Autodock would be my recommendation as well unless there is something new out there that I haven't tracked. - Deepak Singh

Autodock seems to be widely-used and well-regarded. Could also try zdock - more lightweight and good for command-line scripting, parsing. - Neil Saunders

zdock is more protein-protein centric. Did they add small molecule stuff? - Deepak Singh from IM

Ah, that's true. Haven't used it in a while. Autodock would be better for ligands. - Neil Saunders

wondering how difficult it would be to integrate #autodock into #bioclipse or with the #cdk ... - Egon Willighagen

can Autodock actually be scripted from the command line? Or am I restricted to using their GUI to create input files? - Egon Willighagen

I believe they had developed a python based framework - Deepak Singh from IM

they have command line tools but I am still wrapping my head around the basics - Pedro Beltrao

FRED (not Open Source) is very easy to use, but maybe not as accurate as others. If accuracy is the goal it seems that Glide does a good job. - Rajarshi Guha

Glide is definitely state of the art. The one thing about docking though is no one tool is good enough. Pretty much every company I know that does a lot of virtual screening uses two tools - Deepak Singh from IM

What special features in #intellij #idea should I be looking for when testing it? - Egon Willighagen

I'm not going for the looks... well, I did with #bioclipse too :) - Egon Willighagen

I can't point to specific features - but I was able to get a project up and running in 2 minutes with minimal reading. For eclipse I'm still not sure how the workspace can be used efficienly. The whole IDEA experience is just smooth :) - Rajarshi Guha

I've tested IntelliJ a few minutes on my windows partition (*where there is no JDK* , just a JRE). The default code completion was poor compared to eclipse. - Pierre Lindenbaum

+1 to Rajarshi. I never could really understand Eclipse properly, but IntelliJ just works. I did look at the list that comes with the free version, and it's a shame you don't get the facets etc for free (I do use those, especially the GWT one), but it's still really nice to see a base version for free. - Allyson Lister

This is no PR trick... I'm just really impressed with what Arvid achieved! - Egon Willighagen

It'd be interesting to see a description of the caching strategy (yes, I'm too lazy to brwose th code :) - Rajarshi Guha

No one made the SPARQL version yet? - Egon Willighagen

@Egon, I don't know. In my blog spot, I asked if there is a SPARQL version in DBPedia. Moreover, I don't know if SPARQL can do this kind of search without a prior knowledge of the 'depth' of recursion. - Pierre Lindenbaum

http://dbpedia.org/sparql - Egon Willighagen

Yes, but how can you do the recursion stuff ? For example what would be the SPARQL query to find all the sub-Categories of "Category:Scientists" ? - Pierre Lindenbaum

I would need to check the DBPedia OWL, but I hope they defined subCat as being transative... so that with X -subcat-> Y -subcat-> Z, then this should imply X -subCat-> Z ... but have not tried that yet... it would work with the #pellet reasoner in, e.g., #bioclipse - Egon Willighagen

Thanks Egon , nice to know (I've never played with Pellet) . I found this schema: http://downloads.dbpedia.org/3... . ( It seems that they did not use all the categories in WP ?) - Pierre Lindenbaum