Developed & Maintained by BIF Centre, Department of Biochemistry & Biophysics, University of Kalyani, Kalyani, Nadia-741 235, West Bengal India.
Important Web Links
The Protein Databank (PDB) - a depository of protein 3D structures, also cotains information on the entries, like publication, type of experiment (NMR, X-ray crystallography), and much, much more.
PDBe - the European site of the protein data bank. A different type of organization of information, much more exact hits when searching the site for entries.
PDBsum - A lot of visual information (figures), links to other databases, like the those mentioned here and many more.
CATH - protein domain classification database. Very useful when trying to find evoilutionary relatives, in protein homology modeling of multidomain proteins, etc.
SCOP - Another protein classification database. A slightly different way of calssification, when compared to CATH, and sometimes it may be easier to follow.
SwissPDB viewer - for some reason changed name to Deep View, but I think most people still call it SwissPDB viewer. An excelent graphics visualization program for protein, DNA and RNA structures. Many useful features, the ost important probably being the tools for homology modeling: superposition of structures, snalysis of structure-based sequence alignment, hydrogen bonds, etc. It is also possible to use for preparing graphics representation for talks, reports, etc.
Swiss-Model Server- Protein homology modeling server used in the tutorials on this site. There are other servers, but I like the connection between this server and SwissPDB Viewer and the fact that there are different modes of modeling and that I easily can influence the process through the SwissPDB Viewer software (sequence alignment correction, energy estimation, etc). Examples of modeling with this server you can find in the homology modeling part.
Sequences and sequence alignment and analysis tools:
The Expasy server - General proteomics server for protein analysis. The strongest side in my opinion is the SwissProt database, which has changed name to UniProt, Prosite and all the resources related to sequence and function analysis. InterPro protein sequence analysis and classification - This site is extremely useful, e.g., in homology modeling, as described in the tutorial on homology modeling. But it is also useful for finding general functional information on a certain protein.
CLUSTALW2- is used for sequence alignment. Although there are many sites, which use this software, my preference is the EBI server (European Bioinformatics Institute). It provides a lot of options for running the alignment.
Jalview - the best multiple sequence alignment editor I know. To get all the features, it is best to download the program and install it on your own computer. You can always start Jalview when you use the sequence alignment server at EBI.
University of Kalyani, Nadia, West-Bengal, India.
Bioinformatics Infrastructure Facility A DBT (Govt. of India) Sponsored Facility.