J Chem Inf Model - SABRE: ligand/structure-based virtual screening approach using consensus molecular-shape pattern recognition.

Tópicos

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Resumo

We present an efficient and rational ligand/structure shape-based virtual screening approach combining our previous ligand shape-based similarity SABRE (shape-approach-based routines enhanced) and the 3D shape of the receptor binding site. Our approach exploits the pharmacological preferences of a number of known active ligands to take advantage of the structural diversities and chemical similarities, using a linear combination of weighted molecular shape density. Furthermore, the algorithm generates a consensus molecular-shape pattern recognition that is used to filter and place the candidate structure into the binding pocket. The descriptor pool used to construct the consensus molecular-shape pattern consists of four dimensional (4D) fingerprints generated from the distribution of conformer states available to a molecule and the 3D shapes of a set of active ligands computed using SABRE software. The virtual screening efficiency of SABRE was validated using the Database of Useful Decoys (DUD) and the filtered version (WOMBAT) of 10 DUD targets. The ligand/structure shape-based similarity SABRE algorithm outperforms several other widely used virtual screening methods which uses the data fusion of multiscreening tools (2D and 3D fingerprints) and demonstrates a superior early retrieval rate of active compounds (EF(0.1%) = 69.0% and EF(1%) = 98.7%) from a large size of ligand database (~95,000 structures). Therefore, our developed similarity approach can be of particular use for identifying active compounds that are similar to reference molecules and predicting activity against other targets (chemogenomics). An academic license of the SABRE program is available on request.

Resumo Limpo

present effici ration ligandstructur shapebas virtual screen approach combin previous ligand shapebas similar sabr shapeapproachbas routin enhanc d shape receptor bind site approach exploit pharmacolog prefer number known activ ligand take advantag structur divers chemic similar use linear combin weight molecular shape densiti furthermor algorithm generat consensus molecularshap pattern recognit use filter place candid structur bind pocket descriptor pool use construct consensus molecularshap pattern consist four dimension d fingerprint generat distribut conform state avail molecul d shape set activ ligand comput use sabr softwar virtual screen effici sabr valid use databas use decoy dud filter version wombat dud target ligandstructur shapebas similar sabr algorithm outperform sever wide use virtual screen method use data fusion multiscreen tool d d fingerprint demonstr superior earli retriev rate activ compound ef ef larg size ligand databas structur therefor develop similar approach can particular use identifi activ compound similar refer molecul predict activ target chemogenom academ licens sabr program avail request

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