J Chem Inf Model - Atom pair 2D-fingerprints perceive 3D-molecular shape and pharmacophores for very fast virtual screening of ZINC and GDB-17.

Tópicos

{ compound(1573) activ(1297) structur(1058) }
{ algorithm(1844) comput(1787) effici(935) }
{ measur(2081) correl(1212) valu(896) }
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{ monitor(1329) mobil(1314) devic(1160) }
{ research(1218) medic(880) student(794) }
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{ model(2656) set(1616) predict(1553) }
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{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ first(2504) two(1366) second(1323) }
{ activ(1138) subject(705) human(624) }
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{ high(1669) rate(1365) level(1280) }
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{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

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 .

Resumo Limpo

threedimension d molecular shape pharmacophor import determin biolog activ organ molecul howev precis comput dshape general slow virtual screen larg databas reinvestig concept atom pair initi report carhart et al extend schneider et al show simpl atom pair fingerprint apfp count atom pair increas topolog distanc dstructur without atom properti assign correl various represent molecular shape extract dstructur relat dimension atom pair fingerprint extend atom properti xfp provid effici pharmacophor fingerprint good perform ligandbas virtual screen recoveri activ compound decoy dud overlap roc dpharmacophor score function apfp xfp data organ webbas extrem fast nearestneighbor search zinc m compound gdb m random subset freeli access wwwgdbunibech

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