Docking: Do residues from one protein break off during docking?

Author	Message
R.L. Casey Send message Joined: 7 Jun 06 Posts: 91 Credit: 2,728,885 RAC: 0	Message 29474 - Posted: 16 Oct 2006, 19:07:32 UTC The graphic display for at least one DOCxxx WU showed a native structure in which it appeared that part of one of the two chains of residues had been "broken" off from the main chain as was embedded in the other protein some distance from the region of "contact" between the two proteins. Does this in fact happen? If so, is there a "simple" explanation for how that happens? TIA! ID: 29474 · Rating: 0 · rate: / Reply Quote

Chu Send message Joined: 23 Feb 06 Posts: 120 Credit: 112,439 RAC: 0	Message 29477 - Posted: 16 Oct 2006, 20:01:59 UTC - in response to Message 29474. Thanks, R.L.Casey. This points out a minor bug in the graphic for docking. Since the complex structure (the native) is solved independently from the structures of individual protein partners (the ones we are trying to dock), it may have slightly different protein lengths and sequences. We record the length of the first docking partner and use that number to define what is blue and what is red, and this is ok for the "searching", "accepted" and "low" boxes but not for the "native" as that number could be different. This will be fixed in the next update. Thanks again for catching it. The graphic display for at least one DOCxxx WU showed a native structure in which it appeared that part of one of the two chains of residues had been "broken" off from the main chain as was embedded in the other protein some distance from the region of "contact" between the two proteins. Does this in fact happen? If so, is there a "simple" explanation for how that happens? TIA! ID: 29477 · Rating: 0 · rate: / Reply Quote

Michael G.R. Send message Joined: 11 Nov 05 Posts: 264 Credit: 11,247,510 RAC: 0	Message 29478 - Posted: 16 Oct 2006, 20:09:50 UTC - in response to Message 29477. Thanks for the hard work, Chu! ID: 29478 · Rating: 0 · rate: / Reply Quote

R.L. Casey Send message Joined: 7 Jun 06 Posts: 91 Credit: 2,728,885 RAC: 0	Message 29481 - Posted: 16 Oct 2006, 22:19:06 UTC - in response to Message 29477. Thanks, R.L.Casey. This points out a minor bug in the graphic for docking. Since the complex structure (the native) is solved independently from the structures of individual protein partners (the ones we are trying to dock), it may have slightly different protein lengths and sequences. We record the length of the first docking partner and use that number to define what is blue and what is red, and this is ok for the "searching", "accepted" and "low" boxes but not for the "native" as that number could be different. This will be fixed in the next update. Thanks again for catching it. The graphic display for at least one DOCxxx WU showed a native structure in which it appeared that part of one of the two chains of residues had been "broken" off from the main chain as was embedded in the other protein some distance from the region of "contact" between the two proteins. Does this in fact happen? If so, is there a "simple" explanation for how that happens? TIA! Thanks for the info, Chu! It is great to see such significant support from the project--and from other participants, too! ID: 29481 · Rating: 0 · rate: / Reply Quote