovided to look for similar sequence motifs in all the sequence databases like PDB, 90% non-redundant protein chains, Genome database, PIR and Swiss-Prot. The database is being updated at regular intervals and the same can be accessed over the World Wide Web interface at the following URL: http://pranag.physics.iisc.ernet.in/sms/. |