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modelling_software_ft:PHENIX

Filter By

Current Database

  • EMDB [26]

Current status

  • REL [26]

Sample type

  • Protein [23]
  • Complex [22]
  • Ligand [13]
  • Sample [4]
  • Virus [2]

Organism

  • Paracoccus sp. dmf [3]
  • Synechococcus elongatus [2]
  • Enterovirus b [2]
  • Sarbecovirus sp. rhgb07 [2]
  • Oryza sativa [2]
  • Saccharomyces cerevisiae [2]
  • Homo sapiens [2]
  • Mycobacterium tuberculosis [1]
  • Escherichia phage lambda [1]
  • Geobacter metallireducens [1]
  • Spinacia oleracea [1]
  • Oryza sativa [1]
  • Methylosinus sporium [1]
  • (no species) [1]
  • Saccharomyces cerevisiae [1]
  • Escherichia coli [1]
  • Synechococcus virus scbp4 [1]
  • Escherichia coli [1]
  • Salmonella enterica [1]
  • Canis lupus [1]

EM Method

  • Single-particle [24]
  • Helical reconstruction [2]

Resolution

  • ≥ 2Å and < 3Å [14]
  • ≥ 3Å and < 4Å [10]
  • ≥ 8Å and < 12Å [1]
  • ≥ 12Å and < 16Å [1]

Model molecular weight

  • 50-100 kDa [2]
  • 100-250 kDa [6]
  • 250-500 kDa [5]
  • 500-1000 kDa [3]
  • 1-2 MDa [1]
  • 2-5 MDa [2]
  • 5-10 MDa [1]

Release Date

  • 2026 [7]
  • 2025 [5]
  • 2024 [2]
  • 2023 [3]
  • 2022 [3]
  • 2020 [2]
  • 2016 [3]
  • 2014 [1]

Author by name

  • Dhanabalan K [4]
  • Subramanian R [4]
  • Thach T [4]
  • Allison J [3]
  • Brignole EJ [3]
  • Drennan CL [3]
  • Han-hallet Y [3]
  • Kong S [3]
  • Marquez MD [3]
  • Maurya S [3]
  • Park C [3]
  • Perlstein DL [3]
  • Quan S [3]
  • Ramanathan G [3]
  • Vasquez S [3]
  • Vo A [3]
  • Ai X [2]
  • Ashley RE [2]
  • Bischoff AJ [2]
  • Chen WF [2]
  • Conway JF [2]
  • Dong CN [2]
  • Ekundayo B [2]
  • Fosse P [2]
  • Hafenstein S [2]
  • Hou XM [2]
  • Huang LY [2]
  • Lafrance B [2]
  • Lafrance BJ [2]
  • Lau K [2]
  • Lee H [2]
  • Lei DS [2]
  • Li HH [2]
  • Liu NN [2]
  • Makhov AM [2]
  • Mauffret O [2]
  • Newman J [2]
  • Nichols RJ [2]
  • Nogales E [2]
  • Oltrogge LM [2]
  • Organtini LJ [2]
  • Phillips NR [2]
  • Radford DR [2]
  • Rety S [2]
  • Savage DF [2]
  • Shingler KL [2]
  • Valentin-alvarado LE [2]
  • Xi XG [2]
  • Zhang ZL [2]
  • Alvarado S [1]
  • Amara P [1]
  • Ando N [1]
  • Arango N [1]
  • Aversa R [1]
  • Aversa RJ [1]
  • Bailey D [1]
  • Baimukhametov TN [1]
  • Basbous H [1]
  • Boyko KM [1]
  • Breitkopf SB [1]
  • Brown D [1]
  • Bryk R [1]
  • Burnim AA [1]
  • Burtseva AD [1]
  • Cao P [1]
  • Caserta G [1]
  • Chait BT [1]
  • Chang WR [1]
  • Chase J [1]
  • Chen D [1]
  • Cherrier MV [1]
  • Chesnokov YM [1]
  • Chevance FFV [1]
  • Collier P [1]
  • Collier PN [1]
  • Dergalev AA [1]
  • Dobrzynska K [1]
  • Doores KJ [1]
  • Echavarri-erasun C [1]
  • Egelman E [1]
  • Egelman EH [1]
  • Ekundayo BE [1]
  • Enerson B [1]
  • Fitzpatrick JAJ [1]
  • Ford M [1]
  • Fyfe C [1]
  • Ginn J [1]
  • Growney JD [1]
  • Hay AL [1]
  • Heisler I [1]
  • Hong HJ [1]
  • Howarth C [1]
  • Howarth L [1]
  • Hughes KT [1]
  • Hur S [1]
  • Hwang Y [1]
  • Isiorho E [1]
  • Jackson CJ [1]
  • Jeruzalmi D [1]
  • Kang HG [1]

Author by ORCID

  • Drennan CL [3]
  • Perlstein DL [3]
  • Vasquez S [3]
  • Marquez MD [3]
  • Kong S [3]
  • Oltrogge LM [2]
  • Nogales E [2]
  • Ashley RE [2]
  • Rety S [2]
  • Xi XG [2]
  • Organtini LJ [2]
  • Lee H [2]
  • Conway JF [2]
  • Radford DR [2]
  • Makhov AM [2]
  • Nichols RJ [2]
  • Savage DF [2]
  • Lafrance B [2]
  • Bischoff AJ [2]
  • Lei DS [2]
  • Phillips NR [2]
  • Shingler KL [2]
  • Hughes KT [1]
  • Mount J [1]
  • Jeruzalmi D [1]
  • Jackson CJ [1]
  • Maksaev G [1]
  • Pozharski E [1]
  • Ando N [1]
  • Fyfe C [1]
  • Boyko KM [1]
  • Chesnokov YM [1]
  • Lee SJ [1]
  • Yamaguchi T [1]
  • Amara P [1]
  • Nguyen TQ [1]
  • Popov VO [1]
  • Dergalev AA [1]
  • Wu B [1]
  • Schoehn G [1]
  • Xu D [1]
  • Nicolet Y [1]
  • Tetrault D [1]
  • Kochanczyk T [1]
  • Yuan P [1]
  • Hwang Y [1]
  • Subramanian R [1]
  • Fitzpatrick JAJ [1]
  • Collier PN [1]
  • Zheng X [1]
  • Kato T [1]
  • Peisley A [1]
  • Lima CD [1]
  • Magor KE [1]
  • Aversa RJ [1]
  • Burnim AA [1]
  • Paul A [1]
  • Kushnirov VV [1]
  • Burtseva AD [1]
  • Cherrier MV [1]
  • Paya Tormo L [1]
  • Caserta G [1]
  • Ryu B [1]
  • Su L [1]
  • Rubio LM [1]
  • Spence MA [1]
  • Legrand P [1]
  • Walz T [1]
  • Namba K [1]
  • Chevance FFV [1]
  • Sharma K [1]
  • Egelman EH [1]
  • Shatarupa A [1]
  • Martin L [1]
  • Growney JD [1]

Journal

  • ELIFE [6]
  • BIORXIV [5]
  • COMMUN BIOL [4]
  • NAT PLANTS [2]
  • SCI ADV [2]
  • TO BE PUBLISHED [2]
  • J BIOL CHEM [1]
  • J MED CHEM [1]
  • MOL CELL [1]
  • NAT CHEM BIOL [1]
  • NAT COMMUN [1]
  • NATURE [1]
  • NOT PUBLISHED [1]
  • NUCLEIC ACIDS RES [1]

Software

  • PHENIX [26]
  • CRYOSPARC [16]
  • RELION [8]
  • CHIMERA, COOT [1]
  • CRYOLO [1]
  • CTFFIND [1]
  • EMAN, RELION [1]
  • HELICON [1]
  • WARP [1]

Microscope

  • TFS KRIOS [8]
  • FEI TITAN KRIOS [7]
  • FEI TECNAI ARCTICA [3]
  • TFS GLACIOS [3]
  • FEI POLARA 300 [2]
  • FEI TECNAI F20 [1]
  • JEOL CRYO ARM 300 [1]
  • TFS TALOS [1]

Electron Source

  • FIELD EMISSION GUN [26]

Film or detector model

  • GATAN K2 SUMMIT 4K X 4K [5]
  • FEI FALCON IV 4K X 4K [4]
  • GATAN K3 BIOCONTINUUM 6K X 4K [4]
  • GATAN K3 BIOQUANTUM 6K X 4K [4]
  • GATAN K3 6K X 4K [3]
  • FEI FALCON II 4K X 4K [2]
  • FEI FALCON III 4K X 4K [2]
  • GATAN K2 4K X 4K [1]
  • OTHER [1]

External links

  • PDB [23]
  • PDBe-Kb [16]
  • UniProt [16]
  • AlphaFold DB [15]
  • InterPro [15]
  • Pfam [15]
  • Gene Ontology [13]
  • ChEBI [10]
  • ChEMBL [9]
  • DrugBank [7]
  • EMPIAR [3]
  • Complex Portal [2]
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Showing 1 - 10 of 26. Page 1 of 3
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EMD-72223
Download Map
3D View
Cryo-EM structure of Paracoccus Trimethylamine N-oxide Demethylase
CryoEM
Release date: Aug. 26, 2026
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 9q59
Q-score: 0.616
Similar entry percentile: 92%

Thach T, Dhanabalan K, Maurya S, Han-Hallet Y, Quan S, Allison J, Ramanathan G, Subramanian R

eLife (2026) [ DOI: doi:10.7554/elife.109964.2 ]

EMD-72224
Download Map
3D View
Cryo-EM structure of a Paracoccus Trimethylamine N-oxide Demethylase mutant D220A/D367A in Complex with TMAO
CryoEM
Release date: Aug. 26, 2026
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 9q5a
Q-score: 0.613
Similar entry percentile: 92%

Thach T, Dhanabalan K, Maurya S, Han-Hallet Y, Quan S, Allison J, Ramanathan G, Subramanian R

eLife (2026) [ DOI: doi:10.7554/elife.109964.2 ]

EMD-72239
Download Map
3D View
Cryo-EM structure of a Paracoccus Trimethylamine N-oxide Demethylase in complex with DMA, HCHO
CryoEM
Release date: Aug. 26, 2026
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 9q5l
Q-score: 0.568
Similar entry percentile: 77%

Thach T, Dhanabalan K, Maurya S, Han-Hallet Y, Quan S, Allison J, Ramanathan G, Subramanian R

eLife (2026) [ DOI: doi:10.7554/elife.109964.2 ]

EMD-67558
Download Map
3D View
Cryo-EM structure of ex vivo Sup35 prion fibrils from yeast carrying strong PSI variant
CryoEM
Release date: July 22, 2026
Resolution: 2.7 Å
EM Method: Helical reconstruction
Fitted PDBs: 21bq
Q-score: 0.586
Similar entry percentile: 82%

Dergalev AA, Chesnokov YM, Burtseva AD, Kushnirov VV, Boyko KM, Popov VO

To Be Published

EMD-58663
Download Map
3D View
Unbinned map of EMD-53938
CryoEM
Release date: July 8, 2026
Resolution: 2.97 Å
EM Method: Single-particle

Thazuk N, Newman J

To Be Published

EMD-60995
Download Map
3D View
P ring on polyrod-P ring complex from Salmonella TH26292 strain
CryoEM
Release date: March 4, 2026
Resolution: 2.33 Å
EM Method: Single-particle
Fitted PDBs: 9iyc
Q-score: 0.583
Similar entry percentile: 54%

Yamaguchi T, Minamino T, Kato T, Chevance FFV, Hughes KT, Namba K

Commun Biol (2026) [ Pubmed: 42443432 DOI: doi:10.1038/s42003-026-10640-y ]

EMD-49942
Download Map
3D View
Cryo-EM structure of CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 24
CryoEM
Release date: Feb. 4, 2026
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 9nyr
Q-score: 0.34
Similar entry percentile: 32%

Collier PN, Zheng X, Ford M, Weiss M, Chen D, Li K, Growney JD, Yang A, Sathappa M, Breitkopf SB, Enerson B, Liang T, Paul A, Sawant R, Su L, Aversa RJ, Howarth C, Sharma K, Williams J, Kwiatkowski NP

J Med Chem (2025) 68 pp. 18407-18422 [ DOI: doi:10.1021/acs.jmedchem.5c01160 Pubmed: 40833690 ]

EMD-52557
Download Map
3D View
CryoEM structure of holo-GmNifEN
CryoEM
Release date: Nov. 5, 2025
Resolution: 2.86 Å
EM Method: Single-particle
Fitted PDBs: 9i0g
Q-score: 0.52
Similar entry percentile: 56%

Paya Tormo L, Nguyen TQ, Fyfe C, Basbous H, Dobrzynska K, Echavarri-Erasun C, Martin L, Caserta G, Legrand P, Thorn A, Amara P, Schoehn G, Cherrier MV, Rubio LM, Nicolet Y

Nat Chem Biol (2026) 22 pp. 813-821 [ DOI: doi:10.1038/s41589-025-02070-4 Pubmed: 41238839 ]

EMD-53938
Download Map
3D View
Raw data
EMPIAR-12921
Structure of the RhGB07 Prefusion, Closed-state trimeric spike protein
CryoEM
Release date: Sept. 24, 2025
Resolution: 2.97 Å
EM Method: Single-particle
Fitted PDBs: 9rdt
Q-score: 0.485
Similar entry percentile: 44%

Thakur N, Newman J, Ni D, Seow J, Hay AL, Li Y, Upadhyay A, Ekundayo BE, Peacock TP, Lau K, Doores KJ, Bailey D

bioRxiv (2025) [ DOI: doi:10.1101/2025.09.03.673949 ]

EMD-70271
Download Map
3D View
Ecoli DnaB helicase and Phage Lambda loader P with ADP-Mg in a 6:6 stoichiometry ratio.
CryoEM
Release date: July 16, 2025
Resolution: 3.85 Å
EM Method: Single-particle
Fitted PDBs: 9oa2
Q-score: 0.103
Similar entry percentile: 1%

Shatarupa A, Brown D, Olinares PDB, Chase J, Isiorho E, Chait BT, Jeruzalmi D

Nucleic Acids Res (2025) 53 [ DOI: doi:10.1093/nar/gkaf1139 Pubmed: 41312769 ]

Sort by: Download
Showing 1 - 10 of 26. Page 1 of 3
Display:
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Filter By

Current Database

  • EMDB [26]

Current status

  • REL [26]

Sample type

  • Protein [23]
  • Complex [22]
  • Ligand [13]
  • Sample [4]
  • Virus [2]

Organism

  • Paracoccus sp. dmf [3]
  • Synechococcus elongatus [2]
  • Enterovirus b [2]
  • Sarbecovirus sp. rhgb07 [2]
  • Oryza sativa [2]
  • Saccharomyces cerevisiae [2]
  • Homo sapiens [2]
  • Mycobacterium tuberculosis [1]
  • Escherichia phage lambda [1]
  • Geobacter metallireducens [1]
  • Spinacia oleracea [1]
  • Oryza sativa [1]
  • Methylosinus sporium [1]
  • (no species) [1]
  • Saccharomyces cerevisiae [1]
  • Escherichia coli [1]
  • Synechococcus virus scbp4 [1]
  • Escherichia coli [1]
  • Salmonella enterica [1]
  • Canis lupus [1]

EM Method

  • Single-particle [24]
  • Helical reconstruction [2]

Resolution

  • ≥ 2Å and < 3Å [14]
  • ≥ 3Å and < 4Å [10]
  • ≥ 8Å and < 12Å [1]
  • ≥ 12Å and < 16Å [1]

Model molecular weight

  • 50-100 kDa [2]
  • 100-250 kDa [6]
  • 250-500 kDa [5]
  • 500-1000 kDa [3]
  • 1-2 MDa [1]
  • 2-5 MDa [2]
  • 5-10 MDa [1]

Release Date

  • 2026 [7]
  • 2025 [5]
  • 2024 [2]
  • 2023 [3]
  • 2022 [3]
  • 2020 [2]
  • 2016 [3]
  • 2014 [1]

Author by name

  • Dhanabalan K [4]
  • Subramanian R [4]
  • Thach T [4]
  • Allison J [3]
  • Brignole EJ [3]
  • Drennan CL [3]
  • Han-hallet Y [3]
  • Kong S [3]
  • Marquez MD [3]
  • Maurya S [3]
  • Park C [3]
  • Perlstein DL [3]
  • Quan S [3]
  • Ramanathan G [3]
  • Vasquez S [3]
  • Vo A [3]
  • Ai X [2]
  • Ashley RE [2]
  • Bischoff AJ [2]
  • Chen WF [2]
  • Conway JF [2]
  • Dong CN [2]
  • Ekundayo B [2]
  • Fosse P [2]
  • Hafenstein S [2]
  • Hou XM [2]
  • Huang LY [2]
  • Lafrance B [2]
  • Lafrance BJ [2]
  • Lau K [2]
  • Lee H [2]
  • Lei DS [2]
  • Li HH [2]
  • Liu NN [2]
  • Makhov AM [2]
  • Mauffret O [2]
  • Newman J [2]
  • Nichols RJ [2]
  • Nogales E [2]
  • Oltrogge LM [2]
  • Organtini LJ [2]
  • Phillips NR [2]
  • Radford DR [2]
  • Rety S [2]
  • Savage DF [2]
  • Shingler KL [2]
  • Valentin-alvarado LE [2]
  • Xi XG [2]
  • Zhang ZL [2]
  • Alvarado S [1]
  • Amara P [1]
  • Ando N [1]
  • Arango N [1]
  • Aversa R [1]
  • Aversa RJ [1]
  • Bailey D [1]
  • Baimukhametov TN [1]
  • Basbous H [1]
  • Boyko KM [1]
  • Breitkopf SB [1]
  • Brown D [1]
  • Bryk R [1]
  • Burnim AA [1]
  • Burtseva AD [1]
  • Cao P [1]
  • Caserta G [1]
  • Chait BT [1]
  • Chang WR [1]
  • Chase J [1]
  • Chen D [1]
  • Cherrier MV [1]
  • Chesnokov YM [1]
  • Chevance FFV [1]
  • Collier P [1]
  • Collier PN [1]
  • Dergalev AA [1]
  • Dobrzynska K [1]
  • Doores KJ [1]
  • Echavarri-erasun C [1]
  • Egelman E [1]
  • Egelman EH [1]
  • Ekundayo BE [1]
  • Enerson B [1]
  • Fitzpatrick JAJ [1]
  • Ford M [1]
  • Fyfe C [1]
  • Ginn J [1]
  • Growney JD [1]
  • Hay AL [1]
  • Heisler I [1]
  • Hong HJ [1]
  • Howarth C [1]
  • Howarth L [1]
  • Hughes KT [1]
  • Hur S [1]
  • Hwang Y [1]
  • Isiorho E [1]
  • Jackson CJ [1]
  • Jeruzalmi D [1]
  • Kang HG [1]

Author by ORCID

  • Drennan CL [3]
  • Perlstein DL [3]
  • Vasquez S [3]
  • Marquez MD [3]
  • Kong S [3]
  • Oltrogge LM [2]
  • Nogales E [2]
  • Ashley RE [2]
  • Rety S [2]
  • Xi XG [2]
  • Organtini LJ [2]
  • Lee H [2]
  • Conway JF [2]
  • Radford DR [2]
  • Makhov AM [2]
  • Nichols RJ [2]
  • Savage DF [2]
  • Lafrance B [2]
  • Bischoff AJ [2]
  • Lei DS [2]
  • Phillips NR [2]
  • Shingler KL [2]
  • Hughes KT [1]
  • Mount J [1]
  • Jeruzalmi D [1]
  • Jackson CJ [1]
  • Maksaev G [1]
  • Pozharski E [1]
  • Ando N [1]
  • Fyfe C [1]
  • Boyko KM [1]
  • Chesnokov YM [1]
  • Lee SJ [1]
  • Yamaguchi T [1]
  • Amara P [1]
  • Nguyen TQ [1]
  • Popov VO [1]
  • Dergalev AA [1]
  • Wu B [1]
  • Schoehn G [1]
  • Xu D [1]
  • Nicolet Y [1]
  • Tetrault D [1]
  • Kochanczyk T [1]
  • Yuan P [1]
  • Hwang Y [1]
  • Subramanian R [1]
  • Fitzpatrick JAJ [1]
  • Collier PN [1]
  • Zheng X [1]
  • Kato T [1]
  • Peisley A [1]
  • Lima CD [1]
  • Magor KE [1]
  • Aversa RJ [1]
  • Burnim AA [1]
  • Paul A [1]
  • Kushnirov VV [1]
  • Burtseva AD [1]
  • Cherrier MV [1]
  • Paya Tormo L [1]
  • Caserta G [1]
  • Ryu B [1]
  • Su L [1]
  • Rubio LM [1]
  • Spence MA [1]
  • Legrand P [1]
  • Walz T [1]
  • Namba K [1]
  • Chevance FFV [1]
  • Sharma K [1]
  • Egelman EH [1]
  • Shatarupa A [1]
  • Martin L [1]
  • Growney JD [1]

Journal

  • ELIFE [6]
  • BIORXIV [5]
  • COMMUN BIOL [4]
  • NAT PLANTS [2]
  • SCI ADV [2]
  • TO BE PUBLISHED [2]
  • J BIOL CHEM [1]
  • J MED CHEM [1]
  • MOL CELL [1]
  • NAT CHEM BIOL [1]
  • NAT COMMUN [1]
  • NATURE [1]
  • NOT PUBLISHED [1]
  • NUCLEIC ACIDS RES [1]

Software

  • PHENIX [26]
  • CRYOSPARC [16]
  • RELION [8]
  • CHIMERA, COOT [1]
  • CRYOLO [1]
  • CTFFIND [1]
  • EMAN, RELION [1]
  • HELICON [1]
  • WARP [1]

Microscope

  • TFS KRIOS [8]
  • FEI TITAN KRIOS [7]
  • FEI TECNAI ARCTICA [3]
  • TFS GLACIOS [3]
  • FEI POLARA 300 [2]
  • FEI TECNAI F20 [1]
  • JEOL CRYO ARM 300 [1]
  • TFS TALOS [1]

Electron Source

  • FIELD EMISSION GUN [26]

Film or detector model

  • GATAN K2 SUMMIT 4K X 4K [5]
  • FEI FALCON IV 4K X 4K [4]
  • GATAN K3 BIOCONTINUUM 6K X 4K [4]
  • GATAN K3 BIOQUANTUM 6K X 4K [4]
  • GATAN K3 6K X 4K [3]
  • FEI FALCON II 4K X 4K [2]
  • FEI FALCON III 4K X 4K [2]
  • GATAN K2 4K X 4K [1]
  • OTHER [1]

External links

  • PDB [23]
  • PDBe-Kb [16]
  • UniProt [16]
  • AlphaFold DB [15]
  • InterPro [15]
  • Pfam [15]
  • Gene Ontology [13]
  • ChEBI [10]
  • ChEMBL [9]
  • DrugBank [7]
  • EMPIAR [3]
  • Complex Portal [2]