RESUMO
3dSS is a web-based interactive computing server, primarily designed to aid researchers, to superpose two or several 3D protein structures. In addition, the server can be effectively used to find the invariant and common water molecules present in the superposed homologous protein structures. The molecular visualization tool RASMOL is interfaced with the server to visualize the superposed 3D structures with the water molecules (invariant or common) in the client machine. Furthermore, an option is provided to save the superposed 3D atomic coordinates in the client machine. To perform the above, users need to enter Protein Data Bank (PDB)-id(s) or upload the atomic coordinates in PDB format. This server uses a locally maintained PDB anonymous FTP server that is being updated weekly. This program can be accessed through our Bioinformatics web server at the URL http://cluster.physics.iisc.ernet.in/3dss/ or http://10.188.1.15/3dss/.
Assuntos
Software , Homologia Estrutural de Proteína , Gráficos por Computador , Bases de Dados de Proteínas , Internet , Modelos Moleculares , Fosfolipases A/química , Água/químicaRESUMO
The Secondary Structural Elements of Proteins (SSEP) database is an integrated and comprehensive knowledge base for accessing information related to all the secondary-structural elements present in non-redundant (25 and 90%) protein chains. The new version 2.0 of the database contains 2485 and 8595 protein chains from the 25 and 90% non-redundant data sets, respectively. The necessary web interfaces have been developed that enable users to visualize the three-dimensional structure of the secondary-structural element in the client machine using the free molecular-visualization program RASMOL. This source is updated at regular intervals and can be accessed through the bioinformatics web server at the URL http://cluster.physics.iisc.ernet.in/ssep or http://144.16.71.148/ssep/.