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.
Bultinck
Patrick
P
Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium. Patrick.Bultinck@rug.ac.be
Augustynen
Stijn
S
Hilbers
Hans W
HW
Moret
Ed E
EE
Tollenaere
Jan P
JP
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D008956:Models, Chemical; D018716:Molecular Mimicry; D015394:Molecular Structure; D019151:Peptide Library; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013237:Stereoisomerism
D000596:Amino Acids; D019151:Peptide Library; D011506:Proteins