{"title":"结合低温电镜密度图和残馀接触蛋白结构预测-一个案例研究。","authors":"Maytha Alshammari, Jing He","doi":"10.1145/3388440.3414708","DOIUrl":null,"url":null,"abstract":"<p><p>Cryo-electron microscopy is a major structure determination technique for large molecular machines and membrane-associated complexes. Although atomic structures have been determined directly from cryo-EM density maps with high resolutions, current structure determination methods for medium resolution (5 to 10 Å) cryo-EM maps are limited by the availability of structure templates. Secondary structure traces are lines detected from a cryo-EM density map for α-helices and β-strands of a protein. When combined with secondary structure sequence segments predicted from a protein sequence, it is possible to generate a set of likely topologies of α-traces and β-sheet traces. A topology describes the overall folding relationship among secondary structures; it is a critical piece of information for deriving the corresponding atomic structure. We propose a method for protein structure prediction that combines three sources of information: the secondary structure traces detected from the cryo-EM density map, predicted secondary structure sequence segments, and amino acid contact pairs predicted using MULTICOM. A case study shows that using amino acid contact prediction from MULTICOM improves the ranking of the true topology. Our observations convey that using a small set of highly voted secondary structure contact pairs enhances the ranking in all experiments conducted for this case.</p>","PeriodicalId":72044,"journal":{"name":"ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2020-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1145/3388440.3414708","citationCount":"2","resultStr":"{\"title\":\"Combine Cryo-EM Density Map and Residue Contact for Protein Structure Prediction - A Case Study.\",\"authors\":\"Maytha Alshammari, Jing He\",\"doi\":\"10.1145/3388440.3414708\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Cryo-electron microscopy is a major structure determination technique for large molecular machines and membrane-associated complexes. Although atomic structures have been determined directly from cryo-EM density maps with high resolutions, current structure determination methods for medium resolution (5 to 10 Å) cryo-EM maps are limited by the availability of structure templates. Secondary structure traces are lines detected from a cryo-EM density map for α-helices and β-strands of a protein. When combined with secondary structure sequence segments predicted from a protein sequence, it is possible to generate a set of likely topologies of α-traces and β-sheet traces. A topology describes the overall folding relationship among secondary structures; it is a critical piece of information for deriving the corresponding atomic structure. We propose a method for protein structure prediction that combines three sources of information: the secondary structure traces detected from the cryo-EM density map, predicted secondary structure sequence segments, and amino acid contact pairs predicted using MULTICOM. A case study shows that using amino acid contact prediction from MULTICOM improves the ranking of the true topology. Our observations convey that using a small set of highly voted secondary structure contact pairs enhances the ranking in all experiments conducted for this case.</p>\",\"PeriodicalId\":72044,\"journal\":{\"name\":\"ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2020-09-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://sci-hub-pdf.com/10.1145/3388440.3414708\",\"citationCount\":\"2\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. 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Combine Cryo-EM Density Map and Residue Contact for Protein Structure Prediction - A Case Study.
Cryo-electron microscopy is a major structure determination technique for large molecular machines and membrane-associated complexes. Although atomic structures have been determined directly from cryo-EM density maps with high resolutions, current structure determination methods for medium resolution (5 to 10 Å) cryo-EM maps are limited by the availability of structure templates. Secondary structure traces are lines detected from a cryo-EM density map for α-helices and β-strands of a protein. When combined with secondary structure sequence segments predicted from a protein sequence, it is possible to generate a set of likely topologies of α-traces and β-sheet traces. A topology describes the overall folding relationship among secondary structures; it is a critical piece of information for deriving the corresponding atomic structure. We propose a method for protein structure prediction that combines three sources of information: the secondary structure traces detected from the cryo-EM density map, predicted secondary structure sequence segments, and amino acid contact pairs predicted using MULTICOM. A case study shows that using amino acid contact prediction from MULTICOM improves the ranking of the true topology. Our observations convey that using a small set of highly voted secondary structure contact pairs enhances the ranking in all experiments conducted for this case.