SMS 2.0: An Updated Database to Study the Structural Plasticity of Short Peptide Fragments in Non-redundant Proteins
10.1016/S1672-0229(11)60032-6
- Author:
Ravella DHEERAJ
1
;
Kumar Uthaya MUTHUKUMARASAMY
;
Sherlin DURAIRAJ
;
Shankar MANI
;
Vaishnavi Kirti MARTHANDAN
;
Sekar KANAGARAJ
Author Information
1. Bioinformatics Centre(Centre of Excellence in Structural Biology and Bio-computing),Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560012, India
- Keywords:
non-redundant protein chains;
sequence motifs;
3D structure;
structural superposition
- From:
Genomics, Proteomics & Bioinformatics
2012;10(1):44-50
- CountryChina
- Language:Chinese
-
Abstract:
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 theProtein Data Bank (PDB).SMS 2.0 provides information pertaining to the peptide fragments of length 5-14 resi-dues.The entire dataset is divided into three categories,namely,same sequence motifs having similar,intermedi-ate or dissimilar 3D structures.Further,options are provided to facilitate structural superposition using the pro-gram structural alignment of multiple proteins (STAMP) and the popular JAVA plug-in (Jmol) is deployed forvisualization.In addition,functionalities are provided to search for the occurrences of the sequence motifs in otherstructural and sequence databases like PDB,Genome Database (GDB),Protein Information Resource (PIR) andSwiss-Prot.The updated database along with the search engine is available over the World Wide Web through thefollowing URL http://cluster.physics.iisc.emet.in/sms/.
