I am sure that most here have dealt with the issue, when making superpositions of conformationally-different structures, of which regions to align as references and which to call "mobile." Conformational changes can range from very local (e.g., unwinding of a helix) to very diffuse (e.g., subtle but significant rigid body shifts between two domains.) In the first case, it would probably make sense to do a global least-squares fitting, but in the latter, one would do better to fix one of the domains, and show the shift in the other domain. These cases, however, presuppose that one knows which type of case one is dealing with. This could be done by guesswork and trial-and-error, but does anybody know of an approach (e.g., a program) to define the most reasonable way to think about a given conformational change? Variable-size sliding-window least-squares superpositions with comparisons of local versus global rmsd's come to mind, but I do not know whether this has been implemented anywhere, and would not know readily how to set the parameters thereof either.

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Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: [log in to unmask]
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