2021 Ligand Model Challenge Summary Statistics

Challenge Target

beta-galactosidase 1.9 Å (EMD-7770)23
SARS-CoV-2 RNA polymerase 2.5 Å (EMD-30210)17
SARS-Cov-2 ORF3a ion channel 2.1 Å (EMD-22898)21

Polymer Modelling Category

ab initio+optimized22
optimized32
not optimized7

Ligand Modelling Category

independently refit49
optimized12

Effort type

fully automated9
partially automated, some manual steps49
manual3

Ligand initial source

PDB Chemical Component Dictionary (CCD)10
Crystallography Online Database (COD)3
coordinates from PDB entry36
Other12

Ligand restraints software

BUSTER/Grade1
phenix elbow26
ccp4 acedrg6
other34

Modelling software (indicate all used)

AMBER1
ARP/wARP3
CCP-EM3
Chimera31
ChimeraX7
COOT15
CDMD1
DeepTracer8
EMDA3
ISOLDE4
LAFTER2
mainmast2
MDFF10
modeller3
pathwalker3
phenix7
ProSMART3
pymol7
refmac6
rosetta15
Schrodinger7
servalcat3
VMD11

Restraints/Methods (indicate all used)

bond lengths, angles30
dihedrals angles27
planarity27
chirality33
secondary structure-protein21
secondary structure-nucleic acid14
nonbonded (vdW)18
riding hydrogen atoms5
explicit hydrogen atoms23
charge assignments18
molecular dynamics force field28
other31

Atomic Displacement (B) and Occupancy

single overall B value applied to entire model2
grouped B (per residue)6
individual B for each atom23
neigbor restraints11
occupancy refinement or occupancy reduced for specific atoms/residues6
other3
none29

Final model optimization software

Chimera7
COOT3
CDMD4
MDFF10
phenix20
refmac3
rosetta10
Schrodinger1
VMD3

Did you modify the map?

yes4
no57

EMDR information release

yes61