02266nas a2200217 4500008004100000245009000041210006900131260001700200300001400217490000700231520153800238653003401776653003901810653003601849653002301885100002701908700002501935700003101960700001701991856004002008 2019 eng d00aEstablishment of a 3D-structure Database for Chemical Compounds in Indonesian Sponges0 aEstablishment of a 3Dstructure Database for Chemical Compounds i cOctober 2019 a1211-12180 v113 a

Objective: Nowadays, There hasn’t any three-dimensional (3D) chemical structure database yet for biologically active compound in sponges from Indonesian origin. Therefore, this study aimed to create in silico a 3D-structure database of such compound and to evaluate the preferred software for this purpose. Methods: 2D- structure of selected compounds was established using MarvinSketch software. Conversion from 2D- into 3D-structures was evaluated by comparing MarvinSketch, OpenBabel and VegaZZ software packages. Visualization of the respective 3D-structures was perfomed by using PyMOL software. From 68 scientific articles, 212 chemical compounds were selected from 53 Indonesian sponge species. Results: The conversion of 2D-structures of the selected 212 chemical compound into 3D-structures lead to 7118 files, respectively consisting of 2508 files from the MarvinSketch, 1672 files from the OpenBabel and 1051 files from the VegaZZ software. The results based on the extention files were 1043 SDF, 1258 MOL and 2930 PDB format files of the three-dimensional structure. The valid and correct three-dimensional structure of chemical compound were 914 .sdf format files, 916 format .mol files and 72 .pdb format files. From the three-dimensional structures visualization, the database prefers established by using MarvinSketch with SDF or MOL format files since the results is consistent to literature and contain less number of errors.

10a2D-and 3D-chemical structures10a3D-database of chemical structures10aEvaluation of software packages10aIndonesian sponges1 aPrihatiningtyas, Retno1 aSyahdi, Rezi, Riadhi1 aPutra, Masteria, Yunovilsa1 aYanuar, Arry uhttps://www.phcogj.com/article/1002