This subproject is one of many research subprojects utilizing theresources provided by a Center grant funded by NIH/NCRR. The subproject andinvestigator (PI) may have received primary funding from another NIH source,and thus could be represented in other CRISP entries. The institution listed isfor the Center, which is not necessarily the institution for the investigator.Protein loop modeling is often necessary when the initial structure is (a) determined experimentally and lacks data for flexible regions, or (b) constructed computationally and includes poorly built loops. Modeller (see http://salilab.org/modeller for details) from Andrej Sali's lab is a program for comparative protein structure modelling by satisfaction of spatial restraints and includes an implementation of the method described in 'Modeling of loops in protein structures' (Protein Science (2000), 9:1753�1773). When given a protein structure and a loop region, Modeller can generate multiple candidate loop models. However, Modeller does not include a graphical component for displaying these results. To provide a graphical interface to Modeller's loop modeling capabilities, we are designing and implementing 'ModUtil', an extension to UCSF Chimera, that will enable users to model protein loops in a graphical environment, including the generation of candidate structures and evaluation using Chimera tools such as its hydrogen bond finder.
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