SMS 2.0: An Updated Database to Study the Structural Plasticity of Short Peptide Fragments in Non-redundant Proteins

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 corre- sponding 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 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 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/.

Construction of A Non-Redundant Human SH2 Domain Database

Domain database is essential for domain property research. Eliminatingredundant information in database query is very important for database quality. Here we report themanual construction of a non-redundant human SH2 domain database. There are 119 human SH2 domains in110 SH2-containing proteins. Human SH2s were aligned with ClustalX, and a homologous tree wasgenerated. In this tree, proteins with similar known function were classified into the same group.Some proteins in the same group have been reported to have similar binding motifs experimentally.The tree might provide clues about possible functions of hypothetical proteins for furtherexperimental verification.

‘JANE EYRE’:A SIMPLE EXPERIMENT WITH A NON-REDUNDANT BILINGUAL SIMPLIFIED TEXT

What do film subtitles,airport announcements,labels on products for export,simultaneousinterpreters,and vocabulary glosses all have in common?All are bilingual texts,of course,but morethan that they are all redundant,at least for the truly bilingual.Yet there is something irresistiblyseductive about the redundant part of bilingual texts for the language student.To paraphrase OscarWilde,an English student of French can resist almost anything except the temptation to read Englishsubtitles during a French movie or to listen to all four sides of a simultaneously translated argument.Perhaps the temptation lies in our insecurity that we really can understand the original,or in thehopelessly naive quest for the"exact"meaning of language items.With a flick of the eyess.the

Basic belief assignment approximations using degree of non-redundancy for focal element

Dempster-Shafer evidence theory, also called the theory of belief function, is widely used for uncertainty modeling and reasoning. However, when the size and number of focal elements are large, the evidence combination will bring a high computational complexity. To address this issue,various methods have been proposed including the implementation of more efficient combination rules and the simplifications or approximations of Basic Belief Assignments(BBAs). In this paper,a novel principle for approximating a BBA into a simpler one is proposed, which is based on the degree of non-redundancy for focal elements. More non-redundant focal elements are kept in the approximation while more redundant focal elements in the original BBA are removed first. Three types of degree of non-redundancy are defined based on three different definitions of focal element distance, respectively. Two different implementations of this principle for BBA approximations are proposed including a batch and an iterative type. Examples, experiments, comparisons and related analyses are provided to validate proposed approximation approaches.