{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,24]],"date-time":"2025-10-24T07:54:31Z","timestamp":1761292471503},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: One bottleneck in high-throughput protein crystallography is interpreting an electron-density map, that is, fitting a molecular model to the 3D picture crystallography produces. Previously, we developed Acmi (Automatic Crystallographic Map Interpreter), an algorithm that uses a probabilistic model to infer an accurate protein backbone layout. Here, we use a sampling method known as particle filtering to produce a set of all-atom protein models. We use the output of Acmi to guide the particle filter's sampling, producing an accurate, physically feasible set of structures.<\/jats:p><jats:p>Results: We test our algorithm on 10 poor-quality experimental density maps. We show that particle filtering produces accurate all-atom models, resulting in fewer chains, lower sidechain RMS error and reduced R factor, compared to simply placing the best-matching sidechains on Acmi's trace. We show that our approach produces a more accurate model than three leading methods\u2014Textal, Resolve and ARP\/WARP\u2014in terms of main chain completeness, sidechain identification and crystallographic R factor.<\/jats:p><jats:p>Availability: Source code and experimental density maps available at http:\/\/ftp.cs.wisc.edu\/machine-learning\/shavlik-group\/programs\/acmi\/<\/jats:p><jats:p>Contact: \u00a0dimaio@cs.wisc.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm480","type":"journal-article","created":{"date-parts":[[2007,10,13]],"date-time":"2007-10-13T00:33:48Z","timestamp":1192235628000},"page":"2851-2858","source":"Crossref","is-referenced-by-count":26,"title":["Creating protein models from electron-density maps using particle-filtering methods"],"prefix":"10.1093","volume":"23","author":[{"given":"Frank","family":"DiMaio","sequence":"first","affiliation":[{"name":"1 Department of Computer Sciences, 2Department of Biostatistics and Medical Informatics, 3Department of Biochemistry and 4Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA"},{"name":"1 Department of Computer Sciences, 2Department of Biostatistics and Medical Informatics, 3Department of Biochemistry and 4Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dmitry A.","family":"Kondrashov","sequence":"additional","affiliation":[{"name":"1 Department of Computer Sciences, 2Department of Biostatistics and Medical Informatics, 3Department of Biochemistry and 4Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eduard","family":"Bitto","sequence":"additional","affiliation":[{"name":"1 Department of Computer Sciences, 2Department of Biostatistics and Medical Informatics, 3Department of Biochemistry and 4Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ameet","family":"Soni","sequence":"additional","affiliation":[{"name":"1 Department of Computer Sciences, 2Department of Biostatistics and Medical Informatics, 3Department of Biochemistry and 4Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA"},{"name":"1 Department of Computer Sciences, 2Department of Biostatistics and Medical Informatics, 3Department of Biochemistry and 4Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Craig A.","family":"Bingman","sequence":"additional","affiliation":[{"name":"1 Department of Computer Sciences, 2Department of Biostatistics and Medical Informatics, 3Department of Biochemistry and 4Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"suffix":"Jr","given":"George N.","family":"Phillips","sequence":"additional","affiliation":[{"name":"1 Department of Computer Sciences, 2Department of Biostatistics and Medical Informatics, 3Department of Biochemistry and 4Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA"},{"name":"1 Department of Computer Sciences, 2Department of Biostatistics and Medical Informatics, 3Department of Biochemistry and 4Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA"},{"name":"1 Department of Computer Sciences, 2Department of Biostatistics and Medical Informatics, 3Department of Biochemistry and 4Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jude W.","family":"Shavlik","sequence":"additional","affiliation":[{"name":"1 Department of Computer Sciences, 2Department of Biostatistics and Medical Informatics, 3Department of Biochemistry and 4Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA"},{"name":"1 Department of Computer Sciences, 2Department of Biostatistics and Medical Informatics, 3Department of Biochemistry and 4Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2007,10,12]]},"reference":[{"key":"2023041107265196900_","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1109\/78.978374","article-title":"A tutorial on particle filters","volume":"50","author":"Arulampalam","year":"2001","journal-title":"IEEE Trans. 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