PepBuild is an automatic web server for generating an optimized PDB file. Starting with the query protein sequence, the server: Builds the query peptide based on the user's input- · type of amino acid residue, · its nature (protonated /non-protonated), · secondary structure (helix,sheet or coil) · and protecting groups (ACE/BOC and NHE/NME). Calculates the Cartesian coordinates from the internal coordinates and generates a complete PDB file. Runs SCWRL to optimize side chain of amino acid residues. And finally displays the PDB file on standard output.