{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T01:59:00Z","timestamp":1767923940708,"version":"3.49.0"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. The reconstruction process leading to the final 3D map requires an approximate initial model. Generation of an initial model is still an open and challenging problem in single-particle analysis.<\/jats:p>\n               <jats:p>Results: We present a fast and efficient approach to obtain a reliable, low-resolution estimation of the 3D structure of a macromolecule, without any a priori knowledge, addressing the well-known issue of initial volume estimation in the field of single-particle analysis. The input of the algorithm is a set of class average images obtained from individual projections of a biological object at random and unknown orientations by transmission electron microscopy micrographs. The proposed method is based on an initial non-lineal dimensionality reduction approach, which allows to automatically selecting representative small sets of class average images capturing the most of the structural information of the particle under study. These reduced sets are then used to generate volumes from random orientation assignments. The best volume is determined from these guesses using a random sample consensus (RANSAC) approach. We have tested our proposed algorithm, which we will term 3D-RANSAC, with simulated and experimental data, obtaining satisfactory results under the low signal-to-noise conditions typical of cryo-electron microscopy.<\/jats:p>\n               <jats:p>Availability: The algorithm is freely available as part of the Xmipp 3.1 package [ http:\/\/xmipp.cnb.csic.es ].<\/jats:p>\n               <jats:p>Contact: \u00a0jvargas@cnb.csic.es<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu404","type":"journal-article","created":{"date-parts":[[2014,6,29]],"date-time":"2014-06-29T00:12:32Z","timestamp":1404000752000},"page":"2891-2898","source":"Crossref","is-referenced-by-count":66,"title":["Efficient initial volume determination from electron microscopy images of single particles"],"prefix":"10.1093","volume":"30","author":[{"given":"Javier","family":"Vargas","sequence":"first","affiliation":[{"name":"1 Biocomputing Unit, Centro Nacional de Biotecnolog\u00eda-CSIC, C\/Darwin 3 and 2 Escuela Polit\u00e9cnica Superior, Universidad Aut\u00f3noma de Madrid, C\/Francisco Tom\u00e1s y Valiente, 28049, Cantoblanco (Madrid), Spain"}]},{"given":"Ana-Lucia","family":"\u00c1lvarez-Cabrera","sequence":"additional","affiliation":[{"name":"1 Biocomputing Unit, Centro Nacional de Biotecnolog\u00eda-CSIC, C\/Darwin 3 and 2 Escuela Polit\u00e9cnica Superior, Universidad Aut\u00f3noma de Madrid, C\/Francisco Tom\u00e1s y Valiente, 28049, Cantoblanco (Madrid), Spain"}]},{"given":"Roberto","family":"Marabini","sequence":"additional","affiliation":[{"name":"1 Biocomputing Unit, Centro Nacional de Biotecnolog\u00eda-CSIC, C\/Darwin 3 and 2 Escuela Polit\u00e9cnica Superior, Universidad Aut\u00f3noma de Madrid, C\/Francisco Tom\u00e1s y Valiente, 28049, Cantoblanco (Madrid), Spain"}]},{"given":"Jose M.","family":"Carazo","sequence":"additional","affiliation":[{"name":"1 Biocomputing Unit, Centro Nacional de Biotecnolog\u00eda-CSIC, C\/Darwin 3 and 2 Escuela Polit\u00e9cnica Superior, Universidad Aut\u00f3noma de Madrid, C\/Francisco Tom\u00e1s y Valiente, 28049, Cantoblanco (Madrid), Spain"}]},{"given":"C. O. S.","family":"Sorzano","sequence":"additional","affiliation":[{"name":"1 Biocomputing Unit, Centro Nacional de Biotecnolog\u00eda-CSIC, C\/Darwin 3 and 2 Escuela Polit\u00e9cnica Superior, Universidad Aut\u00f3noma de Madrid, C\/Francisco Tom\u00e1s y Valiente, 28049, Cantoblanco (Madrid), Spain"}]}],"member":"286","published-online":{"date-parts":[[2014,6,27]]},"reference":[{"key":"2023012711562677300_btu404-B1","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1093\/bioinformatics\/btt429","article-title":"A pattern matching approach to selection of particles from low-contrast electron micrographs","volume":"29","author":"Abrishami","year":"2013","journal-title":"Bioinformatics"},{"key":"2023012711562677300_btu404-B2","doi-asserted-by":"crossref","first-page":"3286","DOI":"10.1093\/bioinformatics\/bth377","article-title":"Phan3D: design of biological phantoms in 3D electron microscopy","volume":"20","author":"Bilbao-Castro","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012711562677300_btu404-B34","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1006\/jsbi.1996.0020","article-title":"A model-based approach for determining orientations of biological macromolecules imaged by cryo-electron microscopy","volume":"116","author":"Baker","year":"1996","journal-title":"J. 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