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Modeling the structures of proteins and macromolecular assemblies
Author(s) -
Sali Andrej
Publication year - 2006
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.20.5.a851
Subject(s) - resolution (logic) , structural genomics , representation (politics) , characterization (materials science) , function (biology) , computer science , low resolution , biological system , protein structure , protein structure prediction , structural biology , algorithm , high resolution , artificial intelligence , chemistry , nanotechnology , materials science , biology , biochemistry , remote sensing , evolutionary biology , politics , geology , political science , law
The structures of most protein domains will eventually be characterized by structural genomics, which aims to determine most protein folds by experiment, allowing the remaining protein sequences to be modeled with useful accuracy by computational methods. In the case of assemblies, however, the structure is usually obtained by a number of experimental methods of varying accuracy and resolution ( eg , X‐ray crystallography of the subunits, low‐resolution electron microscopy of the assembly, and chemical cross‐linking). Therefore, there is a need for a computational framework that can take into account all available information about the structure of an assembly and calculate at the appropriate resolution all models that are consistent with the given input. To this end, it is useful to express structure determination as an optimization problem. The three components of this approach are (i) representation of an assembly; (ii) a scoring function consisting of individual spatial restraints; and (iii) optimization of the scoring function to obtain the models. This approach will be illustrated by the characterization of several assemblies.