EMDB Solr Search Field Documentation
modelling_software_ft
Names of software packages used during modelling and refinement.
Yes
Yes
Yes
Name: Modelling software (facet)
Type: text
Provenance: Depositor
Archive: EMDB
modelling_software_ft:"PHENIX"
Contains the word:
modelling_software_ft:PHENIX
Partial match:
modelling_software_ft:PHENI*
modelling_software_ft:*HENIX
Has any value:
modelling_software_ft:[* TO *]
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GluN1/GluN3A_ELSL in complex with CGP/Gly/GNE/UCM, LBD-focused, in active conformation (class 2)
Cryo-EM structure of a Paracoccus Trimethylamine N-oxide Demethylase in complex with DMA, HCHO
GluN1/GluN3A_ELSL in complex with CGP/GLY/GNE/UCM, LBD-TMD focused, in active state (class 3)
Cryo-EM structure of a Paracoccus Trimethylamine N-oxide Demethylase mutant (D220A/D367A)in Complex with TMAO
GluN1/GluN3A in complex with CGP and DCKA, TMD focused, in antagonist-bound conformation
GluN1/GluN3A_ELSL in complex with CGP/Gly/GNE/UCM, in pre-open conformation (class 1)
Cryo-EM structure of Paracoccus Trimethylamine N-oxide Demethylase
GluN1/GluN3A in complex with glycine, LBD-TMD focused, in desensitized conformation
GluN1/GluN3A in complex with glycine, TMD focused, in desensitized conformation
GluN1/GluN3A in complex with CGP and DCKA, LBD-focused, in antagonist-bound conformation
GluN1/GluN3A in complex with glycine, LBD focused, in desensitized conformation
Focused-refinement map of the CC dimer in the resting-state GII.3 human norovirus VLP
Focused-refinement map of the CC dimer in the rising-state GII.3 human norovirus VLP
Focused-refinement map of the AB dimer in the resting-state GII.3 human norovirus VLP
Cryo-EM structure of B/Phuket/3037/2013 hemagglutinin trimer in complex with two KL-BHA-3D7 Fab fragments
In situ cryo-EM structure of axonal microtubules from ghost neurons (expanded lattice)
Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-3F4 Fab fragments
In situ cryo-EM structure of axonal microtubules from ghost neurons (compact lattice)
Cryo-EM structure of Gi-coupled GPR84 in complex with OX04539 and PSB-16671
Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-4C2 Fab fragments
In situ cryo-EM structure of axonal cofilactin filaments from ghost neurons
Cryo-EM structure of the kinetoplastid trans-spliceosome (Combined C*/P complex) - PRP22/DHX8 focused map 2
Kinetoplastid trans-spliceosome activated for catalytic step II (C* complex) - Core focused map
Kinetoplastid trans-spliceosome activated for catalytic step II (C* complex) - SNU114-CWC21 focused map
Cryo-EM structure of the kinetoplastid trans-spliceosome (Combined C*/P complex) - PRP22/DHX8 focused map 1
Kinetoplastid trans-spliceosome activated for catalytic step II (C* complex) - U6 LSm ring focused map
Kinetoplastid post-catalytic trans-spliceosome (P complex) - CWC22 focused map
Kinetoplastid trans-spliceosome (Combined C*/P complex) - NTC focused map 3
Kinetoplastid trans-spliceosome activated for catalytic step II (C* complex) - Overall map
Kinetoplastid trans-spliceosome (Combined C*/P complex) - NTC focused map 1
Kinetoplastid trans-spliceosome activated for catalytic step II (C* complex) - U5-40K focused map
Kinetoplastid trans-spliceosome (Combined C*/P complex) - U5 Sm ring focused map
Kinetoplastid trans-spliceosome (Combined C*/P complex) - NTC focused map 2
Kinetoplastid trans-spliceosome activated for catalytic step II (C* complex) - EJC focused map
Kinetoplastid post-catalytic trans-spliceosome (P complex) - Core focused map
Kinetoplastid post-catalytic trans-spliceosome (P complex) - Overall map
Kinetoplastid post-catalytic trans-spliceosome (P complex) - SNU114 focused map
Kinetoplastid trans-spliceosome (Combined C*/P complex) - U2 snRNP focused map
Chlorophyll synthase in complex with the LHC-like protein HliD, apo state
mechanosensitive channel MscS from Francisella tularensis in DDM, asymmetric processing
mechanosensitive channel MscS from Francisella tularensis, mutant K70A
Cryo-Em structure of incomplete encapsulins from Brevibacteriumlinens
mechanosensitive channel MscS from Francisella tularensis in DM, asymmetric processing
mechanosensitive channel MscS from Francisella tularensis, mutant K94A, asymmetric processing
Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7 (focused map: C2 DH core)
Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7 (focused map: Sld3 MRD1:Mcm6)
Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7 (consensus map, 882k particles)
Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7 (focused map: Sld3 MRD2:Mcm4)
Cryo-EM structure of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA (composite map)
Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7 (DH core C-lobe twist state I)
Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7 (focused map: Sld7:Mcm6)
Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7 (DH core C-lobe twist states consensus map, 511k particles)
Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA (consensus map, 107k particles)
Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7 (DH core C-lobe twist state II)
Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7 (DH core C-lobe twist state III)
Cryo-EM map of MCM2-7 DH bound to DNA and two copies of Sld3-Sld7 and Cdc45 (C2 symmetry)
Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA (focused map: Sld3 MRD1/2:Mcm4/6)
Negative stain-EM map of crosslinked gradient purified Sld3-Sld7-Cdc45
Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA (focused map: Sld7:Mcm6)
Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA (focused map: C2 DH core)
Cryo-EM map of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA (focused map: Sld3 STD/Cdc45:Mcm2/5)
Cryo-EM map of MCM2-7 DH bound to DNA and two copies of Sld3-Sld7 and Cdc45 (C1 symmetry)
Cryo-EM consensus map of PSI-LHCI-LHCII supercomplex from Euglena gracilis
Cryo-EM focused refinement map of LHC-(6-9) from Euglena gracilis
Cryo-EM structure of the human KPTN-ITFG2-SZT2(2189-3432) complex
Cryo-EM structure of the human KPTN-ITFG2-C12orf66-SZT2(2189-3432) complex
Focused refinement map of PRP19-LSm region from the human minor spliceosome exon-ligation-ready C* complex
Alpha-7 nicotinic acetylcholine receptor bound to inhibitory bicyclic peptide KP1877 in a resting state
Cryo-EM Structure of Alcohol Dehydrogenase Variant from Gluconobacter oxydans Truncating Membrane-Binding Regions (Form 1)
Cryo-EM Structure of Alcohol Dehydrogenase Variant from Gluconobacter oxydans Truncating Membrane-Binding Regions (Form 2)
Dictyostelium discoideum cytoplasmic dynein motor domain in the presence of ADP (ADP state 2)
Dictyostelium discoideum cytoplasmic dynein motor domain in complex with ADP.Vi (Phi-particle)
Structure of SpCas9 with engineered disulfide bonds (R1210C/V1280C and L1119C/P1128C)
Dictyostelium discoideum cytoplasmic dynein motor domain in the presence of ADP (ADP state 1)
Cryo-EM structure of the human PKR dimer with mitapivat (focused refinement, asymmetric single-bound state A)
Dictyostelium discoideum cytoplasmic dynein motor domain in the absence of nucleotide (Apo state 2)
Cryo-EM structure of the human PKR tetramer with mitapivat (C2 symmetric, dual-bound state)
Cryo-EM structure of helicase DruE in the Druantia anti-phage system elucidates its anti-phage mechanism
Cryo-electron tomogram of His6-tagged D13 assembled into scaffold-like particles from vaccinia virus
Dictyostelium discoideum cytoplasmic dynein motor domain in the presence of ADP (Apo state 1)
Cryo-electron tomogram of in vitro assembly product of untagged D13, Twister
Cryo-EM structure of helicase DruE in the Druantia anti-phage system elucidates its anti-phage mechanism
Cryo-EM structure of helicase DruE in the Druantia anti-phage system elucidates its anti-phage mechanism
Cryo-EM structure of helicase DruE in the Druantia anti-phage system elucidates its anti-phage mechanism
Cryo-EM structure of human pyruvate kinase R (PKR) in complex with FBP
Cryo-EM structure of the human PKR dimer with mitapivat (focused refinement, asymmetric single-bound state B)
Cryo-EM structure of the human PKR dimer with mitapivat (focused refinement, asymmetric dual-bound state)
Structure of hemagglutinin from influenza A virions determined by sub-tomogram averaging
Focused map for area 1 of Vibrio cholerae Avs2 bound to phage terminase
Client peptide-bound structure of a MucD trimer within a 24mer cage
Client peptide-bound structure of a MucD trimer within a 12mer cage
Cryo-EM focused refinement map of LHC-10 of the PSI-LHCI-LHCII supercomplex from Euglena gracilis
Cryo-EM structure of helicase DruE in the Druantia anti-phage system elucidates its anti-phage mechanism
Cryo-EM structure of helicase DruE in the Druantia anti-phage system elucidates its anti-phage mechanism
Cryo-EM structure of helicase DruE in the Druantia anti-phage system elucidates its anti-phage mechanism
Cryo-EM structure of helicase DruE in the Druantia anti-phage system elucidates its anti-phage mechanism
Cryo-EM structure of helicase DruE in the Druantia anti-phage system elucidates its anti-phage mechanism
Cryo-EM structure of helicase DruE in the Druantia anti-phage system elucidates its anti-phage mechanism
Cryo-EM structure of helicase DruE in the Druantia anti-phage system elucidates its anti-phage mechanism
Cryo-EM structure of helicase DruE in the Druantia anti-phage system elucidates its anti-phage mechanism
Cryo-EM structure of helicase DruE in the Druantia anti-phage system elucidates its anti-phage mechanism
Cryo-EM structure of helicase DruE in the Druantia anti-phage system elucidates its anti-phage mechanism
Cryo-EM structure of helicase DruE in the Druantia anti-phage system elucidates its anti-phage mechanism
PEDV HNXX spike trimer with three D0 down in complex with three N19 Fabs
Cryo-EM structure of helicase DruE in the Druantia anti-phage system elucidates its anti-phage mechanism
Cryo-EM Structure of the oligomeric LPOR:Chlide:NADPH Complexes RF-23
Cryo-EM structure of MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-6
Cryo-EM structure of MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-58
Cryo-EM structure of MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-4
Structure of angiotensin II type 1 receptor bound to a b-arrestin biased allosteric modulator stabilized by a synthetic nanobody
Cryo-EM structure of translating Escherichia coli 70S ribosome bound to mRNA, P-site QKF-peptidyl-tRNAPhe, glycyl-tRNAGly in A/T conformation, EF-Tu-GDP, and bottromycin at 2.01A resolution
Negative Stain Electron Microscopy map of the Measles Virus Fusion Glycoprotein Ectodomain in Complex with the Neutralizing Antibody 3D04
Cryo-EM structure of the Escherichia coli 70S ribosome bound to mRNA, P-site fMet-tRNAfMet, glycyl-tRNAGly in A/T conformation, EF-Tu-GDPCP, and bottromycin at 1.99A resolution
Pseudomonas aeruginosa 50S ribosome bound to RsfS (L1 stalk 'in' conformation)
Pseudomonas aeruginosa 50S ribosome bound to RsfS (L1 stalk in 'out' conformation and missing uL1 and tRNA)
Pseudomonas aeruginosa 50S ribosome bound to RsfS (L1 stalk in 'out' conformation)
Pseudomonas aeruginosa 50S ribosome bound to RsfS (L7/L12 Stalk local map)
Hybrid Rubisco containing Arabidopsis thaliana large subunit and Oryza sativa small subunit RbcS1
Hybrid Rubisco containing Arabidopsis thaliana large subunit and Limonium gibertii small subunit
Hybrid Rubisco containing Arabidopsis thaliana large subunit and Sorghum bicolor small subunit
Pseudomonas aeruginosa 50S ribosome bound to RsfS (L1 Stalk domain 'in' conformation)
Pseudomonas aeruginosa 50S ribosome bound to RsfS (L1 Stalk domain 'mid' conformation)
Pseudomonas aeruginosa 50S ribosome bound to RsfS (L1 stalk in 'mid' conformation)
Pseudomonas aeruginosa 50S ribosome bound to RsfS (L1 Stalk domain 'out' conformation)
Pseudomonas aeruginosa 50S ribosome bound to RsfS (L1 Stalk domain 'out' conformation and missing uL1 and tRNA)
A Bundled Antiparallel Cytochrome Nanowire Produced by Desulfuromonas soudanensis WTL
In situ cryo-EM structure of the MS ring RBM3 of the flagellar motor in Borrelia burgdorferi
In situ cryo-EM structure of the flagellar export gate in complex with the FliF RBM12 ring in Borrelia burgdorferi
In situ cryo-EM structure of the MS RBM12 inner ring of the flagellar motor in Borrelia burgdorferi
In situ cryo-EM structure of the MS RBM12 outer ring of the flagellar motor in Borrelia burgdorferi
In situ cryo-EM structure of the FlhA-TMD of the flagellar motor in Borrelia burgdorferi
In situ cryo-EM structure of the export apparatus and MS-ring of the flagellar basal body from Borrelia burgdorferi
Subtomogram average structure of flagellar export apparatus and MS-ring in Borrelia burgdorferi
Consensus map of human FASN aligned by condensing wings (2M particles)
PDB 10RN EMD-75411 Human RNase PNK bound to ATPyS ligand consensus EM map
PDB 10RR EMD-75414 Human RNase PNK bound to AMPPNP ligand + rCAA in PNK active site consensus EM map
PDB 10RN EMD-75411 Human RNase PNK bound to ATPyS ligand focused EM map
PDB 10RR EMD-75414 Human RNase PNK bound to AMPPNP ligand + rCAA in PNK active site focused EM map
Bacterial Proteasome Activator Bpa from Mycobacterium tuberculosis in the dodecameric state
Bacterial Proteasome Activator Bpa from Mycobacterium tuberculosis bound to a native substrate HspR
Bacterial Proteasome Activator Bpa from Mycobacterium tuberculosis in the undecameric state
Cryo-EM map of M. smegmatis 70S complex State M3 (P-tRNA, A-tRNA, Body closed)
Structure of a single human ELF2 transcription factor in complex with a nucleosome
Cryo-EM map of SKM-M. smegmatis 70S complex State M5 (P/E-tRNA, A/P-tRNA)
Structure of two human ELF2 transcription factors in complex with a nucleosome, subclass 1 focused refinement
Cryo-EM map of SKM-M. smegmatis 70S complex State M4 (P/E-tRNA, vacant A-site)
Cryo-EM map of SKM-M. smegmatis 70S complex State M2 (P-tRNA, A-tRNA, Body open)
Structure of two human ELF2 transcription factors in complex with a nucleosome, focused refinement
Cryo-EM map of SKM-M. smegmatis 70S complex State M1 (P-tRNA, vacant A-site)
Structure of two human ELF2 transcription factors in complex with a nucleosome, subclass 1
Cryo-EM Structure of the 13-Mer ATPase Complex YsaN from the Type III Secretion System of Yersinia enterocolitica
Cryo-EM Structure of the 11-Mer ATPase Complex YsaN from the Type III Secretion System of Yersinia enterocolitica
Cryo-EM structure of human ATR-ATRIP complex with ATPgammaS, Chk1 and ETAA1
Cryo-EM structure of human phosphorylate ATR-ATRIP complex with ATPgammaS
Cryo-EM structure of human ATR-ATRIP complex with ATPgammaS, Chk1 and TopBp1
Asymmetric structure of the capsid-portal complex of Lactococcus phage Nocturne116
Structure of the portal and head-tail connector of Lactococcus phage Nocturne116
Cryo-EM structure of the insect sex pheromone receptor ApisOR22-Orco heterocomplex bound with nepetalactone in the closed state.
Cryo electron microscopic analysis of the adduct of syringolin analog with the Mtb 20S proteasome
Cryo-EM Structure of GTP Cyclohydrolase I from Candida albicans bound to 8-oxo GTP at 1.74 A
Cryo-EM structure of human DDB1-CRBN-GSPT1 in complex with GT19630
Cryo-EM structure of amyloidogenic antimicrobial peptide aurein 1.2 polymorph 2 in aqueous solution
Cryo-EM structure of amyloidogenic antimicrobial peptide Aurein 1.2 polymorph 1 in acqueous solution
Cryo-EM structure of amyloidogenic antimicrobial peptide Brevinin-1OKc polymorph 1 in PBS pH 6.5
Cryo-EM structure of amyloidogenic antimicrobial peptide Brevinin-1OKc polymorph 1 in water
Cryo-EM structure of amyloidogenic antimicrobial peptide Brevinin-1OKc polymorph 2 in PBS pH 6.5
CyroEM structure of the complex between Shiga toxin Stx1a B subunit and neutralising Fab fragment of RDS059
CryoEM structure of DruE:ATPgammaS:DNA from Druantia type III - monomer
CryoEM structure of DruE:ATPgammaS:DNA from Druantia type III - dimer 4
Cryo-EM Structure of Native Monomeric Quinol-Dependent Nitric Oxide Reductase from Achromobacter xylosoxidans.
CryoEM structure of DruE:ATPgammaS:DNA from Druantia type III - dimer 1
CryoEM structure of DruE:ATPgammaS:DNA from Druantia type III - dimer 2
CryoEM structure of DruE:ATPgammaS:DNA from Druantia type III - dimer 5
CryoEM structure of DruE:ATPgammaS:DNA from Druantia type III - dimer 3