IMIRS: a high-resolution 3D reconstruction package integrated with a relational image database.
Recent advances in electron cryomicroscopy instrumentation and single particle reconstruction have created opportunities for high-throughput and high-resolution three-dimensional (3D) structure determination of macromolecular complexes. However, it has become impractical and inefficient to rely on conventional text file data management and command-line programs to organize and process the increasing numbers of image data required in high-resolution studies. Here, we present a distributed relational database for managing complex datasets and its integration into our high-resolution software package IMIRS (Image Management and Icosahedral Reconstruction System). IMIRS consists of a complete set of modular programs for icosahedral reconstruction organized under a graphical user interface and provides options for user-friendly, step-by-step data processing as well as automatic reconstruction. We show that the integration of data management with processing in IMIRS automates the tedious tasks of data management, enables data coherence, and facilitates information sharing in a distributed computer and user environment without significantly increasing the time of program execution. We demonstrate the applicability of IMIRS in icosahedral reconstruction toward high resolution by using it to obtain an 8-A 3D structure of an intermediate-sized dsRNA virus.
Liang
Yuyao
Y
Department of Pathology and Laboratory Medicine, University of Texas-Houston Medical School, 77030, USA.
Ke
Eugene Y
EY
Zhou
Z Hong
ZH
D000818:Animals; D001820:Bluetongue virus / Q000737:chemistry / Q000648:ultrastructure; D003195:Computer Communication Networks; D003196:Computer Graphics; D020285:Cryoelectron Microscopy / Q000295:instrumentation; D003626:Data Display; D003628:Database Management Systems; D016208:Databases, Factual; D019281:Dimerization; D004285:Dogs; D001330:Electronic Data Processing; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008958:Models, Molecular; D017993:Parvovirus, Canine / Q000737:chemistry / Q000648:ultrastructure; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012680:Sensitivity and Specificity; D012756:Sheep; D014584:User-Computer Interface; D014764:Viral Proteins / Q000737:chemistry; D014780:Viruses / Q000648:ultrastructure*
D014764:Viral Proteins