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A comparison of the restrained molecular dynamics and distance geometry methods for determining three‐dimensional structures of proteins on the basis of interproton distances
Author(s) -
Clore G.Marius,
Nilges Michael,
Brünger Axel T.,
Karplus Martin,
Gronenborn Angela M.
Publication year - 1987
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/0014-5793(87)81504-1
Subject(s) - chemistry , basis (linear algebra) , molecular dynamics , geometry , crystallography , distance matrix , molecular geometry , dynamics (music) , protein structure , space (punctuation) , chemical physics , molecular physics , physics , molecule , computational chemistry , mathematics , algorithm , computer science , biochemistry , organic chemistry , acoustics , operating system
A direct comparison of the metric matrix distance geometry and restrained molecular dynamics methods for determining three‐dimensional structures of proteins on the basis of interproton distances is presented using crambin as a model system. It is shown that both methods reproduce the overall features of the secondary and tertiary structure (shape and polypeptide fold). The region of conformational space sampled by the converged structures generated by the two methods is similar in size, and in both cases the converged structures are distributed about mean structures which are closer to the X‐ray structure than any of the individual structures. The restrained molecular dynamics structures are superior to those obtained from distance geometry as regards local backbone conformation, side chain positions and non‐bonding energies.