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% 28665412
@Article{khoshouei2017,
Author="Khoshouei, M. and Radjainia, M. and Baumeister, W. and Danev, R. ",
Title="{{C}ryo-{E}{M} structure of haemoglobin at 3.2 Å determined with the {V}olta phase plate}",
Journal="Nat Commun",
Year="2017",
Volume="8",
Pages="16099",
Month="Jun"
}
@Article{perutz1960,
Author="Perutz, M. F. and Rossmann, M. G. and Cullis, A. F. and Muirhead, H. and Will, G. and North, A. C. ",
Title="{{S}tructure of haemoglobin: a three-dimensional {F}ourier synthesis at 5.5-{A}. resolution, obtained by {X}-ray analysis}",
Journal="Nature",
Year="1960",
Volume="185",
Number="4711",
Pages="416--422",
Month="Feb"
}
@Article{martinez2020,
title={{I}ntegration of {C}ryo-{E}{M} {M}odel {B}uilding {S}oftware in {S}cipion},
author={Mart{\'\i}nez, M. and Jim{\'e}nez-Moreno, A. and Maluenda, D. and Ram{\'\i}rez-Aportela, E. and Melero, R. and Cuervo, A. and Conesa, P. and DelCano, L. and Fonseca, Y.C. and Sanchez-Garc{\'\i}a, R. and Strelak, D. and Conesa, J.J. and Fernandez-Gim{\'e}nez, E. and de Isidro, F. and Sorzano, C.O.S. and Carazo, J.M. and Marabini, R. },
journal={J Chem Inf Model},
volume={60},
number={5},
pages={2533--2540},
year={2020},
}
@Article{vilas2018,
title={MonoRes: automatic and accurate estimation of local resolution for electron microscopy maps},
author={Vilas, Jose Luis and G{\'o}mez-Blanco, Josu{\'e} and Conesa, Pablo and Melero, Roberto and de la Rosa-Trev{\'\i}n, Jos{\'e} Miguel and Ot{\'o}n, Joaquin and Cuenca, Jes{\'u}s and Marabini, Roberto and Carazo, Jos{\'e} Mar{\'\i}a and Vargas, Javier and others},
journal={Structure},
volume={26},
number={2},
pages={337--344},
year={2018},
publisher={Elsevier}
}
@Article {Sanchez-Garcia2020.06.12.148296,
author = {Sanchez-Garcia, R and Gomez-Blanco, J and Cuervo, A and Carazo, JM and Sorzano, COS and Vargas, J},
title = {DeepEMhancer: a deep learning solution for cryo-EM volume post-processing},
elocation-id = {2020.06.12.148296},
year = {2020},
doi = {10.1101/2020.06.12.148296},
publisher = {Cold Spring Harbor Laboratory},
abstract = {Cryo-EM maps are valuable sources of information for protein structure modeling. However, due to the loss of contrast at high frequencies, they generally need to be post-processed to improve their interpretability. Most popular approaches, based on B-factor correction, suffer from limitations. For instance, they ignore the heterogeneity in the map local quality that reconstructions tend to exhibit. Aiming to overcome these problems, we present DeepEMhancer, a deep learning approach designed to perform automatic post-processing of cryo-EM maps. Trained on a dataset of pairs of experimental maps and maps sharpened using their respective atomic models, DeepEMhancer has learned how to post-process experimental maps performing masking-like and sharpening-like operations in a single step. DeepEMhancer was evaluated on a testing set of 20 different experimental maps, showing its ability to obtain much cleaner and more detailed versions of the experimental maps. Additionally, we illustrated the benefits of DeepEMhancer on the structure of the SARS-CoV-2 RNA polymerase.Competing Interest StatementThe authors have declared no competing interest.},
URL = {https://www.biorxiv.org/content/early/2020/08/17/2020.06.12.148296},
eprint = {https://www.biorxiv.org/content/early/2020/08/17/2020.06.12.148296.full.pdf},
journal = {bioRxiv}
}
@Article {ramirez2018,
author = {Ram{\'\i}rez-Aportela, Erney and Vilas, Jose Luis and Melero, Roberto and Conesa, Pablo and Mart{\'\i}nez, Marta and Maluenda, David and Mota, Javier and Jim{\'e}nez, Amaya and Vargas, Javier and Marabini, Roberto and Carazo, Jose Maria and Sorzano, Carlos Oscar S.},
title = {Automatic local resolution-based sharpening of cryo-EM maps},
elocation-id = {433284},
year = {2018},
doi = {10.1101/433284},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2018/10/02/433284},
eprint = {https://www.biorxiv.org/content/early/2018/10/02/433284.full.pdf},
journal = {bioRxiv}
}
@Article{Goddard2018,
Author="Goddard, T. D. and Huang, C. C. and Meng, E. C. and Pettersen, E. F. and Couch, G. S. and Morris, J. H. and Ferrin, T. E. ",
Title="{{U}{C}{S}{F} {C}himera{X}: {M}eeting modern challenges in visualization and analysis}",
Journal="Protein Sci.",
Year="2018",
Volume="27",
Number="1",
Pages="14--25",
Month="01"
}
@Article{pearson2013,
Author="Pearson, W. R. ",
Title="{{A}n introduction to sequence similarity ("homology") searching}",
Journal="Curr Protoc Bioinformatics",
Year="2013",
Volume="Chapter 3",
Pages="Unit3.1",
Month="Jun"
}
@Article{kryshtafovych2018,
Author="Kryshtafovych, A. and Monastyrskyy, B. and Fidelis, K. and Moult, J. and Schwede, T. and Tramontano, A. ",
Title="{{E}valuation of the template-based modeling in {C}{A}{S}{P}12}",
Journal="Proteins",
Year="2018",
Volume="86 Suppl 1",
Pages="321--334",
Month="Mar"
}
@Article{altschul1997,
Author="Altschul, S. F. and Madden, T. L. and Schaffer, A. A. and Zhang, J. and Zhang, Z. and Miller, W. and Lipman, D. J. ",
Title="{{G}apped {B}{L}{A}{S}{T} and {P}{S}{I}-{B}{L}{A}{S}{T}: a new generation of protein database search programs}",
Journal="Nucleic Acids Res.",
Year="1997",
Volume="25",
Number="17",
Pages="3389--3402",
Month="Sep"
}
@Article{camardella1992,
Author="Camardella, L. and Caruso, C. and D'Avino, R. and di Prisco, G. and Rutigliano, B. and Tamburrini, M. and Fermi, G. and Perutz, M. F. ",
Title="{{H}aemoglobin of the antarctic fish {P}agothenia bernacchii. {A}mino acid sequence, oxygen equilibria and crystal structure of its carbonmonoxy derivative}",
Journal="J. Mol. Biol.",
Year="1992",
Volume="224",
Number="2",
Pages="449--460",
Month="Mar"
}
@Article{sali1993,
Author="Sali, A. and Blundell, T. L. ",
Title="{{C}omparative protein modelling by satisfaction of spatial restraints}",
Journal="J. Mol. Biol.",
Year="1993",
Volume="234",
Number="3",
Pages="779--815",
Month="Dec"
}
@Article{Liebschner2019,
Author="Liebschner, D. and Afonine, P. V. and Baker, M. L. and Bunk?czi, G. and Chen, V. B. and Croll, T. I. and Hintze, B. and Hung, L. W. and Jain, S. and McCoy, A. J. and Moriarty, N. W. and Oeffner, R. D. and Poon, B. K. and Prisant, M. G. and Read, R. J. and Richardson, J. S. and Richardson, D. C. and Sammito, M. D. and Sobolev, O. V. and Stockwell, D. H. and Terwilliger, T. C. and Urzhumtsev, A. G. and Videau, L. L. and Williams, C. J. and Adams, P. D. ",
Title="{{M}acromolecular structure determination using {X}-rays, neutrons and electrons: recent developments in {P}henix}",
Journal="Acta Crystallogr D Struct Biol",
Year="2019",
Volume="75",
Number="Pt 10",
Pages="861--877",
Month="Oct"
}
@Article{emsley2010,
Author="Emsley, P. and Lohkamp, B. and Scott, W. G. and Cowtan, K. ",
Title="{{F}eatures and development of {C}oot}",
Journal="Acta Crystallogr. D Biol. Crystallogr.",
Year="2010",
Volume="66",
Number="Pt 4",
Pages="486--501",
Month="Apr"
}
@Article{afonine2018a,
author = "Afonine, Pavel V. and Poon, Billy K. and Read, Randy J. and Sobolev, Oleg V. and Terwilliger, Thomas C. and Urzhumtsev, Alexandre and Adams, Paul D.",
title = "{Real-space refinement in {\it PHENIX} for cryo-EM and crystallography}",
journal = "Acta Crystallographica Section D",
year = "2018",
volume = "74",
number = "6",
pages = "531--544",
month = "Jun",
doi = {10.1107/S2059798318006551},
url = {https://doi.org/10.1107/S2059798318006551},
abstract = {This article describes the implementation of real-space refinement in the {\it phenix.real_space_refine} program from the {\it PHENIX} suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, {\it phenix.real_space_refine} makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6{\AA} or better shows significant improvement of the models and of the fit of these models to the target maps.},
keywords = {real-space refinement, cryo-EM, crystallography, map interpolation, atomic-centered targets, PHENIX},
}
@Article{vagin2004,
Author="Vagin, A. A. and Steiner, R. A. and Lebedev, A. A. and Potterton, L. and McNicholas, S. and Long, F. and Murshudov, G. N. ",
Title="{{R}{E}{F}{M}{A}{C}5 dictionary: organization of prior chemical knowledge and guidelines for its use}",
Journal="Acta Crystallogr. D Biol. Crystallogr.",
Year="2004",
Volume="60",
Number="Pt 12 Pt 1",
Pages="2184--2195",
Month="Dec"
}
@Article{barad2015,
Author="Barad, B. A. and Echols, N. and Wang, R. Y. and Cheng, Y. and DiMaio, F. and Adams, P. D. and Fraser, J. S. ",
Title="{{E}{M}{R}inger: side chain-directed model and map validation for 3{D} cryo-electron microscopy}",
Journal="Nat. Methods",
Year="2015",
Volume="12",
Number="10",
Pages="943--946",
Month="Oct"
}
@Article{davis2004,
Author="Davis, I. W. and Murray, L. W. and Richardson, J. S. and Richardson, D. C. ",
Title="{{M}{O}{L}{P}{R}{O}{B}{I}{T}{Y}: structure validation and all-atom contact analysis for nucleic acids and their complexes}",
Journal="Nucleic Acids Res.",
Year="2004",
Volume="32",
Number="Web Server issue",
Pages="W615--619",
Month="Jul"
}
@Article{afonine2018b,
Author="Afonine, P. V. and Klaholz, B. P. and Moriarty, N. W. and Poon, B. K. and Sobolev, O. V. and Terwilliger, T. C. and Adams, P. D. and Urzhumtsev, A. ",
Title="{{N}ew tools for the analysis and validation of cryo-{E}{M} maps and atomic models}",
Journal="Acta Crystallogr D Struct Biol",
Year="2018",
Volume="74",
Number="Pt 9",
Pages="814--840",
Month="Sep"
}
@Misc{zwartUrl,
Author = "Zwart, P. and Afonine, P. and Grosse-Kunstleve, R.W.",
Title = "Superimposing two {P}{D}{B} files with superpose\_pdbs",
Year = "2017",
Note = "\url{https://www.phenix-online.org/documentation/reference/superpose_pdbs.html}, Accessed: 2018-10-31"
}
@Article{williams2018,
Author="Williams, C. J. and Headd, J. J. and Moriarty, N. W. and Prisant, M. G. and Videau, L. L. and Deis, L. N. and Verma, V. and Keedy, D. A. and Hintze, B. J. and Chen, V. B. and Jain, S. and Lewis, S. M. and Arendall, W. B. and Snoeyink, J. and Adams, P. D. and Lovell, S. C. and Richardson, J. S. and Richardson, D. C. ",
Title="{M}ol{P}robity: {M}ore and better reference data for improved all-atom structure validation",
Journal="Protein Sci.",
Year="2018",
Volume="27",
Number="1",
Pages="293--315",
Month="01"
}
@Article{PerezIllana2021,
Author="Pérez-Illana, M. and Martínez, M. and Condezo, G. N. and Hernando-Pérez, M. and Mangroo, C. and Brown, M. and Marabini, R. and San Martín, C. ",
Title="{{C}ryo-{E}{M} structure of enteric adenovirus {H}{A}d{V}-{F}41 highlights structural variations among human adenoviruses}",
Journal="Sci Adv",
Year="2021",
Volume="7",
Number="9",
Month="02"
}
@Article{brown2015,
Author="Brown, A. and Long, F. and Nicholls, R. A. and Toots, J. and Emsley, P. and Murshudov, G. ",
Title="{{T}ools for macromolecular model building and refinement into electron cryo-microscopy reconstructions}",
Journal="Acta Crystallogr. D Biol. Crystallogr.",
Year="2015",
Volume="71",
Number="Pt 1",
Pages="136--153",
Month="Jan"
}
@Article{kovalevskiy2018,
Author="Kovalevskiy, O. and Nicholls, R. A. and Long, F. and Carlon, A. and Murshudov, G. N. ",
Title="{{O}verview of refinement procedures within {R}{E}{F}{M}{A}{C}5: utilizing data from different sources}",
Journal="Acta Crystallogr D Struct Biol",
Year="2018",
Volume="74",
Number="Pt 3",
Pages="215--227",
Month="03"
}
% 35235791
@Article{tacan,
Author="Chen, X. and Wang, Y. and Li, Y. and Lu, X. and Chen, J. and Li, M. and Wen, T. and Liu, N. and Chang, S. and Zhang, X. and Yang, X. and Shen, Y. ",
Title="{{C}ryo-{E}{M} structure of the human {T}{A}{C}{A}{N} in a closed state}",
Journal="Cell Rep",
Year="2022",
Volume="38",
Number="9",
Pages="110445",
Month="03"
}
% alphafold
% 31693199
@Article{alphafold,
Author="Heo, L. and Feig, M. ",
Title="{{H}igh-accuracy protein structures by combining machine-learning with physics-based refinement}",
Journal="Proteins",
Year="2020",
Volume="88",
Number="5",
Pages="637--642",
Month="05"
}
% 34265844
@Article{jumper2021,
Author="Jumper, J. and Evans, R. and Pritzel, A. and Green, T. and Figurnov, M. and Ronneberger, O. and Tunyasuvunakool, K. and Bates, R. and Žídek, A. and Potapenko, A. and Bridgland, A. and Meyer, C. and Kohl, S. A. A. and Ballard, A. J. and Cowie, A. and Romera-Paredes, B. and Nikolov, S. and Jain, R. and Adler, J. and Back, T. and Petersen, S. and Reiman, D. and Clancy, E. and Zielinski, M. and Steinegger, M. and Pacholska, M. and Berghammer, T. and Bodenstein, S. and Silver, D. and Vinyals, O. and Senior, A. W. and Kavukcuoglu, K. and Kohli, P. and Hassabis, D. ",
Title="{{H}ighly accurate protein structure prediction with {A}lpha{F}old}",
Journal="Nature",
Year="2021",
Volume="596",
Number="7873",
Pages="583--589",
Month="08"
}
% 34282049
@Article{baek2021,
Author="Baek, M. and DiMaio, F. and Anishchenko, I. and Dauparas, J. and Ovchinnikov, S. and Lee, G. R. and Wang, J. and Cong, Q. and Kinch, L. N. and Schaeffer, R. D. and Millán, C. and Park, H. and Adams, C. and Glassman, C. R. and DeGiovanni, A. and Pereira, J. H. and Rodrigues, A. V. and van Dijk, A. A. and Ebrecht, A. C. and Opperman, D. J. and Sagmeister, T. and Buhlheller, C. and Pavkov-Keller, T. and Rathinaswamy, M. K. and Dalwadi, U. and Yip, C. K. and Burke, J. E. and Garcia, K. C. and Grishin, N. V. and Adams, P. D. and Read, R. J. and Baker, D. ",
Title="{{A}ccurate prediction of protein structures and interactions using a three-track neural network}",
Journal="Science",
Year="2021",
Volume="373",
Number="6557",
Pages="871--876",
Month="08"
}
% 34409941
@Article{rong2021,
Author="Rong, Y. and Jiang, J. and Gao, Y. and Guo, J. and Song, D. and Liu, W. and Zhang, M. and Zhao, Y. and Xiao, B. and Liu, Z. ",
Title="{{T}{M}{E}{M}120{A} contains a specific coenzyme {A}-binding site and might not mediate poking- or stretch-induced channel activities in cells}",
Journal="Elife",
Year="2021",
Volume="10",
Month="08"
}
% 34374645
@Article{xue2021,
Author="Xue, J. and Han, Y. and Baniasadi, H. and Zeng, W. and Pei, J. and Grishin, N. V. and Wang, J. and Tu, B. P. and Jiang, Y. ",
Title="{{T}{M}{E}{M}120{A} is a coenzyme {A}-binding membrane protein with structural similarities to {E}{L}{O}{V}{L} fatty acid elongase}",
Journal="Elife",
Year="2021",
Volume="10",
Month="08"
}
% 35235791
@Article{chen2022,
Author="Chen, X. and Wang, Y. and Li, Y. and Lu, X. and Chen, J. and Li, M. and Wen, T. and Liu, N. and Chang, S. and Zhang, X. and Yang, X. and Shen, Y. ",
Title="{{C}ryo-{E}{M} structure of the human {T}{A}{C}{A}{N} in a closed state}",
Journal="Cell Rep",
Year="2022",
Volume="38",
Number="9",
Pages="110445",
Month="03"
}
@Article {AlphaFold-Multimer2021,
Author="Evans, R. and O'Neill, Michael and Pritzel, Alexander and Antropova, Natasha and Senior, Andrew and Green, Tim and {\v{Z}}{\'\i}dek, Augustin and Bates, Russ and Blackwell, Sam and Yim, Jason and Ronneberger, Olaf and Bodenstein, Sebastian and Zielinski, Michal and Bridgland, Alex and Potapenko, Anna and Cowie, Andrew and Tunyasuvunakool, Kathryn and Jain, Rishub and Clancy, Ellen and Kohli, Pushmeet and Jumper, John and Hassabis, Demis",
Title="{{P}rotein complex prediction with {A}lpha{F}old-{M}ultimer}",
Journal="bioRxiv",
Year="2021",
elocation-id={2021.10.04.463034},
doi="10.1101/2021.10.04.463034",
URL="https://www.biorxiv.org/content/early/2021/10/04/2021.10.04.463034",
eprint="https://www.biorxiv.org/content/early/2021/10/04/2021.10.04.463034.full.pdf",
}@inproceedings{
jamali2023modelangelo,
title={A Graph Neural Network Approach to Automated Model Building in Cryo-EM Maps},
author={Kiarash Jamali and Dari Kimanius and Sjors HW Scheres},
booktitle={International Conference on Learning Representations},
year={2023},
url={https://openreview.net/forum?id=65XDF_nwI61}
}