Namdinator – automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps
Model building into experimental maps is a key element of structural biology, but can be both time consuming and error prone for low-resolution maps. Here we present Namdinator , an easy-to-use tool that enables the user to run a molecular dynamics flexible fitting simulation followed by real-space...
Uložené v:
| Vydané v: | IUCrJ Ročník 6; číslo 4; s. 526 - 531 |
|---|---|
| Hlavní autori: | , , , , , |
| Médium: | Journal Article |
| Jazyk: | English |
| Vydavateľské údaje: |
England
International Union of Crystallography
01.07.2019
|
| Predmet: | |
| ISSN: | 2052-2525, 2052-2525 |
| On-line prístup: | Získať plný text |
| Tagy: |
Pridať tag
Žiadne tagy, Buďte prvý, kto otaguje tento záznam!
|
| Abstract | Model building into experimental maps is a key element of structural biology, but can be both time consuming and error prone for low-resolution maps. Here we present
Namdinator
, an easy-to-use tool that enables the user to run a molecular dynamics flexible fitting simulation followed by real-space refinement in an automated manner through a pipeline system.
Namdinator
will modify an atomic model to fit within cryo-EM or crystallography density maps, and can be used advantageously for both the initial fitting of models, and for a geometrical optimization step to correct outliers, clashes and other model problems. We have benchmarked
Namdinator
against 39 deposited cryo-EM models and maps, and observe model improvements in 34 of these cases (87%). Clashes between atoms were reduced, and the model-to-map fit and overall model geometry were improved, in several cases substantially. We show that
Namdinator
is able to model large-scale conformational changes compared to the starting model.
Namdinator
is a fast and easy tool for structural model builders at all skill levels.
Namdinator
is available as a web service (https://namdinator.au.dk), or it can be run locally as a command-line tool. |
|---|---|
| AbstractList | A pipeline tool called Namdinator is presented that enables the user to run a molecular dynamics flexible fitting (MDFF) simulation in a fully automated manner, online or locally. This provides a fast and easy way to create suitable initial models for both cryo-EM and crystallography, and help fix errors in the final steps of model building. Model building into experimental maps is a key element of structural biology, but can be both time consuming and error prone for low-resolution maps. Here we present Namdinator, an easy-to-use tool that enables the user to run a molecular dynamics flexible fitting simulation followed by real-space refinement in an automated manner through a pipeline system. Namdinator will modify an atomic model to fit within cryo-EM or crystallography density maps, and can be used advantageously for both the initial fitting of models, and for a geometrical optimization step to correct outliers, clashes and other model problems. We have benchmarked Namdinator against 39 deposited cryo-EM models and maps, and observe model improvements in 34 of these cases (87%). Clashes between atoms were reduced, and the model-to-map fit and overall model geometry were improved, in several cases substantially. We show that Namdinator is able to model large-scale conformational changes compared to the starting model. Namdinator is a fast and easy tool for structural model builders at all skill levels. Namdinator is available as a web service (https://namdinator.au.dk), or it can be run locally as a command-line tool. Model building into experimental maps is a key element of structural biology, but can be both time consuming and error prone for low-resolution maps. Here we present Namdinator, an easy-to-use tool that enables the user to run a molecular dynamics flexible fitting simulation followed by real-space refinement in an automated manner through a pipeline system. Namdinator will modify an atomic model to fit within cryo-EM or crystallography density maps, and can be used advantageously for both the initial fitting of models, and for a geometrical optimization step to correct outliers, clashes and other model problems. We have benchmarked Namdinator against 39 deposited cryo-EM models and maps, and observe model improvements in 34 of these cases (87%). Clashes between atoms were reduced, and the model-to-map fit and overall model geometry were improved, in several cases substantially. We show that Namdinator is able to model large-scale conformational changes compared to the starting model. Namdinator is a fast and easy tool for structural model builders at all skill levels. Namdinator is available as a web service (https://namdinator.au.dk), or it can be run locally as a command-line tool.Model building into experimental maps is a key element of structural biology, but can be both time consuming and error prone for low-resolution maps. Here we present Namdinator, an easy-to-use tool that enables the user to run a molecular dynamics flexible fitting simulation followed by real-space refinement in an automated manner through a pipeline system. Namdinator will modify an atomic model to fit within cryo-EM or crystallography density maps, and can be used advantageously for both the initial fitting of models, and for a geometrical optimization step to correct outliers, clashes and other model problems. We have benchmarked Namdinator against 39 deposited cryo-EM models and maps, and observe model improvements in 34 of these cases (87%). Clashes between atoms were reduced, and the model-to-map fit and overall model geometry were improved, in several cases substantially. We show that Namdinator is able to model large-scale conformational changes compared to the starting model. Namdinator is a fast and easy tool for structural model builders at all skill levels. Namdinator is available as a web service (https://namdinator.au.dk), or it can be run locally as a command-line tool. Model building into experimental maps is a key element of structural biology, but can be both time consuming and error prone for low-resolution maps. Here we present Namdinator, an easy-to-use tool that enables the user to run a molecular dynamics flexible fitting simulation followed by real-space refinement in an automated manner through a pipeline system. Namdinator will modify an atomic model to fit within cryo-EM or crystallography density maps, and can be used advantageously for both the initial fitting of models, and for a geometrical optimization step to correct outliers, clashes and other model problems. We have benchmarked Namdinator against 39 deposited cryo-EM models and maps, and observe model improvements in 34 of these cases (87%). Clashes between atoms were reduced, and the model-to-map fit and overall model geometry were improved, in several cases substantially. We show that Namdinator is able to model large-scale conformational changes compared to the starting model. Namdinator is a fast and easy tool for structural model builders at all skill levels. Namdinator is available as a web service (https://namdinator.au.dk), or it can be run locally as a command-line tool. Model building into experimental maps is a key element of structural biology, but can be both time consuming and error prone for low-resolution maps. Here we present , an easy-to-use tool that enables the user to run a molecular dynamics flexible fitting simulation followed by real-space refinement in an automated manner through a pipeline system. will modify an atomic model to fit within cryo-EM or crystallography density maps, and can be used advantageously for both the initial fitting of models, and for a geometrical optimization step to correct outliers, clashes and other model problems. We have benchmarked against 39 deposited cryo-EM models and maps, and observe model improvements in 34 of these cases (87%). Clashes between atoms were reduced, and the model-to-map fit and overall model geometry were improved, in several cases substantially. We show that is able to model large-scale conformational changes compared to the starting model. is a fast and easy tool for structural model builders at all skill levels. is available as a web service (https://namdinator.au.dk), or it can be run locally as a command-line tool. Model building into experimental maps is a key element of structural biology, but can be both time consuming and error prone for low-resolution maps. Here we present Namdinator , an easy-to-use tool that enables the user to run a molecular dynamics flexible fitting simulation followed by real-space refinement in an automated manner through a pipeline system. Namdinator will modify an atomic model to fit within cryo-EM or crystallography density maps, and can be used advantageously for both the initial fitting of models, and for a geometrical optimization step to correct outliers, clashes and other model problems. We have benchmarked Namdinator against 39 deposited cryo-EM models and maps, and observe model improvements in 34 of these cases (87%). Clashes between atoms were reduced, and the model-to-map fit and overall model geometry were improved, in several cases substantially. We show that Namdinator is able to model large-scale conformational changes compared to the starting model. Namdinator is a fast and easy tool for structural model builders at all skill levels. Namdinator is available as a web service (https://namdinator.au.dk), or it can be run locally as a command-line tool. |
| Author | Karlsen, Jesper Lykkegaard Juhl, Jonathan Nissen, Poul Boesen, Thomas Pedersen, Bjørn Panyella Kidmose, Rune Thomas |
| Author_xml | – sequence: 1 givenname: Rune Thomas orcidid: 0000-0001-9699-2494 surname: Kidmose fullname: Kidmose, Rune Thomas – sequence: 2 givenname: Jonathan orcidid: 0000-0001-5076-0321 surname: Juhl fullname: Juhl, Jonathan – sequence: 3 givenname: Poul orcidid: 0000-0003-0948-6628 surname: Nissen fullname: Nissen, Poul – sequence: 4 givenname: Thomas orcidid: 0000-0002-5633-6844 surname: Boesen fullname: Boesen, Thomas – sequence: 5 givenname: Jesper Lykkegaard orcidid: 0000-0002-3146-2414 surname: Karlsen fullname: Karlsen, Jesper Lykkegaard – sequence: 6 givenname: Bjørn Panyella orcidid: 0000-0001-7860-7230 surname: Pedersen fullname: Pedersen, Bjørn Panyella |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/31316797$$D View this record in MEDLINE/PubMed |
| BookMark | eNp9ks9u1DAQxi1URMvSB-CCLHHhEvCfOI4vSKgqUKnAAThHE9vZeuXEi-2g7o0Db8Ab8iQ43VK1ReLk0fj3fZ4Zz2N0MIXJIvSUkpeUEvnqMyOCMcEEVYTIhqoH6GhJVUvu4FZ8iI5T2hBCKGVC1vQROuSU00YqeYR-foTRuAlyiPj3j18Y5hxGyE7jMXirZw8Rm90Eo9MJD95eut5bPLic3bTGYcApx1nnOYIvCmN9wm7KAeu4C9XpBwyTWeKUwfuwjrC92GF7ubXRjXbKiwi26Ql6OIBP9vj6XKGvb0-_nLyvzj-9Ozt5c17pWvFcgahbrUHaVjHOyGCZ4H0t6tpazkzTMz1AS8BQTqCWUmpeA221JVIKM4DlK3S29zUBNt221ABx1wVw3VUixHUHsfTubdcw01MpiCBM1AJIL5XSTQNcGC14eXiFXu-9tnM_WqNLN2UGd0zv3kzuoluH713TkLa5MnhxbRDDt9mm3I0uaes9TDbMqSt_qxSlrWgK-vweuglznMqoClUr1XIh20I9u13RTSl_P7sAdA_oGFKKdrhBKOmWner-2amikfc02uWyH2Fpyvn_KP8AU1HR0A |
| CitedBy_id | crossref_primary_10_1371_journal_ppat_1010583 crossref_primary_10_1016_j_str_2020_12_008 crossref_primary_10_1038_s41467_025_63451_w crossref_primary_10_1038_s41586_020_2772_0 crossref_primary_10_1002_wcms_1542 crossref_primary_10_1016_j_molcel_2022_04_027 crossref_primary_10_1042_BST20210674 crossref_primary_10_1016_j_celrep_2025_116061 crossref_primary_10_1038_s41594_022_00912_6 crossref_primary_10_1073_pnas_2312276120 crossref_primary_10_1371_journal_pcbi_1013367 crossref_primary_10_1038_s41467_024_47174_y crossref_primary_10_7554_eLife_92307 crossref_primary_10_1038_s41586_025_08896_1 crossref_primary_10_1038_s41594_025_01543_3 crossref_primary_10_1126_science_abk0154 crossref_primary_10_1038_s44298_025_00112_1 crossref_primary_10_1038_s41586_024_07601_y crossref_primary_10_7554_eLife_86784 crossref_primary_10_1038_s41586_024_07814_1 crossref_primary_10_1038_s41586_019_1344_7 crossref_primary_10_1038_s41467_022_31068_y crossref_primary_10_15252_embj_2022112351 crossref_primary_10_1016_j_str_2022_12_014 crossref_primary_10_7554_eLife_84427_3 crossref_primary_10_1038_s41422_023_00778_3 crossref_primary_10_7554_eLife_52983 crossref_primary_10_1038_s41586_024_08337_5 crossref_primary_10_1371_journal_pone_0291131 crossref_primary_10_1016_j_cell_2024_01_005 crossref_primary_10_1038_s41467_024_48312_2 crossref_primary_10_1038_s41594_022_00799_3 crossref_primary_10_1038_s41594_024_01261_2 crossref_primary_10_1038_s41477_025_02056_z crossref_primary_10_1016_j_neuron_2021_02_009 crossref_primary_10_1126_science_abg3074 crossref_primary_10_3389_fimmu_2023_1111385 crossref_primary_10_1038_s41594_020_00517_x crossref_primary_10_1093_nar_gkae1111 crossref_primary_10_1016_j_molcel_2021_06_019 crossref_primary_10_1073_pnas_2115849118 crossref_primary_10_1016_j_cell_2023_09_007 crossref_primary_10_1016_j_isci_2025_113314 crossref_primary_10_1038_s41467_022_33174_3 crossref_primary_10_1038_s41594_019_0364_1 crossref_primary_10_1371_journal_pgen_1011749 crossref_primary_10_15252_embj_2018100825 crossref_primary_10_7554_eLife_80901 crossref_primary_10_7554_eLife_92307_3 crossref_primary_10_1038_s41586_023_06599_z crossref_primary_10_1038_s41467_021_27881_6 crossref_primary_10_1093_nar_gkac625 crossref_primary_10_1038_s44318_024_00081_w crossref_primary_10_1038_s41589_023_01326_1 crossref_primary_10_1016_j_cell_2024_06_041 crossref_primary_10_1038_s41467_020_19456_8 crossref_primary_10_1016_j_jsb_2020_107546 crossref_primary_10_1016_j_str_2023_05_013 crossref_primary_10_1038_s41467_024_51754_3 crossref_primary_10_1073_pnas_2419732121 crossref_primary_10_1038_s41467_020_20321_x crossref_primary_10_15252_embj_2021110411 crossref_primary_10_1093_nar_gkaa456 crossref_primary_10_1016_j_jbc_2025_110686 crossref_primary_10_15252_embj_2022111857 crossref_primary_10_1038_s41422_023_00869_1 crossref_primary_10_1016_j_molcel_2022_03_007 crossref_primary_10_1038_s41594_021_00698_z crossref_primary_10_1038_s41467_022_28079_0 crossref_primary_10_1038_s41586_020_2665_2 crossref_primary_10_1016_j_cell_2021_05_012 crossref_primary_10_1038_s41467_024_48251_y crossref_primary_10_1038_s41467_020_19482_6 crossref_primary_10_1126_sciadv_adv7296 crossref_primary_10_1038_s41467_024_53773_6 crossref_primary_10_1016_j_molcel_2022_08_012 crossref_primary_10_1038_s41467_024_46864_x crossref_primary_10_1093_nar_gkaa429 crossref_primary_10_1371_journal_ppat_1011174 crossref_primary_10_1038_s41467_020_19785_8 crossref_primary_10_7554_eLife_84617 crossref_primary_10_1016_j_cub_2023_11_057 crossref_primary_10_1126_science_abe9403 crossref_primary_10_1128_jvi_01376_24 crossref_primary_10_1073_pnas_2220542120 crossref_primary_10_1186_s12951_025_03243_y crossref_primary_10_1073_pnas_2100198118 crossref_primary_10_1002_pro_5073 crossref_primary_10_1016_j_jmb_2022_167458 crossref_primary_10_1038_s41594_022_00729_3 crossref_primary_10_1038_s41477_021_00992_0 crossref_primary_10_1038_s41586_024_07813_2 crossref_primary_10_1038_s41594_023_01205_2 crossref_primary_10_7554_eLife_89755 crossref_primary_10_1016_j_str_2023_09_009 crossref_primary_10_1038_s41586_021_03650_9 crossref_primary_10_1038_s41467_020_19847_x crossref_primary_10_1016_j_devcel_2020_04_019 crossref_primary_10_1038_s42003_021_02222_x crossref_primary_10_1038_s41586_025_08773_x crossref_primary_10_1038_s41586_022_04829_4 crossref_primary_10_1038_s41594_020_0478_5 crossref_primary_10_1016_j_seta_2023_103370 crossref_primary_10_1038_s41594_024_01243_4 crossref_primary_10_1038_s41467_020_18874_y crossref_primary_10_1038_s41586_020_2087_1 crossref_primary_10_1038_s41586_022_04883_y crossref_primary_10_3390_ijms241914785 crossref_primary_10_1016_j_molcel_2020_06_032 crossref_primary_10_1016_j_molcel_2020_09_008 crossref_primary_10_1038_s41467_022_34997_w crossref_primary_10_1038_s41467_024_45242_x crossref_primary_10_1038_s41467_022_30673_1 crossref_primary_10_1038_s41467_023_36590_1 crossref_primary_10_1038_s41467_024_55171_4 crossref_primary_10_1038_s41586_021_03555_7 crossref_primary_10_1016_j_molcel_2021_07_005 crossref_primary_10_1038_s41467_022_31748_9 crossref_primary_10_1126_science_adl1356 crossref_primary_10_1038_s41594_022_00905_5 crossref_primary_10_1038_s41586_023_06691_4 crossref_primary_10_1016_j_str_2020_09_001 crossref_primary_10_1038_s41594_019_0359_y crossref_primary_10_1038_s41586_024_07287_2 crossref_primary_10_1038_s41467_025_56118_z crossref_primary_10_1073_pnas_2417370122 crossref_primary_10_7554_eLife_74175 crossref_primary_10_1038_s41596_022_00757_9 crossref_primary_10_1038_s41563_025_02295_7 crossref_primary_10_1093_nar_gkaf119 crossref_primary_10_1038_s41594_023_01010_x crossref_primary_10_1038_s41467_022_33228_6 crossref_primary_10_1038_s41586_021_03906_4 crossref_primary_10_1038_s41467_024_48759_3 crossref_primary_10_7554_eLife_86784_3 crossref_primary_10_1038_s41586_024_07347_7 crossref_primary_10_1038_s41467_025_56796_9 crossref_primary_10_1073_pnas_2315018121 crossref_primary_10_1038_s41477_025_01984_0 crossref_primary_10_1016_j_cell_2024_02_013 crossref_primary_10_1038_s41467_025_59133_2 crossref_primary_10_1016_j_molcel_2024_06_013 crossref_primary_10_1038_s41586_022_05255_2 crossref_primary_10_1016_j_cell_2022_11_014 crossref_primary_10_1038_s44319_025_00392_x crossref_primary_10_1016_j_jbc_2022_102357 crossref_primary_10_1016_j_ijbiomac_2020_01_282 crossref_primary_10_1016_j_str_2023_08_014 crossref_primary_10_7554_eLife_84427 crossref_primary_10_1016_j_molcel_2023_05_034 crossref_primary_10_1073_pnas_2502425122 crossref_primary_10_1038_s41467_025_60232_3 crossref_primary_10_1126_science_abe8526 crossref_primary_10_1038_s41564_019_0530_6 crossref_primary_10_1038_s41467_020_20735_7 crossref_primary_10_1016_j_jsb_2023_107995 crossref_primary_10_1038_s41586_019_1896_6 crossref_primary_10_1038_s41467_023_40483_8 crossref_primary_10_1038_s41467_023_40422_7 crossref_primary_10_1016_j_cell_2019_08_038 crossref_primary_10_1126_science_abq2844 crossref_primary_10_1038_s41467_022_32004_w crossref_primary_10_1038_s41564_022_01235_4 crossref_primary_10_1038_s41467_024_55772_z crossref_primary_10_1038_s41467_020_15517_0 crossref_primary_10_1038_s41467_022_33504_5 crossref_primary_10_7554_eLife_81977 crossref_primary_10_1021_acsinfecdis_5c00368 crossref_primary_10_1126_science_ady0241 crossref_primary_10_1093_nar_gkac1232 crossref_primary_10_1073_pnas_2315575121 crossref_primary_10_1038_s41586_020_2696_8 crossref_primary_10_1038_s41594_020_0468_7 crossref_primary_10_26508_lsa_202201796 crossref_primary_10_1038_s41586_023_06746_6 crossref_primary_10_7554_eLife_89755_4 crossref_primary_10_3390_molecules25010082 crossref_primary_10_1038_s41586_023_06140_2 crossref_primary_10_1038_s41467_023_36604_y crossref_primary_10_1038_s41467_025_57729_2 crossref_primary_10_1073_pnas_2110936119 crossref_primary_10_1038_s41467_025_58410_4 crossref_primary_10_1038_s41586_022_04470_1 crossref_primary_10_1128_jvi_00929_23 crossref_primary_10_1038_s41467_022_31564_1 crossref_primary_10_15252_embj_2020106807 crossref_primary_10_1038_s41467_022_32690_6 crossref_primary_10_1107_S205225252401217X crossref_primary_10_1038_s41586_020_2088_0 crossref_primary_10_1038_s41467_022_30402_8 crossref_primary_10_1016_j_molcel_2024_01_023 crossref_primary_10_7554_eLife_87167 crossref_primary_10_1038_s41467_022_33698_8 crossref_primary_10_1016_j_molcel_2020_07_013 crossref_primary_10_1038_s41586_023_05723_3 crossref_primary_10_1038_s42003_024_06437_6 crossref_primary_10_1016_j_jbc_2022_102553 crossref_primary_10_1038_s41594_024_01218_5 crossref_primary_10_1038_s41467_020_17791_4 crossref_primary_10_1038_s41467_024_47506_y crossref_primary_10_1038_s41594_023_00992_y crossref_primary_10_1016_j_molcel_2021_05_032 crossref_primary_10_15252_embj_2022112440 crossref_primary_10_1016_j_jmb_2024_168747 crossref_primary_10_1038_s41467_020_18243_9 crossref_primary_10_26508_lsa_202000858 crossref_primary_10_1016_j_cell_2024_08_044 crossref_primary_10_1038_s41467_020_14735_w crossref_primary_10_1111_jnc_16179 crossref_primary_10_1016_j_molcel_2020_07_008 crossref_primary_10_1038_s41589_025_01981_6 crossref_primary_10_7554_eLife_87167_3 crossref_primary_10_1038_s41467_024_49693_0 crossref_primary_10_1038_s41586_023_06690_5 crossref_primary_10_15252_embr_202153597 crossref_primary_10_1126_science_adn9560 crossref_primary_10_1038_s41594_023_01190_6 crossref_primary_10_1038_s41594_025_01665_8 |
| Cites_doi | 10.1016/0263-7855(96)00018-5 10.1107/S2052252519000277 10.1016/0022-2836(92)90582-5 10.1126/science.1251652 10.1016/j.cell.2015.12.055 10.1107/S2059798318009324 10.1016/S0969-2126(96)00018-4 10.1016/j.str.2012.08.007 10.1002/jcc.20289 10.1002/jcc.23354 10.1021/jp061976m 10.1038/nature24046 10.1006/jmbi.2002.5438 10.1107/S0907444909052925 10.1021/acs.jctc.7b00125 10.1016/j.str.2017.07.012 10.1039/C4FD00005F 10.1021/ct200563j 10.1016/j.ymeth.2009.04.005 10.1002/jcc.20084 10.1038/nature24627 10.1016/j.str.2008.03.005 |
| ContentType | Journal Article |
| Copyright | 2019. This article is published under https://creativecommons.org/licenses/by/4.0/ (“the License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. Rune Thomas Kidmose et al. 2019 2019 |
| Copyright_xml | – notice: 2019. This article is published under https://creativecommons.org/licenses/by/4.0/ (“the License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. – notice: Rune Thomas Kidmose et al. 2019 2019 |
| DBID | AAYXX CITATION NPM 7SR 7U5 8BQ 8FD 8FE 8FG ABJCF ABUWG AFKRA AZQEC BENPR BGLVJ CCPQU D1I DWQXO EHMNL HCIFZ JG9 KB. L7M PDBOC PHGZM PHGZT PIMPY PKEHL PQEST PQGLB PQQKQ PQUKI PRINS 7X8 5PM DOA |
| DOI | 10.1107/S2052252519007619 |
| DatabaseName | CrossRef PubMed Engineered Materials Abstracts Solid State and Superconductivity Abstracts METADEX Technology Research Database ProQuest SciTech Collection ProQuest Technology Collection Materials Science & Engineering Collection ProQuest Central (Alumni) ProQuest Central UK/Ireland ProQuest Central Essentials - QC ProQuest Central Technology collection ProQuest One Community College ProQuest Materials Science Collection ProQuest Central Korea UK & Ireland Database SciTech Premium Collection Materials Research Database Materials Science Database Advanced Technologies Database with Aerospace Materials Science Collection ProQuest Central Premium ProQuest One Academic (New) Publicly Available Content Database ProQuest One Academic Middle East (New) ProQuest One Academic Eastern Edition (DO NOT USE) One Applied & Life Sciences ProQuest One Academic (retired) ProQuest One Academic UKI Edition ProQuest Central China MEDLINE - Academic PubMed Central (Full Participant titles) DOAJ Directory of Open Access Journals |
| DatabaseTitle | CrossRef PubMed Publicly Available Content Database Materials Research Database Technology Collection Technology Research Database ProQuest One Academic Middle East (New) ProQuest Central Essentials Materials Science Collection ProQuest Central (Alumni Edition) SciTech Premium Collection ProQuest One Community College ProQuest Central China ProQuest Central ProQuest One Applied & Life Sciences Engineered Materials Abstracts ProQuest Central Korea Materials Science Database ProQuest Central (New) Advanced Technologies Database with Aerospace ProQuest Materials Science Collection ProQuest One Academic Eastern Edition ProQuest Technology Collection ProQuest SciTech Collection METADEX UK & Ireland Database ProQuest One Academic UKI Edition Materials Science & Engineering Collection Solid State and Superconductivity Abstracts ProQuest One Academic ProQuest One Academic (New) MEDLINE - Academic |
| DatabaseTitleList | MEDLINE - Academic PubMed Publicly Available Content Database CrossRef |
| Database_xml | – sequence: 1 dbid: DOA name: DOAJ Directory of Open Access Journals url: https://www.doaj.org/ sourceTypes: Open Website – sequence: 2 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 3 dbid: KB. name: Materials Science Database url: http://search.proquest.com/materialsscijournals sourceTypes: Aggregation Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Engineering |
| DocumentTitleAlternate | Namdinator |
| EISSN | 2052-2525 |
| EndPage | 531 |
| ExternalDocumentID | oai_doaj_org_article_62db1750502545a0b799c66a35dc5325 PMC6608625 31316797 10_1107_S2052252519007619 |
| Genre | Journal Article |
| GrantInformation_xml | – fundername: Aarhus Institute of Advanced Studies, Aarhus Universitet – fundername: H2020 European Research Council grantid: 637372 – fundername: Natur og Univers, Det Frie Forskningsråd grantid: DFF-4002-00052 |
| GroupedDBID | 5VS 8FE 8FG AAFWJ AAYXX ABJCF ABUWG ADBBV AENEX AFFHD AFKRA AFPKN ALMA_UNASSIGNED_HOLDINGS AOIJS BCNDV BENPR BGLVJ BPHCQ CCPQU CITATION D1I EBS EHMNL EJD GROUPED_DOAJ H13 HCIFZ HYE IAO ITC KB. KQ8 M48 M~E OK1 PDBOC PGMZT PHGZM PHGZT PIMPY PQGLB PQQKQ PROAC RCJ ROL RPM ZBA 3V. NPM 7SR 7U5 8BQ 8FD AZQEC DWQXO JG9 L7M PKEHL PQEST PQUKI PRINS 7X8 5PM |
| ID | FETCH-LOGICAL-c493t-a548cca7e892320fe253b4544ee32d6b2cfa80ad130a4777c34a18ce0775dfae3 |
| IEDL.DBID | KB. |
| ISICitedReferencesCount | 245 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000473692700006&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| ISSN | 2052-2525 |
| IngestDate | Tue Oct 14 18:58:03 EDT 2025 Tue Nov 04 02:01:32 EST 2025 Sun Nov 09 10:24:14 EST 2025 Fri Jul 25 11:59:38 EDT 2025 Thu Jan 02 23:04:08 EST 2025 Sat Nov 29 01:43:45 EST 2025 Tue Nov 18 21:47:00 EST 2025 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 4 |
| Keywords | crystallography MDFF automation web services molecular dynamics flexible fitting flexible fitting molecular dynamics cryo-EM model-fitting |
| Language | English |
| License | This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited. |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c493t-a548cca7e892320fe253b4544ee32d6b2cfa80ad130a4777c34a18ce0775dfae3 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 |
| ORCID | 0000-0002-5633-6844 0000-0001-7860-7230 0000-0003-0948-6628 0000-0001-9699-2494 0000-0001-5076-0321 0000-0002-3146-2414 |
| OpenAccessLink | https://www.proquest.com/docview/2249983578?pq-origsite=%requestingapplication% |
| PMID | 31316797 |
| PQID | 2249983578 |
| PQPubID | 2035043 |
| PageCount | 6 |
| ParticipantIDs | doaj_primary_oai_doaj_org_article_62db1750502545a0b799c66a35dc5325 pubmedcentral_primary_oai_pubmedcentral_nih_gov_6608625 proquest_miscellaneous_2259911856 proquest_journals_2249983578 pubmed_primary_31316797 crossref_primary_10_1107_S2052252519007619 crossref_citationtrail_10_1107_S2052252519007619 |
| PublicationCentury | 2000 |
| PublicationDate | 2019-07-01 |
| PublicationDateYYYYMMDD | 2019-07-01 |
| PublicationDate_xml | – month: 07 year: 2019 text: 2019-07-01 day: 01 |
| PublicationDecade | 2010 |
| PublicationPlace | England |
| PublicationPlace_xml | – name: England – name: Chester |
| PublicationTitle | IUCrJ |
| PublicationTitleAlternate | IUCrJ |
| PublicationYear | 2019 |
| Publisher | International Union of Crystallography |
| Publisher_xml | – name: International Union of Crystallography |
| References | Pettersen (eh5002_bb16) 2004; 25 Müller (eh5002_bb14) 1996; 4 Müller (eh5002_bb15) 1992; 224 Kühlbrandt (eh5002_bb11) 2014; 343 Humphrey (eh5002_bb10) 1996; 14 Subramaniam (eh5002_bb20) 2019; 6 Stone (eh5002_bb19) 2014; 169 Alford (eh5002_bb4) 2017; 13 Trabuco (eh5002_bb23) 2009; 49 Afonine (eh5002_bb2) 2013; 4 Vashisth (eh5002_bb24) 2012; 20 Matthies (eh5002_bb13) 2016; 164 eh5002_bb18 eh5002_bb8 Phillips (eh5002_bb17) 2005; 26 Tanner (eh5002_bb21) 2011; 7 Blees (eh5002_bb5) 2017; 551 Trabuco (eh5002_bb22) 2008; 16 Adams (eh5002_bb1) 2010; 66 Lou (eh5002_bb12) 2006; 110 Farnung (eh5002_bb7) 2017; 550 Wlodawer (eh5002_bb25) 2017; 25 Huang (eh5002_bb9) 2013; 34 Chacón (eh5002_bb6) 2002; 317 Afonine (eh5002_bb3) 2018; 74 |
| References_xml | – volume: 14 start-page: 33 year: 1996 ident: eh5002_bb10 publication-title: J. Mol. Graph. doi: 10.1016/0263-7855(96)00018-5 – volume: 6 start-page: 1 year: 2019 ident: eh5002_bb20 publication-title: IUCrJ doi: 10.1107/S2052252519000277 – volume: 224 start-page: 159 year: 1992 ident: eh5002_bb15 publication-title: J. Mol. Biol. doi: 10.1016/0022-2836(92)90582-5 – ident: eh5002_bb8 – volume: 343 start-page: 1443 year: 2014 ident: eh5002_bb11 publication-title: Science doi: 10.1126/science.1251652 – volume: 164 start-page: 747 year: 2016 ident: eh5002_bb13 publication-title: Cell doi: 10.1016/j.cell.2015.12.055 – volume: 74 start-page: 814 year: 2018 ident: eh5002_bb3 publication-title: Acta Cryst. D doi: 10.1107/S2059798318009324 – volume: 4 start-page: 147 year: 1996 ident: eh5002_bb14 publication-title: Structure doi: 10.1016/S0969-2126(96)00018-4 – volume: 20 start-page: 1453 year: 2012 ident: eh5002_bb24 publication-title: Structure doi: 10.1016/j.str.2012.08.007 – volume: 26 start-page: 1781 year: 2005 ident: eh5002_bb17 publication-title: J. Comput. Chem. doi: 10.1002/jcc.20289 – volume: 34 start-page: 2135 year: 2013 ident: eh5002_bb9 publication-title: J. Comput. Chem. doi: 10.1002/jcc.23354 – volume: 110 start-page: 12796 year: 2006 ident: eh5002_bb12 publication-title: J. Phys. Chem. B doi: 10.1021/jp061976m – volume: 550 start-page: 539 year: 2017 ident: eh5002_bb7 publication-title: Nature doi: 10.1038/nature24046 – volume: 317 start-page: 375 year: 2002 ident: eh5002_bb6 publication-title: J. Mol. Biol. doi: 10.1006/jmbi.2002.5438 – volume: 66 start-page: 213 year: 2010 ident: eh5002_bb1 publication-title: Acta Cryst. D doi: 10.1107/S0907444909052925 – volume: 13 start-page: 3031 year: 2017 ident: eh5002_bb4 publication-title: J. Chem. Theory Comput. doi: 10.1021/acs.jctc.7b00125 – volume: 25 start-page: 1589 year: 2017 ident: eh5002_bb25 publication-title: Structure doi: 10.1016/j.str.2017.07.012 – volume: 169 start-page: 265 year: 2014 ident: eh5002_bb19 publication-title: Faraday Discuss. doi: 10.1039/C4FD00005F – volume: 4 start-page: 43 year: 2013 ident: eh5002_bb2 publication-title: Comput. Crystallogr. Newsl. – volume: 7 start-page: 3635 year: 2011 ident: eh5002_bb21 publication-title: J. Chem. Theory Comput. doi: 10.1021/ct200563j – volume: 49 start-page: 174 year: 2009 ident: eh5002_bb23 publication-title: Methods doi: 10.1016/j.ymeth.2009.04.005 – volume: 25 start-page: 1605 year: 2004 ident: eh5002_bb16 publication-title: J. Comput. Chem. doi: 10.1002/jcc.20084 – ident: eh5002_bb18 – volume: 551 start-page: 525 year: 2017 ident: eh5002_bb5 publication-title: Nature doi: 10.1038/nature24627 – volume: 16 start-page: 673 year: 2008 ident: eh5002_bb22 publication-title: Structure doi: 10.1016/j.str.2008.03.005 |
| SSID | ssj0001125741 |
| Score | 2.5809808 |
| Snippet | Model building into experimental maps is a key element of structural biology, but can be both time consuming and error prone for low-resolution maps. Here we... A pipeline tool called Namdinator is presented that enables the user to run a molecular dynamics flexible fitting (MDFF) simulation in a fully automated... |
| SourceID | doaj pubmedcentral proquest pubmed crossref |
| SourceType | Open Website Open Access Repository Aggregation Database Index Database Enrichment Source |
| StartPage | 526 |
| SubjectTerms | Automation Computer simulation cryo-EM Crystallography flexible fitting MDFF model-fitting Molecular dynamics molecular dynamics flexible fitting Optimization Outliers (statistics) Research Letters Web services |
| SummonAdditionalLinks | – databaseName: DOAJ Directory of Open Access Journals dbid: DOA link: http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV1Li9RAEG5k8aAH8W10lRY8CWE7_UyOKrt4cRBU2FuofgQHZpJlM7vgzcP-g_2H_hKruzNDRkUv3kJ3Bzpd1amv0pXvI-QVeNfUrraldcaXGK-hrKX1ZVVpV7vKAIQsNmEWi_r0tPk4k_qKNWGZHjgv3JHm3mKIYyr-tq2AWdM0TmsQyjsleGIvRdQzS6bS1xWM2ybJVnKmeMkVV9ORJqY7R59iY2zDaJjy-L2glLj7_wQ4f62bnAWik7vkzoQg6Zs883vkRujvk9szXsEH5GoBa4xJMZ-mP75fU7jYDImala63arjUZyn6kXaREtOuAu2WqQaaDh3NrLKRkYMmqZyRLvvNQN35t6E8_kCh9_EageVqS3lN51IBdA1n40Py5eT487v35SS3UDrZiE0JmLygPU2oEfRx1gWuhJVKyhAE99py10HNwGPUA2mMcUJCVbsQSfR8B0E8Igf90IcnhKpKSMfwXSFYkJoz24gOZBXQeFJ57grCtuvduomLPEpirNqUkzDT_maigrze3XKWiTj-NvhtNOJuYOTQTg3oWe3kWe2_PKsgh1sXaKeNPbaIeDBBjRRBBXm568YtGc9ZoA_DRRyjEHUjENIFeZw9ZjcTUUXqgcYUxOz50t5U93v65ddE-611TD_V0__xbM_ILUR-Ta47PiQH6FXhObnpLjfL8fxF2ks_AScaIVU priority: 102 providerName: Directory of Open Access Journals |
| Title | Namdinator – automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/31316797 https://www.proquest.com/docview/2249983578 https://www.proquest.com/docview/2259911856 https://pubmed.ncbi.nlm.nih.gov/PMC6608625 https://doaj.org/article/62db1750502545a0b799c66a35dc5325 |
| Volume | 6 |
| WOSCitedRecordID | wos000473692700006&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| journalDatabaseRights | – providerCode: PRVAON databaseName: DOAJ Directory of Open Access Journals customDbUrl: eissn: 2052-2525 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0001125741 issn: 2052-2525 databaseCode: DOA dateStart: 20140101 isFulltext: true titleUrlDefault: https://www.doaj.org/ providerName: Directory of Open Access Journals – providerCode: PRVHPJ databaseName: ROAD: Directory of Open Access Scholarly Resources customDbUrl: eissn: 2052-2525 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0001125741 issn: 2052-2525 databaseCode: M~E dateStart: 20140101 isFulltext: true titleUrlDefault: https://road.issn.org providerName: ISSN International Centre – providerCode: PRVPQU databaseName: Materials Science Database customDbUrl: eissn: 2052-2525 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0001125741 issn: 2052-2525 databaseCode: KB. dateStart: 20140101 isFulltext: true titleUrlDefault: http://search.proquest.com/materialsscijournals providerName: ProQuest – providerCode: PRVPQU databaseName: ProQuest Central customDbUrl: eissn: 2052-2525 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0001125741 issn: 2052-2525 databaseCode: BENPR dateStart: 20140101 isFulltext: true titleUrlDefault: https://www.proquest.com/central providerName: ProQuest – providerCode: PRVPQU databaseName: ProQuest Publicly Available Content Database customDbUrl: eissn: 2052-2525 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0001125741 issn: 2052-2525 databaseCode: PIMPY dateStart: 20140101 isFulltext: true titleUrlDefault: http://search.proquest.com/publiccontent providerName: ProQuest – providerCode: PRVPQU databaseName: UK & Ireland Database customDbUrl: eissn: 2052-2525 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0001125741 issn: 2052-2525 databaseCode: EHMNL dateStart: 20140101 isFulltext: true titleUrlDefault: https://search.proquest.com/ukireland providerName: ProQuest |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV1Lj9MwEB6xuxzYA-9HYKmMxAkprBPbcXJCFHUFQltVPKRyihzbgUpt0m26SNw48A_4h_wSxk7SbQHthVvkONJIHs98Y0--D-CpMjpLdVqEhZYmxHytwpQXJoyiRKc6kkrZVmxCjsfpdJpNugO3pmur7GOiD9Sm1u6M_BhTDVYGjpvlxfIsdKpR7na1k9DYgwPHkuCkG94On1-csWD2xozZXWZioXP8PqYIOIT7XZP6Cn4nHXnW_n9BzT87JrdS0MmN_zX-JlzvwCd52XrLLbhiq9twuEVJeAd-jNUC05krxcmv7z-JOl_XntWVLHohXWJaFfuGlI5Ns5hbUs58-zSpS9IS0joyD-JVdhoyq9Y10atvdTg6Jaoy7hkx6bxnyybbKgNkoZbNXfh4Mvrw6nXYKTWEmmdsHSqse9AVpE0RL8a0tLFgBRecW8tikxSxLlVKlcGEqbiUUjOuolRbx79nSmXZPdiv6so-ACIixjXFMMOo5UlMi4yVike2wMAhTKwDoP2C5bqjMXdqGvPclzNU5n-tcQDPNp8sWw6PyyYPnRdsJjr6bT9Qrz7n3W7Ok9gUiLuocFwCQlE0LtNJopgwWrBYBHDU-0HexYQmv3CCAJ5sXuNudlc0qrL1uZsjELAjhkoCuN-63MYSFjnWgkwGIHecccfU3TfV7ItnDE8SV7mKh5eb9QiuIRzM2mbkI9hHf7GP4ar-up41qwHsyWk6gIPhaDx5N_BnFwO_3XBs8uZ08uk3g7k0NA |
| linkProvider | ProQuest |
| linkToHtml | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw1V3LbtNAFL0qKRKw4P0wFBgk2CBZHc94_FggxKNVozZRJIpUVu54ZgyWEjvEKSg7FvwB_8FH8SXc8SNNAHXXBbsonkRX9pl7z50ZnwPwVGoVRypK3VSF2sV6Ld3IT7XreYGKlBdKaRqziXA4jI6O4tEG_OzehbHHKrucWCdqXSq7Rr6NpQY7A6vN8nL62bWuUXZ3tbPQaGCxbxZfsWWrXvTf4vN9xtjuzuGbPbd1FXCVH_O5K5GjY9ihiZDbMJoZJnjqC983hjMdpExlMqJSY3KXfhiGivvSi5SxWnE6k4bj_16ATR_BHvVgc9QfjD6cruogX8Aa3W6fYmu1_Y5RpDjCviBK6zWDtQJY-wT8i9z-eUZzpejtXvvfbtd1uNrSa_KqmQ83YMMUN-HKiujiLfg-lBMs2Haxgfz69oPIk3lZ69aSSWcVTPSikJNcVSSzeqHp2JAsrw-IkzIjjeSulSshtY9QRfJiXhI1W5TuzoDIQtvPyLrHnR44WfVRIBM5rW7D-3O5DXegV5SFuQdEeNxXFBMpp8YPGE1jnknfMymmRqGZcoB2AElUK9Ru_ULGSd2w0TD5C1MOPF_-ZNqolJw1-LVF3XKgFRivvyhnH5M2XyUB0ykySyqsWoKQFIOLVRBILrQSnAkHtjrcJW3Wq5JT0DnwZHkZ85XdhJKFKU_sGIEtCbLEwIG7DcSXkXDP6jLEoQPhGvjXQl2_UuSfak30ILC9ubh_dliP4dLe4eAgOegP9x_AZSS_cXP0egt6iB3zEC6qL_O8mj1qJzaB4_OeHL8BTG-OXQ |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Namdinator+%E2%80%93+automatic+molecular+dynamics+flexible+fitting+of+structural+models+into+cryo-EM+and+crystallography+experimental+maps&rft.jtitle=IUCrJ&rft.au=Kidmose%2C+Rune+Thomas&rft.au=Juhl%2C+Jonathan&rft.au=Nissen%2C+Poul&rft.au=Boesen%2C+Thomas&rft.date=2019-07-01&rft.issn=2052-2525&rft.eissn=2052-2525&rft.volume=6&rft.issue=4&rft.spage=526&rft.epage=531&rft_id=info:doi/10.1107%2FS2052252519007619&rft.externalDBID=n%2Fa&rft.externalDocID=10_1107_S2052252519007619 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=2052-2525&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=2052-2525&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=2052-2525&client=summon |