The right people to look at for this are found in the structure prediction community; a series of algorithms were developed to compare different predictions of the same structure. Look for papers from about CASP-3 (John Mount) or pick up any recent CASP and look at how they compare the different predictions and follow the literature back.
Adrian > On 10 Apr 2017, at 00:44, Gert Vriend <[email protected]> wrote: > > Arthur Lesk (at Penn state Univ, I think)m is the only one I know who has > worked on this topic. I suggest you ask him. The topic you elude to is > commonly known as the Russian Doll Effect. > > If you want to discuss the topic, feel free to Skype me. > > Greetings > > Gert Vriend > > > On 10-4-2017 1:37, Reza Khayat wrote: >> Hi, >> >> My initial e-mail may have been a bit vague so I'll try to be more specific. >> Superposing the structures and comparing them against one another, while >> appropriate, is a subjective way to do the analysis as I would have to >> subjectively define a threshold that would indicate a difference between the >> structures. My threshold may be grossly different than someone else's >> threshold. I am interested in an objective criterion. One where strong >> emphasis has been put on error analysis and error modeling in terms of both >> the refined structure and the underlying data. I realize that defining such >> criterion is by no means trivial. Thanks again for the help. >> >> Best wishes, >> Reza >> >> Reza Khayat, PhD >> Assistant Professor >> City College of New York >> Department of Chemistry >> New York, NY 10031 >> >> ________________________________________ >> From: Reza Khayat >> Sent: Sunday, April 9, 2017 6:07 PM >> To: CCP4 bulletin board >> Subject: Structure comparison >> >> Hi, >> >> I have refined several structures of a protein from different space groups >> and would like to compare them to one another. Is there a program/software >> suite that would provide an objective comparison of the structures and >> identify regions where the structures are sufficiently different from one >> another to warrant a closer look? I think the most important aspect of the >> analysis would be defining a threshold (possibly based on resolution and >> structure statistics) that would identify sufficient difference between >> structures. Thanks. >> >> Best wishes, >> Reza >> >> Reza Khayat, PhD >> Assistant Professor >> City College of New York >> Department of Chemistry >> New York, NY 10031
