FindEM--a fast, efficient program for automatic selection of particles from electron micrographs. 2004

A M Roseman
Medical Research Council-Laboratory of Molecular Biology, Hills Road, England, Cambridge CB2 2QH, UK. roseman@mrc-lmb.cam.ac.uk

The FindEM particle picking program was tested on the publicly available keyhole limpet hemocyanin (KLH) dataset, and the results were submitted for the "bakeoff" contest at the recent particle picking workshop (Zhu et al., 2003b). Two alternative ways of using the program are demonstrated and the results are compared. The first of these approximates exhaustive projection matching with a full set of expected views, which need to be known. This could correspond to the task of extending a known structure to higher resolution, for which many 1000's of additional images are required. The second procedure illustrates use of multivariate statistical analysis (MSA) to filter a preliminary set of candidate particles containing a high proportion of false particles. This set was generated using the FindEM program to search with one template that crudely represents the expected views. Classification of the resultant set of candidate particles then allows the desired classes to be selected while the rest can be ignored. This approach requires no prior information of the structure and is suitable for the initial investigation of an unknown structure--the class averages indicate the symmetry and oligomeric state of the particles. Potential improvements in speed and accuracy are discussed.

UI MeSH Term Description Entries
D007091 Image Processing, Computer-Assisted A technique of inputting two-dimensional or three-dimensional images into a computer and then enhancing or analyzing the imagery into a form that is more useful to the human observer. Biomedical Image Processing,Computer-Assisted Image Processing,Digital Image Processing,Image Analysis, Computer-Assisted,Image Reconstruction,Medical Image Processing,Analysis, Computer-Assisted Image,Computer-Assisted Image Analysis,Computer Assisted Image Analysis,Computer Assisted Image Processing,Computer-Assisted Image Analyses,Image Analyses, Computer-Assisted,Image Analysis, Computer Assisted,Image Processing, Biomedical,Image Processing, Computer Assisted,Image Processing, Digital,Image Processing, Medical,Image Processings, Medical,Image Reconstructions,Medical Image Processings,Processing, Biomedical Image,Processing, Digital Image,Processing, Medical Image,Processings, Digital Image,Processings, Medical Image,Reconstruction, Image,Reconstructions, Image
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D008974 Mollusca A phylum of the kingdom Metazoa. Mollusca have soft, unsegmented bodies with an anterior head, a dorsal visceral mass, and a ventral foot. Most are encased in a protective calcareous shell. It includes the classes GASTROPODA; BIVALVIA; CEPHALOPODA; Aplacophora; Scaphopoda; Polyplacophora; and Monoplacophora. Molluscs,Mollusks,Mollusc,Molluscas,Mollusk
D010363 Pattern Recognition, Automated In INFORMATION RETRIEVAL, machine-sensing or identification of visible patterns (shapes, forms, and configurations). (Harrod's Librarians' Glossary, 7th ed) Automated Pattern Recognition,Pattern Recognition System,Pattern Recognition Systems
D011487 Protein Conformation The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). Conformation, Protein,Conformations, Protein,Protein Conformations
D006433 Hemocyanins Metalloproteins that function as oxygen transport proteins in the HEMOLYMPH of MOLLUSKS and ARTHROPODS. They are characterized by two copper atoms, coordinated with HISTIDINE residues, that reversibly bind a single oxygen molecule; they do not contain HEME groups. Hemocyanin,alpha-Haemocyanin,alpha-Hemocyanin,alpha-Hemocyanins,alpha Haemocyanin,alpha Hemocyanin,alpha Hemocyanins
D000465 Algorithms A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task. Algorithm
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D001330 Electronic Data Processing Applications that store and process large quantities of data. Automatic Data Processing,Bar Codes,Computer Data Processing,Data Processing, Automatic,Information Processing, Automatic,Optical Readers,Information Processing,Automatic Information Processing,Bar Code,Codes, Bar,Data Processing, Computer,Data Processing, Electronic,Optical Reader,Processing, Automatic Data,Processing, Automatic Information,Processing, Computer Data,Processing, Electronic Data,Processing, Information
D012984 Software Sequential operating programs and data which instruct the functioning of a digital computer. Computer Programs,Computer Software,Open Source Software,Software Engineering,Software Tools,Computer Applications Software,Computer Programs and Programming,Computer Software Applications,Application, Computer Software,Applications Software, Computer,Applications Softwares, Computer,Applications, Computer Software,Computer Applications Softwares,Computer Program,Computer Software Application,Engineering, Software,Open Source Softwares,Program, Computer,Programs, Computer,Software Application, Computer,Software Applications, Computer,Software Tool,Software, Computer,Software, Computer Applications,Software, Open Source,Softwares, Computer Applications,Softwares, Open Source,Source Software, Open,Source Softwares, Open,Tool, Software,Tools, Software

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