J Chem Inf Model - REPROVIS-DB: a benchmark system for ligand-based virtual screening derived from reproducible prospective applications.

Tópicos

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Resumo

Benchmark calculations are essential for the evaluation of virtual screening (VS) methods. Typically, classes of known active compounds taken from the medicinal chemistry literature are divided into reference molecules (search templates) and potential hits that are added to background databases assumed to consist of compounds not sharing this activity. Then VS calculations are carried out, and the recall of known active compounds is determined. However, conventional benchmarking is affected by a number of problems that reduce its value for method evaluation. In addition to often insufficient statistical validation and the lack of generally accepted evaluation standards, the artificial nature of typical benchmark settings is often criticized. Retrospective benchmark calculations generally overestimate the potential of VS methods and do not scale with their performance in prospective applications. In order to provide additional opportunities for benchmarking that more closely resemble practical VS conditions, we have designed a publicly available compound database (DB) of reproducible virtual screens (REPROVIS-DB) that organizes information from successful ligand-based VS applications including reference compounds, screening databases, compound selection criteria, and experimentally confirmed hits. Using the currently available 25 hand-selected compound data sets, one can attempt to reproduce successful virtual screens with other than the originally applied methods and assess their potential for practical applications.

Resumo Limpo

benchmark calcul essenti evalu virtual screen vs method typic class known activ compound taken medicin chemistri literatur divid refer molecul search templat potenti hit ad background databas assum consist compound share activ vs calcul carri recal known activ compound determin howev convent benchmark affect number problem reduc valu method evalu addit often insuffici statist valid lack general accept evalu standard artifici natur typic benchmark set often critic retrospect benchmark calcul general overestim potenti vs method scale perform prospect applic order provid addit opportun benchmark close resembl practic vs condit design public avail compound databas db reproduc virtual screen reprovisdb organ inform success ligandbas vs applic includ refer compound screen databas compound select criteria experiment confirm hit use current avail handselect compound data set one can attempt reproduc success virtual screen origin appli method assess potenti practic applic

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