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MIPS (metal interactions in protein structures) is a database of metals in the three-dimensional macromolecular structures available in the Protein Data Bank. Bound metal ions in proteins have both catalytic and structural functions. The proposed database serves as an open resource for the analysis and visualization of all metals and their interactions with macromolecular (protein and nucleic acid) structures. MIPS can be searched via a user-friendly interface, and the interactions between metals and protein molecules, and the geometric parameters, can be viewed in both textual and graphical format using the freely available graphics plug-in Jmol. MIPS is updated regularly, by means of programmed scripts to find metal-containing proteins from newly released protein structures. The database is useful for studying the properties of coordination between metals and protein molecules. It also helps to improve understanding of the relationship between macromolecular structure and function. This database is intended to serve the scientific community working in the areas of chemical and structural biology, and is freely available to all users, around the clock, at http://dicsoft2.physics.iisc.ernet.in/mips/. [ABSTRACT FROM AUTHOR]

The identification of sequence (amino acids or nucleotides) motifs in a particular order in biological sequences has proved to be of interest. This paper describes a computing server, SSMBS, which can locate and display the occurrences of user-defined biologically important sequence motifs (a maximum of five) present in a specific order in protein and nucleotide sequences. While the server can efficiently locate motifs specified using regular expressions, it can also find occurrences of long and complex motifs. The computation is carried out by an algorithm developed using the concepts of quantifiers in regular expressions. The web server is available to users around the clock at http://dicsoftl.physics.iisc.ernet.in/ssmbs/. [ABSTRACT FROM AUTHOR]

MLDB (macromolecule ligand database) is a knowledgebase containing ligands co-crystallized with the three-dimensional structures available in the Protein Data Bank. The proposed knowledgebase serves as an open resource for the analysis and visualization of all ligands and their interactions with macro-molecular structures. MLDB can be used to search ligands, and their interactions can be visualized both in text and graphical formats. MLDB will be updated at regular intervals (weekly) with automated Perl scripts. The knowledgebase is intended to serve the scientific community working in the areas of molecular and structural biology. It is available free to users around the clock and can be accessed at http://dicsoft2.physics.iisc.ernet.in/mldb/. [ABSTRACT FROM AUTHOR]

By exploiting the fast-growing Internet technology, the interactive computing server Water Analysis Package (WAP, version 2.0) has been updated with more flexible options to better understand the role of the water O atoms present in three-dimensional macromolecular (protein or nucleic acid) structures. The updated robust server facilitates the computation and visualization of water molecules from various hydration shells, interfacial water molecules and those water molecules that stabilize various secondary structural elements. It is also possible to detect the interactions of water molecules with various parts (polar atoms, nonpolar atoms, main-chain and side-chain atoms) of the protein molecule. Furthermore, a molecular graphics visualization program is interfaced to display the nature of the interactions of the water molecules. The Protein Data Bank archive interfaced with the server is updated every week; hence users get to analyse the latest structures. The computing server can be obtained from http://dicsoft2.physics.iisc.ernet.in/wap/. [ABSTRACT FROM AUTHOR]