%0 Journal Article %1 Awale2014APfp %A Awale, Mahendra %A Reymond, Jean-Louis %D 2014 %J Journal of Chemical Information and Modeling %K 2d-pharmacophore fingerprint molecular-fingerprint pharmacophore %N 7 %P 1892-1907 %R 10.1021/ci500232g %T Atom Pair 2D-Fingerprints Perceive 3D-Molecular Shape and Pharmacophores for Very Fast Virtual Screening of ZINC and GDB-17 %U http://dx.doi.org/10.1021/ci500232g %V 54 %X Three-dimensional (3D) molecular shape and pharmacophores are important determinants of the biological activity of organic molecules; however, a precise computation of 3D-shape is generally too slow for virtual screening of very large databases. A reinvestigation of the concept of atom pairs initially reported by Carhart et al. and extended by Schneider et al. showed that a simple atom pair fingerprint (APfp) counting atom pairs at increasing topological distances in 2D-structures without atom property assignment correlates with various representations of molecular shape extracted from the 3D-structures. A related 55-dimensional atom pair fingerprint extended with atom properties (Xfp) provided an efficient pharmacophore fingerprint with good performance for ligand-based virtual screening such as the recovery of active compounds from decoys in DUD, and overlap with the ROCS 3D-pharmacophore scoring function. The APfp and Xfp data were organized for web-based extremely fast nearest-neighbor searching in ZINC (13.5 M compounds) and GDB-17 (50 M random subset) freely accessible at www.gdb.unibe.ch.

@article{Awale2014APfp, abstract = { Three-dimensional (3D) molecular shape and pharmacophores are important determinants of the biological activity of organic molecules; however, a precise computation of 3D-shape is generally too slow for virtual screening of very large databases. A reinvestigation of the concept of atom pairs initially reported by Carhart et al. and extended by Schneider et al. showed that a simple atom pair fingerprint (APfp) counting atom pairs at increasing topological distances in 2D-structures without atom property assignment correlates with various representations of molecular shape extracted from the 3D-structures. A related 55-dimensional atom pair fingerprint extended with atom properties (Xfp) provided an efficient pharmacophore fingerprint with good performance for ligand-based virtual screening such as the recovery of active compounds from decoys in DUD, and overlap with the ROCS 3D-pharmacophore scoring function. The APfp and Xfp data were organized for web-based extremely fast nearest-neighbor searching in ZINC (13.5 M compounds) and GDB-17 (50 M random subset) freely accessible at www.gdb.unibe.ch. }, added-at = {2017-03-10T02:15:12.000+0100}, author = {Awale, Mahendra and Reymond, Jean-Louis}, biburl = {https://www.bibsonomy.org/bibtex/2d4e18d963bff768b86964f2539a96d74/salotz}, description = {Atom Pair 2D-Fingerprints Perceive 3D-Molecular Shape and Pharmacophores for Very Fast Virtual Screening of ZINC and GDB-17 - Journal of Chemical Information and Modeling (ACS Publications)}, doi = {10.1021/ci500232g}, eprint = {http://dx.doi.org/10.1021/ci500232g}, interhash = {01b55b975c93cfb8e43b9951863249f5}, intrahash = {d4e18d963bff768b86964f2539a96d74}, journal = {Journal of Chemical Information and Modeling}, keywords = {2d-pharmacophore fingerprint molecular-fingerprint pharmacophore}, note = {PMID: 24988038}, number = 7, pages = {1892-1907}, timestamp = {2017-03-10T02:15:12.000+0100}, title = {Atom Pair 2D-Fingerprints Perceive 3D-Molecular Shape and Pharmacophores for Very Fast Virtual Screening of ZINC and GDB-17}, url = {http://dx.doi.org/10.1021/ci500232g}, volume = 54, year = 2014 }