A method for finding candidate conformations for molecular replacement using relative rotation between domains of a known structure.

ABSTRACT: This paper presents a methodology to obtain candidate conformations of multidomain proteins for use in molecular replacement. For each separate domain, the orientational relationship between the template and the target structure is obtained using standard molecular replacement. The orientational relationships of the domains are then used to calculate the relative rotation between the domains in the target conformation by using pose-estimation techniques from the field of robotics and computer vision. With the angle of relative rotation between the domains as a cost function, iterative normal-mode analysis is used to drive the template structure to a candidate conformation that matches the X-ray crystallographic data obtained for the target conformation. The selection of the correct intra-p

SUBMITTER: Jeong JI 

PROVIDER: S-EPMC2836325 | biostudies-literature | 2006 Apr

REPOSITORIES: biostudies-literature