De novo modeling in cryo-EM density maps with Pathwalking
Open accessAbstract
As electron cryo-microscopy (cryo-EM) can now frequently achieve near atomic resolution, accurate interpretation of these density maps in terms of atomistic detail has become paramount in deciphering macromolecular structure and function. However, there are few software tools for modeling protein structure from cryo-EM density maps in this resolution range. Here, we present an extension of our original Pathwalking protocol, which can automatically trace a protein backbone directly from a near-atomic resolution (3-6Å) density map. The original Pathwalking approach utilized a Traveling Salesman Problem solver for backbone tracing, but manual adjustment was still required during modeling. In the new version, human intervention is minimized and we provide a more robust approach for backbone modeling. This includes iterative secondary structure identification, termini detection and the ability to model multiple subunits without prior segmentation. Overall, the new Pathwalking procedure provides a more complete and robust tool for annotating protein structure function in near-atomic resolution density maps.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Electron density images from x-ray crystallography or cryo-electron microscopy produce proximity constraints representable as networks of atoms linked to other atoms in close spatial proximity.
“At the atomic scale, electron density images generated by x-ray crystallography (Adams et al., 2002; Kleywegt et al., 2004; Yang et al., 2016) or cryo-electron microscopy (cryo-EM) (Chen et al., 2016; Frenz et al., 2017; Hryc et al., 2017) produce proximity constraints that can be represented as networks of atoms (nodes) linked to other atoms determined to be in close spatial proximity (edges).”
From Mapping the multiscale structure of biological systems (2021) · cites this paper as Chen et al., 2016
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
UCSF Chimera—A visualization system for exploratory research and analysis
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20084 · Cited by 45,260 · see citing works
EMAN2: An extensible image processing suite for electron microscopy
Tang, G., Peng, L., Baldwin, P. R., Mann, D. S., Jiang, W., Rees, I., & Ludtke, S. J. (2006) · Journal of Structural Biology · doi:10.1016/j.jsb.2006.05.009 · Cited by 2,914 · see citing works
Li, X.-M., Mooney, P., Zheng, S., Booth, C., Braunfeld, M. B., Gubbens, S., Agard, D., & Cheng, Y.-F. (2013) · Nature Methods · doi:10.1038/nmeth.2472 · Cited by 1,866 · see citing works
Structural determinants of water permeation through aquaporin-1
Murata, K., Mitsuoka, K., Hirai, T., Walz, T., Agre, P. C., Heymann, J. B., Engel, A. H., & Fujiyoshi, Y. (2000) · Nature · doi:10.1038/35036519 · Cited by 1,810 · see citing works
The Traveling salesman problem: a computational study
(2007) · Choice Reviews Online · doi:10.5860/choice.45-0928 · Cited by 1,726 · see citing works
Structure of the TRPV1 ion channel determined by electron cryo-microscopy
Liao, M., Cao, E., Julius, D. J., & Cheng, Y. (2013) · Nature · doi:10.1038/nature12822 · Cited by 1,696 · see citing works
TRPV1 structures in distinct conformations reveal activation mechanisms
Cao, E., Liao, M., Cheng, Y., & Julius, D. J. (2013) · Nature · doi:10.1038/nature12823 · Cited by 1,034 · see citing works
Single-Particle Cryo-EM at Crystallographic Resolution
Cheng, Y. (2015) · Cell · doi:10.1016/j.cell.2015.03.049 · Cited by 581 · see citing works
Structure of the Yeast Mitochondrial Large Ribosomal Subunit
Amunts, A., Brown, A., Bai, X., Llacer, J. L., Hussain, T., Emsley, P., Long, F., Murshudov, G. N., Scheres, S. H. W., & Ramakrishnan, V. (2014) · Science · doi:10.1126/science.1249410 · Cited by 580 · see citing works
2.2 Å resolution cryo-EM structure of β-galactosidase in complex with a cell-permeant inhibitor
Bartesaghi, A., Merk, A., Banerjee, S., Matthies, D., Wu, X., Milne, J. L. S., & Subramaniam, S. (2015) · Science · doi:10.1126/science.aab1576 · Cited by 438 · see citing works
General k-opt submoves for the Lin–Kernighan TSP heuristic
Helsgaun, K. (2009) · Mathematical Programming Computation · doi:10.1007/s12532-009-0004-6 · Cited by 421 · see citing works
Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction
Zhang, X., Settembre, E. C., Xu, C., Dormitzer, P. R., Bellamy, R., Harrison, S. C., & Grigorieff, N. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0711623105 · Cited by 367 · see citing works
Structure of the E. coli ribosome–EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM
Fischer, N., Neumann, P., Konevega, A. L., Bock, L. V., Ficner, R., Rodnina, M. V., & Stark, H. (2015) · Nature · doi:10.1038/nature14275 · Cited by 356 · see citing works
Jiang, W., Baker, M. L., Ludtke, S. J., & Chiu, W. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4633 · Cited by 300 · see citing works
Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta
DiMaio, F., Tyka, M. D., Baker, M. L., Chiu, W., & Baker, D. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.07.008 · Cited by 295 · see citing works
3.88 Å structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy
Yu, X., Jin, L., & Zhou, Z. (2008) · Nature · doi:10.1038/nature06893 · Cited by 282 · see citing works
Atomic structure of anthrax protective antigen pore elucidates toxin translocation
Jiang, J., Pentelute, B. L., Collier, R. J., & Zhou, Z. H. (2015) · Nature · doi:10.1038/nature14247 · Cited by 255 · see citing works
Gating machinery of InsP3R channels revealed by electron cryomicroscopy
Fan, G., Baker, M. L., Wang, Z., Baker, M. R., Sinyagovskiy, P. A., Chiu, W., Ludtke, S. J., & Serysheva, I. I. (2015) · Nature · doi:10.1038/nature15249 · Cited by 228 · see citing works
4.4 Å cryo‐EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus
Zhang, R., Hryc, C. F., Cong, Y., Liu, X., Jakana, J., Gorchakov, R. V., Baker, M. L., Weaver, S. C., & Chiu, W. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.261 · Cited by 222 · see citing works
Backbone structure of the infectious ε15 virus capsid revealed by electron cryomicroscopy
Jiang, W., Baker, M. L., Jakana, J., Weigele, P., King, J. W., & Chiu, W. (2008) · Nature · doi:10.1038/nature06665 · Cited by 214 · see citing works
Mechanism of folding chamber closure in a group II chaperonin
Zhang, J., Baker, M. L., Schroeder, G. F., Douglas, N. R., Reißmann, S., Jakana, J., Dougherty, M., Fu, C., Levitt, M., Ludtke, S. J., et al. (2010) · Nature · doi:10.1038/nature08701 · Cited by 209 · see citing works
Coat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolutions
Jiang, W., Li, Z., Zhang, Z., Baker, M. L., Prevelige, P. E., & Chiu, W. (2003) · Nature Structural Biology · doi:10.1038/nsb891 · Cited by 207 · see citing works
Identification of Secondary Structure Elements in Intermediate-Resolution Density Maps
Baker, M. L., Ju, T., & Chiu, W. K. (2007) · Structure · doi:10.1016/j.str.2006.11.008 · Cited by 202 · see citing works
De Novo Backbone Trace of GroEL from Single Particle Electron Cryomicroscopy
Ludtke, S. J., Baker, M. L., Chen, D.-H., Song, J., Chuang, D., & Chiu, W. (2008) · Structure · doi:10.1016/j.str.2008.02.007 · Cited by 175 · see citing works
Campbell, M. G., Veesler, D., Cheng, A., Potter, C. S., & Carragher, B. O. (2015) · eLife · doi:10.7554/elife.06380 · Cited by 163 · see citing works
Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus
Liu, X., Zhang, Q., Murata, K., Baker, M. L., Sullivan, M. B., Fu, C., Dougherty, M. T., Schmid, M. F., Osburne, M. S., Chisholm, S. W., et al. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1823 · Cited by 148 · see citing works
Electron Cryomicroscopy of Biological Machines at Subnanometer Resolution
Chiu, W., Baker, M. L., Jiang, W., Dougherty, M., & Schmid, M. F. (2005) · Structure · doi:10.1016/j.str.2004.12.016 · Cited by 140 · see citing works
Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus.
Zhou, Z., Baker, M. L., Jiang, W., Dougherty, M., Jakana, J., Dong, G., Lu, G., & Chiu, W. (2001) · Nature Structural Biology · doi:10.1038/nsb1001-868 · Cited by 132 · see citing works
CLICK—topology-independent comparison of biomolecular 3D structures
Nguyen, M. N., Tan, K. P., & Madhusudhan, M. S. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr393 · Cited by 130 · see citing works
An atomic model of brome mosaic virus using direct electron detection and real-space optimization
Wang, Z., Hryc, C. F., Bammes, B. E., Afonine, P. V., Jakana, J., Chen, D.-H., Liu, X., Baker, M. L., Kao, C. C., Ludtke, S. J., et al. (2014) · Nature Communications · doi:10.1038/ncomms5808 · Cited by 120 · see citing works
Combining X-Ray Crystallography and Electron Microscopy
Rossmann, M. G., Morais, M. C., Leiman, P. G., & Zhang, W. (2005) · Structure · doi:10.1016/j.str.2005.01.005 · Cited by 118 · see citing works
Serysheva, I. I., Ludtke, S. J., Baker, M. L., Cong, Y., Topf, M., Eramian, D., Šali, A., Hamilton, S. L., & Chiu, W. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803189105 · Cited by 115 · see citing works
Refinement of Protein Structures by Iterative Comparative Modeling and CryoEM Density Fitting
Topf, M., Baker, M. L., Martı́-Renom, M. A., Chiu, W., & Šali, A. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.01.062 · Cited by 110 · see citing works
Topf, M., Baker, M. L., John, B., Chiu, W., & Šali, A. (2004) · Journal of Structural Biology · doi:10.1016/j.jsb.2004.11.004 · Cited by 91 · see citing works
Pintilie, G. D., & Chiu, W. K. (2012) · Biopolymers · doi:10.1002/bip.22074 · Cited by 83 · see citing works
Cryo-EM of macromolecular assemblies at near-atomic resolution
Baker, M. L., Zhang, J., Ludtke, S. J., & Chiu, W. (2010) · Nature Protocols · doi:10.1038/nprot.2010.126 · Cited by 81 · see citing works
Baker, M. L., Hryc, C. F., Zhang, Q., Wu, W., Jakana, J., Haase‐Pettingell, C., Afonine, P. V., Adams, P. D., King, J. W., Jiang, W., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1309947110 · Cited by 72 · see citing works
Structure of an Xrcc4–DNA ligase IV yeast ortholog complex reveals a novel BRCT interaction mode
Dore, A. S., Furnham, N., Davies, O. R., Sibanda, B. L., Chirgadze, D. Y., Jackson, S. P., Pellegrini, L., & Blundell, T. L. (2006) · DNA repair · doi:10.1016/j.dnarep.2005.11.004 · Cited by 61 · see citing works
Cryo-EM structure of a transcribing cypovirus
Yang, C., Ji, G., Liu, H., Zhang, K., Liu, G., Sun, F., Zhu, P., & Cheng, L. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1200206109 · Cited by 57 · see citing works
Structure-Based Characterization of Multiprotein Complexes
Wiederstein, M., Gruber, M., Frank, K., Melo, F., & Sippl, M. J. (2014) · Structure · doi:10.1016/j.str.2014.05.005 · Cited by 51 · see citing works
Finding the right fit: chiseling structures out of cryo-electron microscopy maps
Villa, E., & Lasker, K. (2014) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2014.04.001 · Cited by 48 · see citing works
Automated segmentation of molecular subunits in electron cryomicroscopy density maps
Baker, M. L., Yu, Z., Chiu, W., & Bajaj, C. (2006) · Journal of Structural Biology · doi:10.1016/j.jsb.2006.05.013 · Cited by 48 · see citing works
Computational methods for constructing protein structure models from 3D electron microscopy maps
Esquivel‐Rodríguez, J., & Kihara, D. (2013) · Journal of Structural Biology · doi:10.1016/j.jsb.2013.06.008 · Cited by 45 · see citing works
Gorgon and pathwalking: Macromolecular modeling tools for subnanometer resolution density maps
Baker, M. L., Baker, M. R., Hryc, C. F., Ju, T., & Chiu, W. (2012) · Biopolymers · doi:10.1002/bip.22065 · Cited by 44 · see citing works
Baker, M. R., Rees, I., Ludtke, S. J., Chiu, W., & Baker, M. L. (2012) · Structure · doi:10.1016/j.str.2012.01.008 · Cited by 42 · see citing works
Zhu, J., Cheng, L., Fang, Q., Zhou, Z. H., & Honig, B. H. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.01.041 · Cited by 41 · see citing works
Architecture of the Herpes Simplex Virus Major Capsid Protein Derived from Structural Bioinformatics
Baker, M. L., Jiang, W., Bowman, B. R., Zhou, Z., Quiocho, F. A., Rixon, F. J., & Chiu, W. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00696-x · Cited by 33 · see citing works
Analyses of Subnanometer Resolution Cryo-EM Density Maps
Baker, M. L., Baker, M. R., Hryc, C. F., & DiMaio, F. (2010) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(10)83001-0 · Cited by 24 · see citing works
Protruding knob-like proteins violate local symmetries in an icosahedral marine virus
Gipson, P., Baker, M. L., Raytcheva, D., Haase‐Pettingell, C., Piret, J., King, J. W., & Chiu, W. (2014) · Nature Communications · doi:10.1038/ncomms5278 · Cited by 23 · see citing works
Flagged first, then by citations
1 of the 50 references couldn’t be matched to a known paper.
Research works printed but not linked: 4
- [38]Baker Matthew L Ju Tao Chiu Wah Identification of Secondary Structure Elements in Intermediate-Resolution Density Maps Structure 15 1 7 19 2007 17223528 PMC1810566
- [43]Ludtke Steven J Baker Matthew L Chen Dong Hua Song Jiu Li Chuang David T Chiu Wah De Novo Backbone Trace of GroEL from Single Particle Electron Cryomicroscopy Structure 16 3 441 448 2008 18334219
- [47]Liao Maofu Cao Erhu Julius David Cheng Yifan Structure of the TRPV1 ion channel determined by electron cryo-microscopy Nature 504 7478 107 12 2013 24305160 PMC4078027
- [52]Baker Matthew L Baker Mariah R Hryc Corey F DiMaio Frank Analyses of Subnanometer Resolution Cryo-EM Density Maps 483 2010 PMC3107677 20888467
Cited by
Sorted by citations
Liebschner, D. C., Afonine, P. V., Baker, M. L., Bunkòczi, G., Chen, V. B., Croll, T. I., Hintze, B. J., Hung, L., Jain, S., McCoy, A. J., et al. (2019) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798319011471 · Cited by 6,709 · see citing works
A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps
Terwilliger, T. C., Adams, P. D., Afonine, P. V., & Sobolev, O. V. (2018) · Nature Methods · doi:10.1038/s41592-018-0173-1 · Cited by 170 · see citing works
De novo main-chain modeling for EM maps using MAINMAST
Terashi, G., & Kihara, D. (2018) · Nature Communications · doi:10.1038/s41467-018-04053-7 · Cited by 137 · see citing works
RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps
Frenz, B., Walls, A. C., Egelman, E. H., Veesler, D., & DiMaio, F. (2017) · Nature Methods · doi:10.1038/nmeth.4340 · Cited by 116 · see citing works
Protein secondary structure detection in intermediate-resolution cryo-EM maps using deep learning
Subramaniya, S. R. M. V., Terashi, G., & Kihara, D. (2019) · Nature Methods · doi:10.1038/s41592-019-0500-1 · Cited by 99 · see citing works
Mapping the multiscale structure of biological systems
Schaffer, L. V., & Ideker, T. (2021) · Cell Systems · doi:10.1016/j.cels.2021.05.012 · Cited by 75 · see citing works
Giri, N., Roy, R. S., & Cheng, J. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102536 · Cited by 59 · see citing works
Hybrid methods for combined experimental and computational determination of protein structure
Seffernick, J. T., & Lindert, S. (2020) · The Journal of Chemical Physics · doi:10.1063/5.0026025 · Cited by 66 · see citing works
Predicting Protein Complex Structure from Surface-Induced Dissociation Mass Spectrometry Data
Seffernick, J. T., Harvey, S. R., Wysocki, V. H., & Lindert, S. (2019) · ACS Central Science · doi:10.1021/acscentsci.8b00912 · Cited by 53 · see citing works
Simulation-Based Methods for Model Building and Refinement in Cryoelectron Microscopy
Dodd, T., Yan, C., & Ivanov, I. N. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00087 · Cited by 52 · see citing works
Cryo_fit: Democratization of flexible fitting for cryo-EM
Kim, D. N., Moriarty, N. W., Kırmızıaltın, S., Afonine, P. V., Poon, B. K., Sobolev, O. V., Adams, P. D., & Sanbonmatsu, K. Y. (2019) · Journal of Structural Biology · doi:10.1016/j.jsb.2019.05.012 · Cited by 47 · see citing works
Wang, X., Alnabati, E., Aderinwale, T. W., Subramaniya, S. R. M. V., Terashi, G., & Kihara, D. (2021) · Nature Communications · doi:10.1038/s41467-021-22577-3 · Cited by 47 · see citing works
Zhou, N., Wang, H., & Wang, J. (2017) · Scientific Reports · doi:10.1038/s41598-017-02725-w · Cited by 44 · see citing works
Cryo‐EM map interpretation and protein model‐building using iterative map segmentation
Terwilliger, T. C., Adams, P. D., Afonine, P. V., & Sobolev, O. V. (2019) · Protein Science · doi:10.1002/pro.3740 · Cited by 37 · see citing works
Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps
Alnabati, E., & Kihara, D. (2019) · Molecules · doi:10.3390/molecules25010082 · Cited by 36 · see citing works
Finding the needle in the haystack: towards solving the protein-folding problem computationally
Li, B., Fooksa, M., Heinze, S., & Meiler, J. (2017) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2017.1380596 · Cited by 35 · see citing works
DiMaio, F., & Chiu, W. (2016) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2016.06.003 · Cited by 34 · see citing works
Full-length de novo protein structure determination from cryo-EM maps using deep learning
He, J., & Huang, S. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab357 · Cited by 33 · see citing works
StarMap: a user-friendly workflow for Rosetta-driven molecular structure refinement
Lugmayr, W., Kotov, V., Goessweiner‐Mohr, N., Wald, J., DiMaio, F., & Marlovits, T. C. (2022) · Nature Protocols · doi:10.1038/s41596-022-00757-9 · Cited by 32 · see citing works
Current approaches for automated model building into cryo-EM maps using Buccaneer with CCP-EM
Hoh, S. W., Burnley, B. T., & Cowtan, K. D. (2020) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798320005513 · Cited by 31 · see citing works
EMNUSS: a deep learning framework for secondary structure annotation in cryo-EM maps
He, J., & Huang, S. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab156 · Cited by 31 · see citing works
Si, D., Nakamura, A., Tang, R., Guan, H., Hou, J., Firozi, A., Cao, R., Hippe, K., & Zhao, M. (2021) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1542 · Cited by 30 · see citing works
Interpretation of medium resolution cryoEM maps of multi-protein complexes
Casañal, A., Shakeel, S., & Passmore, L. A. (2019) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2019.06.009 · Cited by 29 · see citing works
Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images
Dasgupta, B., Miyashita, O., & Tama, F. (2019) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2019.129420 · Cited by 28 · see citing works
CryoAtom improves model building for cryo-EM
Su, B., Huang, K., Peng, Z., Amunts, A., & Yang, J. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01713-3 · Cited by 37 · see citing works
CryoEM-based hybrid modeling approaches for structure determination
Cassidy, C. K., Himes, B. A., Luthey-Schulten, Z. A., & Zhang, P. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.10.002 · Cited by 22 · see citing works
Chen, M., Toader, B., & Lederman, R. R. (2023) · Journal of Molecular Biology · doi:10.1016/j.jmb.2023.168014 · Cited by 22 · see citing works
Structural interpretation of cryo-EM image reconstructions
Beckers, M., Mann, D., & Sachse, C. (2020) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2020.07.004 · Cited by 21 · see citing works
Cryo‐electron microscopy targets in CASP13: Overview and evaluation of results
Kryshtafovych, A., Malhotra, S., Monastyrskyy, B., Cragnolini, T., Joseph, A. P., Chiu, W., & Topf, M. (2019) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25817 · Cited by 20 · see citing works
Richardson, J. S., Williams, C. J., Videau, L. L., Chen, V. B., & Richardson, D. C. (2018) · Journal of Structural Biology · doi:10.1016/j.jsb.2018.08.007 · Cited by 20 · see citing works
Tools for the cryo-EM gold rush: going from the cryo-EM map to the atomistic model
Kim, D. N., & Sanbonmatsu, K. Y. (2017) · Bioscience Reports · doi:10.1042/bsr20170072 · Cited by 19 · see citing works
Enhancing cryo-EM maps with 3D deep generative networks for assisting protein structure modeling
Subramaniya, S. R. M. V., Terashi, G., & Kihara, D. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad494 · Cited by 19 · see citing works
Chen, S., Zhang, S., Fang, X., Lin, L., Zhao, H., & Yang, Y. (2024) · Nature Communications · doi:10.1038/s41467-024-53116-5 · Cited by 19 · see citing works
Zhu, Z., Deng, Z., Wang, Q., Wang, Y., Zhang, D., Xu, R., Guo, L., & Wen, H. (2022) · Frontiers in Pharmacology · doi:10.3389/fphar.2022.939555 · Cited by 17 · see citing works
DiIorio, M. C., & Kulczyk, A. (2023) · Micromachines · doi:10.3390/mi14091674 · Cited by 17 · see citing works
De novo main-chain modeling with MAINMAST in 2015/2016 EM Model Challenge
Terashi, G., & Kihara, D. (2018) · Journal of Structural Biology · doi:10.1016/j.jsb.2018.07.013 · Cited by 17 · see citing works
Farrell, D. P., Anishchenko, I. V., Shakeel, S., Lauko, A., Passmore, L. A., Baker, D. A., & DiMaio, F. (2020) · IUCrJ · doi:10.1107/s2052252520009306 · Cited by 16 · see citing works
Refinement of AlphaFold2 models against experimental and hybrid cryo-EM density maps
Alshammari, M., Wriggers, W., Sun, J., & He, J. (2022) · QRB Discovery · doi:10.1017/qrd.2022.13 · Cited by 12 · see citing works
Tüting, C., Schmidt, L., Skalidis, I., Sinz, A., & Kastritis, P. L. (2023) · PROTEOMICS · doi:10.1002/pmic.202200096 · Cited by 14 · see citing works
Mori, T., Terashi, G., Matsuoka, D., Kihara, D., & Sugita, Y. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c00230 · Cited by 15 · see citing works
Chen, M., & Baker, M. L. (2018) · Journal of Structural Biology · doi:10.1016/j.jsb.2018.09.005 · Cited by 15 · see citing works
Super Resolution Cryo-EM Maps with 3D Deep Generative Networks
Subramaniya, S. R. M. V., Terashi, G., & Kihara, D. (2021) · Biophysical Journal · doi:10.1016/j.bpj.2020.11.1801 · Cited by 14 · see citing works
The accuracy of protein models automatically built into cryo-EM maps with ARP/wARP
Chojnowski, G., Sobolev, E. V., Heuser, P., & Lamzin, V. S. (2021) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798320016332 · Cited by 14 · see citing works
Integrating model simulation tools and cryo‐electron microscopy
Beton, J. G., Cragnolini, T., Kaleel, M., Mulvaney, T., Sweeney, A., & Topf, M. (2022) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1642 · Cited by 11 · see citing works
AAnchor: CNN guided detection of anchor amino acids in high resolution cryo-EM density maps
Rozanov, M., & Wolfson, H. J. (2018) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm.2018.8621288 · Cited by 12 · see citing works
Advancing structure modeling from cryo-EM maps with deep learning
Li, S., Terashi, G., Zhang, Z., & Kihara, D. (2025) · Biochemical Society Transactions · doi:10.1042/bst20240784 · Cited by 14 · see citing works
Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps
Kim, D. N., Gront, D., & Sanbonmatsu, K. Y. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00090 · Cited by 12 · see citing works
Wang, F., Banerjee, V., Barria, C., Ramírez, S., Allison, T., Gorski, D., Evans, H., Nguyen, Q., Harrison, D., Al‐Lahham, R., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-66146-4 · Cited by 11 · see citing works
Zhang, Q., Gao, Y., Baker, M. L., Liu, S., Jia, X., Xu, H., He, J., Kaelber, J. T., Weng, S., & Jiang, W. (2023) · PLoS Pathogens · doi:10.1371/journal.ppat.1011341 · Cited by 9 · see citing works
Hryc, C. F., & Baker, M. L. (2022) · Biomolecules · doi:10.3390/biom12060773 · Cited by 9 · see citing works
Wang, Y., Shekhar, M., Thifault, D., Williams, C. J., McGreevy, R., Richardson, J. S., Singharoy, A., & Tajkhorshid, E. (2018) · Journal of Structural Biology · doi:10.1016/j.jsb.2018.08.003 · Cited by 9 · see citing works
Improved model building for cryo-EM maps using local attention and 3D rotary position embeddingPreprint
Su, B., Huang, K., Peng, Z., Amunts, A., & Yang, J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.13.623164 · Cited by 8 · see citing works
Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge
Terwilliger, T. C., Adams, P. D., Afonine, P. V., & Sobolev, O. V. (2018) · Journal of Structural Biology · doi:10.1016/j.jsb.2018.07.016 · Cited by 7 · see citing works
Deciphering Protein Secondary Structures and Nucleic Acids in Cryo-EM Maps Using Deep Learning
Cao, H., He, J., Li, T., & Huang, S. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c01971 · Cited by 7 · see citing works
Miyashita, O., & Tama, F. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102653 · Cited by 5 · see citing works
SEGEM: a Fast and Accurate Automated Protein Backbone Structure Modeling Method for Cryo-EM
Chen, S., Zhang, S., Li, X., Liu, Y., & Yang, Y. (2021) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm52615.2021.9669647 · Cited by 4 · see citing works
Protein Structure Modeling from Cryo-EM Map Using MAINMAST and MAINMAST-GUI Plugin
Terashi, G., Zha, Y., & Kihara, D. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0708-4_19 · Cited by 4 · see citing works
Zhang, C., Condon, A., & Duc, K. D. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf322 · Cited by 3 · see citing works
Yamamori, Y., & Tomii, K. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23041977 · Cited by 3 · see citing works
Deep Learning for Assignment of Protein Secondary Structure Elements from Cɑ Coordinates
Nasr, K. A., Sekmen, A., Bilgin, B., Jones, C., & Koku, A. B. (2021) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm52615.2021.9669538 · Cited by 3 · see citing works
Full-length de novo protein structure determination from cryo-EM maps using deep learningPreprint
He, J., & Huang, S.-Y. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.28.271981 · Cited by 3 · see citing works
SegmA: Residue Segmentation of cryo-EM density maps
Rozanov, M., & Wolfson, H. J. (2023) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm58861.2023.10385980 · Cited by 2 · see citing works
Sekmen, A., Nasr, K. A., Bilgin, B., Koku, A. B., & Jones, C. (2023) · Biomolecules · doi:10.3390/biom13060923 · Cited by 2 · see citing works
Subspace Modeling for Classification of Protein Secondary Structure Elements from Cα Trace
Sekmen, A., Nasr, K. A., & Jones, C. (2021) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm52615.2021.9669762 · Cited by 2 · see citing works
Wang, X., Alnabati, E., Aderinwale, T. W., Subramaniya, S. R. M. V., Terashi, G., & Kihara, D. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.22.262675 · Cited by 2 · see citing works
DeepCryoRNA: deep learning-based RNA structure reconstruction from cryo-EM mapsPreprint
Li, J., & Chen, S. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.05.647396 · Cited by 2 · see citing works
Accurate Macromolecular Complex Modeling for Cryo-EM with CryoZetaPreprint
Zhang, Z., Li, S., Farheen, F., Kagaya, Y., Liu, B., Ibtehaz, N., Terashi, G., Nakamura, T., Zhu, H., Khan, K., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.13.705846 · Cited by 3 · see citing works
Application of conformational space annealing to the protein structure modeling using cryo‐EM maps
Park, J., Joung, I., Joo, K., & Lee, J. (2023) · Journal of Computational Chemistry · doi:10.1002/jcc.27200 · Cited by 1 · see citing works
Deep learning–based postprocessing and model building for cryo-electron microscopy maps
Li, T., & Huang, S. (2025) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2025.103196 · Cited by 1 · see citing works
Role of artificial intelligence in advancing cryo electron microscopy
Borar, P., & Polley, S. (2026) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2026.01.030 · Cited by 1 · see citing works
Connecting the dots: deep learning-based automated model building methods in cryo-EM
Bansia, H., & des Georges, A. (2026) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2025.1613399 · Cited by 2 · see citing works
Li, B. (2018) · ProQuest Demo Repository
Waugh, D. S., & Lountos, G. T. (2020) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.736739195.793573835
Alshammari, M., Wriggers, W. R., Sun, J., et al. (2022) · QRB Discovery · doi:10.1017/qrd.2022.13.pr4
Alshammari, M., Wriggers, W. R., Sun, J., et al. (2022) · QRB Discovery · doi:10.1017/qrd.2022.13.pr5
Alshammari, M., Wriggers, W. R., Sun, J., et al. (2022) · QRB Discovery · doi:10.1017/qrd.2022.13.pr3
Alshammari, M., Wriggers, W. R., Sun, J., et al. (2022) · QRB Discovery · doi:10.1017/qrd.2022.13.pr2
Alshammari, M., Wriggers, W. R., Sun, J., et al. (2022) · QRB Discovery · doi:10.1017/qrd.2022.13.pr1
Deep Learning Approach to Identify Protein’s Secondary Structure Elements
Bataineh, M. H., Nasr, K. A., Mu, R. R., & Alamri, M. (2024) · Lecture notes in computer science · doi:10.1007/978-981-97-5128-0_38
Zhang, C., Condon, A., & Duc, K. D. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.03.02.641021
Liu, H., Wu, Y., Zhang, W., Xu, H., Guo, Z., Meng, F., Men, X., & Guo, A. C. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.05.657588
Computational Approaches for Protein–DNA/RNA Complex Modeling for Cryo‐EM Maps
Jain, A., Cao, K., & Kihara, D. (2026) · Current Protocols · doi:10.1002/cpz1.70409
- Authors
- Chen, M., Baldwin, P. R., Ludtke, S. J., & Baker, M. L.
- Affiliations
- Baylor College of Medicine (US)
- Corresponding author
- Baker, Matthew L.
- Venue
- Journal of Structural Biology
- Publisher
- Elsevier BV
- Published
- 2016-12
- Volume
- 196
- Issue
- 3
- Pages
- 289-298
- ISSN
- 1047-8477 (ISSN-L)
- PMC
- PMC5118137
- OpenAlex
- W2506310782
- Cited by
- 82
- References
- 50
- Citations by year
- 2026: 4 · 2025: 9 · 2024: 3 · 2023: 10 · 2022: 11 · 2021: 11 · 2020: 10 · 2019: 9 · 2018: 9 · 2017: 5 · 2016: 1
- FWCI
- 4.18
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (am, 351 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Journal of Structural Biology (acceptedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (R01GM080139, P41GM103832, R01GM079429, R21GM100229)
- National Science Foundation (DBI-1408887)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- cryo-EM density maps, near-atomic resolution, traveling salesman problem
- MeSH terms
- Algorithms, Models, Molecular, Protein Conformation, Proteins, Software, Protein Structure, Secondary, Cryoelectron Microscopy
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
