The Dengue virus M protein is a 75 amino acid polypeptide with two helical transmembranes (TM). The TM domain oligomerizes to form an ion channel, facilitating viral release from the host cells. The M protein has a critical role in the virus entry and life cycle, making it a potent drug target. The oligomerization of the monomeric protein was studied using ab initio modeling and molecular dynamics (MD) simulation in an implicit membrane environment. The representative structures obtained showed pentamer as the most stable oligomeric state, resembling an ion channel. Glutamic acid, threonine, serine, tryptophan, alanine, isoleucine form the pore-lining residues of the pentameric channel, conferring an overall negative charge to the channel with approximate length of 51.9 Å. Residue interaction analysis (RIN) for M protein shows that Ala94, Leu95, Ser112, Glu124, and Phe155 are the central hub residues representing the physicochemical interactions between domains. The virtual screening with 165 different ion channel inhibitors from the ion channel library shows monovalent ion channel blockers, namely lumacaftor, glipizide, gliquidone, glisoxepide, and azelnidipine to be the inhibitors with high docking scores. Understanding the three-dimensional structure of M protein will help design therapeutics and vaccines for Dengue infection.

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/.

In the past few decades,scientists from all over the world have taken a keen interest in novel functional units such as small regulatory RNAs,small open reading frames,pseudogenes,transposons,integrase binding attB/attP sites,repeat elements within the bacterial intergenic regions (IGRs) and in the analysis of those “junk” regions for genomic complexity.Here we have developed a web server,named Junker,to facilitate the in-depth analysis of IGRs for examining their length distribution,four-quadrant plots,GC percentage and repeat details.Upon selection of a particular bacterial genome,the physical genome map is displayed as a multiple loci with options to view any loci of interest in detail.In addition,an IGR statistics module has been created and implemented in the web server to analyze the length distribution of the IGRs and to understand the disordered grouping of IGRs across the genome by generating the four-quadrant plots.The proposed web server is freely available at the URL http://pranag.phy sics.iisc.ernet.in/junker/.

Small RNAs (sRNAs) are non-coding transcripts exerting their functions in the cells directly.Identification of sRNAs is a difficult task due to the lack of clear sequence and structural biases.Most sRNAs are identified within genus specific intergenic regions in related genomes.However,several of these regions remain un-annotated due to lack of sequence homology and/or potent statistical identification tools.A computational engine has been built to search within the intergenic regions to identify and roughly annotate new putative sRNA regions in Enterobacteriaceae genomes.It utilizes experimentally known sRNA data and their flanking genes/KEGG Orthology (KO) numbers as templates to identify similar sRNA regions in related query genomes.The search engine not only has the capability to locate putative intergenic regions for specific sRNAs,but also has the potency to locate conserved,shuffled or deleted gene clusters in query genomes.Because it uses the KO terms for locating functionally important regions such as sRNAs,any further KO number assignment to additional genes will increase the sensitivity.The PsRNA server is used for the identification of putative sRNA regions through the information retrieved from the sRNA of interest.The computing engine is available online at http://boioserver1.physics.iisc.ernet.in/psrna/and http://bicmku.in:8081/psrna/.