AcknowledgmentsThis work was supported by Grant OTKA 72771 and the New Hungary Development Plan Projects T��MOP-4.2.1/B-09/1/KONV-2010-0005 and T��MOP-4.2.2-08/1-2008-0013 and G��bor Baross OMFB-00339/2010.
Virtual screening refers to the use of a computer-based method selleckchem Abiraterone to process compounds from a library or database of compounds in order to identify and select ones that are likely to possess a desired biological activity, such as the ability to inhibit the action of a particular therapeutic target. The selection of molecules with a virtual screening algorithm should yield a higher proportion of active compounds, as assessed by experiment, relative to a random selection of the same number of molecules [1].

Over recent decades, drug discovery companies have used combinatorial chemistry approaches to create large and diverse libraries of structures; therefore large arrays of compounds are formed by combining sets of different types of reagents, called building blocks, in a systematic and repetitive way. These libraries can be used as a source of new potential drugs, since the compounds in the libraries can be randomly tested or screened to find good drug compounds. Increasing the capabilities of testing compounds using chemoinformatic technologies such as high-throughput screening (HTS) enables hundreds of thousands of these compounds to be tested in a short time. Computers can be used to aid this process in a number of ways; for example, in the creation of virtual combinatorial libraries which can be much larger than their real counterparts.

There are two methods for screening those libraries, looking into active sites of interest and looking for similarities to a known active compound. Recently, searching chemical databases has been done using computers instead of experiment, and this is known as the virtual screening technique Cilengitide [2�C9].Chemical information systems offer three principal types of searching facility. Early systems provided two types of retrieval mechanisms: structure searching and substructure searching. These mechanisms were later complemented by another access mechanism: similarity searching. There are many studies in the literature associated with the measurement of molecular similarity [10�C13]. However, the most common approaches are based on 2D fingerprints, with the similarity between a reference structure and a database structure computed using association coefficients such as the Tanimoto coefficient [1, 14].Several methods have been used to further optimise the measures of similarity between molecules, including weighting, standardization, and data fusion [15�C18].