Generate: A program for 3-D structure generation and conformational analysis of peptides and peptidomimetics

The program Generate, aimed at generating 3‐D structures for peptides and peptidomimetics, is presented. The algorithm is based on a build‐up procedure, using a library of conformations of amino acid residues. This library is built from conformational analysis of amino acids placed in a di‐ or tripeptide environment to mimic the surroundings of the amino acid in a true peptide, considering different positions of the residue in the peptide chain (peptidyl fragment, NH +3‐terminus or COO−‐terminus). Cis‐trans isomerism in the amide bonds is taken into account by construction of rotamer libraries for different isomers. Water solvation is included through the GB/SA model. New amino acid residues can easily be added to the libraries, making it possible to generate conformations of peptidomimetics. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 746–754, 2002