TM-align is used in the protein structure prediction community. -Jack Tanner
Sent from Jack's iPhone > On Apr 10, 2017, at 8:45 PM, Goldman, Adrian <[email protected]> > wrote: > > 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
