title: The signature molecular descriptor. 2. Enumerating molecules from their extended valence sequences.
abstract: We present a new algorithm that enumerates molecular structures matching a predefined extended valence sequence or signature. The algorithm can construct molecular structures composed of about 50 non-hydrogen atoms in CPU seconds time scale. The algorithm is run to produce all molecular structures matching the binding affinities (IC(50)) of some HIV-1 protease inhibitors. The algorithm is also used to compute the degeneracy, or the number of molecular structures, corresponding to a given signature. Signature degeneracy is systematically studied for varying signature heights on four molecular series, alkanes, alcohols, fullerene-type structures, and peptides. Signature degeneracy is compared with similar results obtained with popular topological indices (TIs). As a general rule, we find that signature degeneracy decreases as the signature height increases. We also find that alkanes, alcohols, and fullerene-type structures comprising n non-hydrogen atoms are uniquely characterized by signatures of height n/4, while peptides up to 4000 amino acids can be singled out with signatures of heights as small as 2 and 3.
authors.affiliation: Sandia National Laboratories, P.O. Box 969, MS 9951, Livermore, California 94551, USA. jfaulon@sandia.gov
authors.forename: Jean-Loup
authors.initials: JL
authors.lastname: Faulon
authors.forename: Carla J
authors.initials: CJ
authors.lastname: Churchwell
authors.forename: Donald P
authors.initials: DP
authors.lastname: Visco
mesh_terms: D000465:Algorithms; D002626:Chemistry, Pharmaceutical / Q000379:methods; D017076:Computer-Aided Design; D017320:HIV Protease Inhibitors / Q000737:chemistry / Q000494:pharmacology; D006838:Hydrocarbons / Q000737:chemistry; D020128:Inhibitory Concentration 50; D007536:Isomerism; D008956:Models, Chemical; D015394:Molecular Structure; D010455:Peptides / Q000737:chemistry
chemical_list: D017320:HIV Protease Inhibitors; D006838:Hydrocarbons; D010455:Peptides