I have used MOE, Discovery Studio and Ligand Scout for Pharmacophore screening of large databases using clusters and was happy with that. But now I changed to another place with very low budget so we can not buy these academic licenses anymore. Therefore I wonder if you could recommend me open source (or free) pharmacophore screening software, where both database generation and screening can be carried out in a cluster (in this aspect, what I basically need is that processed can be separated individually, and then results merged together)
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Depending on what you want there are a variety of options. RDKit has support for pharmacophore definitions but I think you need to write code to put it together (ie it's not a prepackaged app). SilicosIT provides Align-IT but this is more for pharmacophore based alignments. The Pharmer tool from U Pittsburgh is nice prepackaged solution which is also employed in a web interface to allow screening against ZINC. Finally the CDK provides a command line tool, but only supports simple pharamcophore (e.g., no torsional or volume constraints) and a crude visualization via JMol.
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