What do the two names (e.g. 1ATN_r_u and 1HE1_r_u) in the circle at the lower left
of the graphics window mean?
This two String represents the pdb (Protein Data Bank) codes of the 2 proteins which are currently being docked. These proteins come from the protein docking benchmark. They have been selected because they are all known to take part in at least one identified protein-protein complex and they cover a wide range of protein structures and functions without redundancy. You can have more information about this protein by visiting the links below using the first four characters of the protein name at the end.
For the examples above this would be:
http://www.rcsb.org/pdb/explore/explore.do?structureId=1ATN
http://www.rcsb.org/pdb/explore/explore.do?structureId=1HE1
The two proteins are illustrated in the large circle area of the graphics window and color coded to match their name. Please see the following reference for more details on the protein benchmark we are working with: J.Mintseris, K, Wiehe, B. Pierce, R. Anderson, R. Chen, J. Janin and Z.Weng,Protein-protein docking benchmark 2.0: An update, Proteins 20, 214 (2005) http://www3.interscience.wiley.com/cgi-bin/abstract/110548133/ABSTRACT
What do the Erelec and Etmin mean in the circle at the upper left
of the graphics window?
The aim of the docking process is to find the best way to associate 2 proteins in order to form a protein-protein complex (and see whether these two proteins are likely to interact, should they ever meet in the "real world", i.e. in a biological system). The quality of the protein-protein interaction can be evaluated via an interaction energy Etmin (expressed in kcal/mol). Erelec is the electrostatic contribution of the interaction energy, which depends on the electric charges that are located all over the protein. The more negative the Etmin is, the stronger the protein-protein interaction.
Please see the following reference for more details on how the interaction energy between two protein is calculated : M. Zacharias, Protein-protein docking with a reduced protein model accounting for side-chain flexibility, Protein Science 12,1271 (2003) http://protsci.highwire.org/cgi/content/abstract/12/6/1271
What does current progress mean?
The computation power of your computer is used to determine the best possible structure for the protein-protein complex by minimizing the interaction energy between the two proteins. The current progress represents the progression of the docking program while exploring the space of the docking positions.
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