MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field
An increasing number of protein complex structures are determined by cryo-electron microscopy (cryo-EM). When individual protein structures have been determined and are available, an important task in structure modeling is to fit the individual structures into the density map. Here, we designed a me...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-07-01
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| Series: | Frontiers in Molecular Biosciences |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmolb.2022.935411/full |
| _version_ | 1818188986750861312 |
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| author | Eman Alnabati Juan Esquivel-Rodriguez Genki Terashi Daisuke Kihara Daisuke Kihara |
| author_facet | Eman Alnabati Juan Esquivel-Rodriguez Genki Terashi Daisuke Kihara Daisuke Kihara |
| author_sort | Eman Alnabati |
| collection | DOAJ |
| description | An increasing number of protein complex structures are determined by cryo-electron microscopy (cryo-EM). When individual protein structures have been determined and are available, an important task in structure modeling is to fit the individual structures into the density map. Here, we designed a method that fits the atomic structures of proteins in cryo-EM maps of medium to low resolutions using Markov random fields, which allows probabilistic evaluation of fitted models. The accuracy of our method, MarkovFit, performed better than existing methods on datasets of 31 simulated cryo-EM maps of resolution 10 Å, nine experimentally determined cryo-EM maps of resolution less than 4 Å, and 28 experimentally determined cryo-EM maps of resolution 6 to 20 Å. |
| first_indexed | 2024-12-11T23:35:39Z |
| format | Article |
| id | doaj.art-22cba81fae8148c991e6e85f482ca476 |
| institution | Directory Open Access Journal |
| issn | 2296-889X |
| language | English |
| last_indexed | 2024-12-11T23:35:39Z |
| publishDate | 2022-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Molecular Biosciences |
| spelling | doaj.art-22cba81fae8148c991e6e85f482ca4762022-12-22T00:45:53ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2022-07-01910.3389/fmolb.2022.935411935411MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random FieldEman Alnabati0Juan Esquivel-Rodriguez1Genki Terashi2Daisuke Kihara3Daisuke Kihara4Department of Computer Science, Purdue University, West Lafayette, IN, United StatesComputer Engineering School, Costa Rica Institute of Technology, Cartago, Costa RicaDepartment of Biological Sciences, Purdue University, West Lafayette, IN, United StatesDepartment of Computer Science, Purdue University, West Lafayette, IN, United StatesDepartment of Biological Sciences, Purdue University, West Lafayette, IN, United StatesAn increasing number of protein complex structures are determined by cryo-electron microscopy (cryo-EM). When individual protein structures have been determined and are available, an important task in structure modeling is to fit the individual structures into the density map. Here, we designed a method that fits the atomic structures of proteins in cryo-EM maps of medium to low resolutions using Markov random fields, which allows probabilistic evaluation of fitted models. The accuracy of our method, MarkovFit, performed better than existing methods on datasets of 31 simulated cryo-EM maps of resolution 10 Å, nine experimentally determined cryo-EM maps of resolution less than 4 Å, and 28 experimentally determined cryo-EM maps of resolution 6 to 20 Å.https://www.frontiersin.org/articles/10.3389/fmolb.2022.935411/fullprotein modelingcryo-EMMarkov random fieldstructure fittingprotein structure prediction |
| spellingShingle | Eman Alnabati Juan Esquivel-Rodriguez Genki Terashi Daisuke Kihara Daisuke Kihara MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field Frontiers in Molecular Biosciences protein modeling cryo-EM Markov random field structure fitting protein structure prediction |
| title | MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field |
| title_full | MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field |
| title_fullStr | MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field |
| title_full_unstemmed | MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field |
| title_short | MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field |
| title_sort | markovfit structure fitting for protein complexes in electron microscopy maps using markov random field |
| topic | protein modeling cryo-EM Markov random field structure fitting protein structure prediction |
| url | https://www.frontiersin.org/articles/10.3389/fmolb.2022.935411/full |
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