PepBuild: a web server for building structure data of peptides/proteins.

PepBuild, a web server, will aid in designing and building a capped or uncapped peptide/protein with known secondary and tertiary structure. The user can build a peptide/protein by choosing the required amino acid residue with regular secondary structure. The torsional angles can be supplied by the user, if desired. The server also allows the user to add relevant protecting groups at the N- and/or C-terminal of the peptide. The amino acid side chains of the designed peptide are optimized using rotameric libraries. Finally, the server provides the option of displaying the result or downloading the complete file in PDB (Protein Data Bank) format. This PDB file can later be used as an input for various molecular simulation programs or for graphical display. The web server is available at http://www.imtech.res.in/bvs/pepbuild/.