title: SMS: sequence, motif and structure--a database on the structural rigidity of peptide fragments in non-redundant proteins.
abstract: 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/.
authors.affiliation: Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India.
authors.forename: Bhagavathimuthu
authors.initials: B
authors.lastname: Balamurugan
authors.forename: M N A Mohd
authors.initials: MN
authors.lastname: Roshan
authors.forename: Daliah
authors.initials: D
authors.lastname: Michael
authors.forename: Majumder
authors.initials: M
authors.lastname: Ambaree
authors.forename: Subramanyam
authors.initials: S
authors.lastname: Divya
authors.forename: Hanumanthagowda
authors.initials: H
authors.lastname: Keerthana
authors.forename: Mahadev
authors.initials: M
authors.lastname: Seemanthini
authors.forename: Kanagaraj
authors.initials: K
authors.lastname: Sekar
mesh_terms: D000595:Amino Acid Sequence; D018360:Crystallography, X-Ray; D030562:Databases, Protein / Q000592:standards*; D007091:Image Processing, Computer-Assisted; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D015203:Reproducibility of Results
chemical_list: D010446:Peptide Fragments