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

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