########################### # Panagiotis L. Kastritis # # Luca Parca ############## # EMBL Heidelberg ######### ########################### These files were generated as part of the publication: Ori et al. (..) Please refer to http://www.bork.embl.de/Docu/variable_complexes/ for more information. Here are the tgz files for all HADDOCK/CNS runs. They have the standard directory format of each HADDOCK run. For more information on directory structure and resulting energies, please consult the following websites: http://milou.science.uu.nl/services/HADDOCK2.2/ http://www.wenmr.eu/wenmr/haddock-web-server-tutorial/ On youtube: http://www.youtube.com/watch?v=5eS8BAOJ6es http://www.youtube.com/watch?v=InwxoiVy3QQ A webinar: https://www.youtube.com/watch?v=vF4VZjzVUKk&feature=em-subs_digest Column explanations --------------------------- Complex ID ID of the complex Name_complex the name of the complex Protein 1 First member selected from the protein complex Protein 2 Second member selected from the protein complex Any variable member? Indicates whether any of the members were labeled as variable PDB The PDB file used for the calculation of interface properties Chain 2 Corresponding chain for protein 1 Chain 1 Corresponding chain for protein 2 Apolar_all The overall apolar surface area of the complex, calculated with NACCESS, in A2 Apolar_1 The overall apolar surface area of the first chain, calculated with NACCESS, in A2 Apolar_2 The overall apolar surface area of the second chain, calculated with NACCESS, in A2 Buried_Apolar The apolar surface area in the interface of the complex, calculated with NACCESS, in A2 Polar_all The overall apolar surface area of the complex, calculated with NACCESS, in A2 Polar_1 The overall polar surface area of the first chain, calculated with NACCESS, in A2 Polar_2 The overall polar surface area of the second chain, calculated with NACCESS, in A2 Buried_Polar The polar surface area of the complex, calculated with NACCESS, in A2 Total_BSA The overall buried surface area of the complex, calculated with NACCESS, in A2 Haddock_score The average energy score of the top 4 structures of the protein complex, calculated with CNS/HADDOCK Van_der_Waals The average van der Waals energy score of the top 4 structures of the protein complex, calculated with CNS/HADDOCK Electrostatics The average Electrostatic energy score of the top 4 structures of the protein complex, calculated with CNS/HADDOCK Desolvation The average Desolvation energy score of the top 4 structures of the protein complex, calculated with CNS/HADDOCK Total_BSA_CNS The average buried surface area of the top 4 structures of the protein complex, calculated with CNS/HADDOCK -Please cite the original paper if you use these data: ############################################################################################# HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. Dominguez C, Boelens R, Bonvin AM. J Am Chem Soc. 2003 Feb 19;125(7):1731-7. ############################################################################################# -If you use the webserver, you can cite the 2015 webserver paper of HADDOCK ############################################################################################# The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. van Zundert GC, Rodrigues JP, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond AS, van Dijk M, de Vries SJ, Bonvin AM. J Mol Biol. 2015 Sep 26. pii: S0022-2836(15)00537-9. doi: 10.1016/j.jmb.2015.09.014. [Epub ahead of print] ############################################################################################# -For the HADDOCK scoring function relative to binding affinity and the usage of the refinement interface, please cite the following: ############################################################################################# 1. Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark. Kastritis PL, Bonvin AM. J Proteome Res. 2010 May 7;9(5):2216-25. doi: 10.1021/pr9009854. Erratum in: J Proteome Res. 2011 Feb 4;10(2):921-2. 2. Proteins feel more than they see: fine-tuning of binding affinity by properties of the non-interacting surface. Kastritis PL, Rodrigues JP, Folkers GE, Boelens R, Bonvin AM. J Mol Biol. 2014 Jul 15;426(14):2632-52. doi: 10.1016/j.jmb.2014.04.017. Epub 2014 Apr 25. #############################################################################################