http://rosettadesigngroup.com/blog/58/10-protein-protein-interface-prediction-servers/ Trading tips and news on modeling proteins, DNA, RNA, small molecules, folding, docking, design..... Mon, 07 May 2012 09:52:00 +0000 hourly 1 http://wordpress.org/?v=3.0 http://rosettadesigngroup.com/blog/58/10-protein-protein-interface-prediction-servers/comment-page-1/#comment-18248 Rosetta Web Servers | Macromolecular Modeling Blog ™ Fri, 17 Dec 2010 14:55:07 +0000 http://rosettadesigngroup.com/blog/?p=58#comment-18248 [...] The RosettaDock protein-protein docking server predicts the structure of protein complexes given the structures of the individual components and an approximate binding orientation. The server uses the Rosetta 2.1 protein structure modeling suite. It’s important to note that this is a “Local docking” server, i.e. the input complex should be in the approximate binding site. RosettaDock has a module that can handle “Global docking” (i.e. with no information on the binding site) but this is too computational demanding for a web-server. (You can detect initial potential binding sites using protein interface predictors). [...] [...] The RosettaDock protein-protein docking server predicts the structure of protein complexes given the structures of the individual components and an approximate binding orientation. The server uses the Rosetta 2.1 protein structure modeling suite. It’s important to note that this is a “Local docking” server, i.e. the input complex should be in the approximate binding site. RosettaDock has a module that can handle “Global docking” (i.e. with no information on the binding site) but this is too computational demanding for a web-server. (You can detect initial potential binding sites using protein interface predictors). [...]

]]> http://rosettadesigngroup.com/blog/58/10-protein-protein-interface-prediction-servers/comment-page-1/#comment-148 Nir London Tue, 18 Nov 2008 21:53:23 +0000 http://rosettadesigngroup.com/blog/?p=58#comment-148 Thanks Lisa, I actually didn't know of that one. I'll try it out. Thanks Lisa, I actually didn’t know of that one. I’ll try it out.

]]> http://rosettadesigngroup.com/blog/58/10-protein-protein-interface-prediction-servers/comment-page-1/#comment-144 Lisa Lambert Tue, 18 Nov 2008 19:19:06 +0000 http://rosettadesigngroup.com/blog/?p=58#comment-144 I was wondering why SHARP2 wasn't on the list. It provides several different models and you can see quickly if any of the patches are in an area of interest. Website: http://www.bioinformatics.sussex.ac.uk/SHARP2/sharp2.html Reference: Murakami,Y. & Jones, S. (2006) SHARP2 ; Protein-Protein Predictions using Patch Analysis. Bioinformatics vol. 22, pp.1794-1795. I was wondering why SHARP2 wasn’t on the list. It provides several different models and you can see quickly if any of the patches are in an area of interest. Website: http://www.bioinformatics.sussex.ac.uk/SHARP2/sharp2.html
Reference: Murakami,Y. & Jones, S. (2006) SHARP2 ; Protein-Protein Predictions using Patch Analysis. Bioinformatics vol. 22, pp.1794-1795.

]]>