title: SMS 2.0: an updated database to study the structural plasticity of short peptide fragments in non-redundant proteins.
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 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/.
authors.affiliation: Bioinformatics Centre (Centre of Excellence in Structural Biology and Bio-computing), Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560012, India.
authors.forename: Dheeraj
authors.initials: D
authors.lastname: Ravella
authors.forename: Muthukumarasamy Uthaya
authors.initials: MU
authors.lastname: Kumar
authors.forename: Durairaj
authors.initials: D
authors.lastname: Sherlin
authors.forename: Mani
authors.initials: M
authors.lastname: Shankar
authors.forename: Marthandan Kirti
authors.initials: MK
authors.lastname: Vaishnavi
authors.forename: Kanagaraj
authors.initials: K
authors.lastname: Sekar
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D008958:Models, Molecular; D010446:Peptide Fragments; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*
chemical_list: D010446:Peptide Fragments; D011506:Proteins