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+optimized	22
optimized	32
not optimized	7

Ligand Modelling Category

independently refit	49
optimized	12

Effort type

fully automated	9
partially automated, some manual steps	49
manual	3

Ligand initial source

PDB Chemical Component Dictionary (CCD)	10
Crystallography Online Database (COD)	3
coordinates from PDB entry	36
Other	12

Ligand restraints software

BUSTER/Grade	1
phenix elbow	26
ccp4 acedrg	6
other/MD Force Field	13
other/PyRosetta	7
other/Multiple Sources	7
other/COOT mon_lib	3
other/CGENFF	1
other/Schrodinger LigPrep	1
other/Antechamber	1
other/OpenBabel	1

Modelling software (indicate all used)

AMBER	1
ARP/wARP	3
CCP-EM	3
Chimera	31
ChimeraX	7
COOT	15
CDMD	1
DeepTracer	8
EMDA	3
ISOLDE	4
LAFTER	2
mainmast	2
MDFF	10
modeller	3
pathwalker	3
phenix	7
ProSMART	3
pymol	7
refmac	6
rosetta	15
Schrodinger	7
servalcat	3
VMD	11

Restraints/Methods (indicate all used)

bond lengths, angles	30
dihedrals angles	27
planarity	27
chirality	33
secondary structure-protein	21
secondary structure-nucleic acid	14
nonbonded (vdW)	18
riding hydrogen atoms	5
explicit hydrogen atoms	23
charge assignments	18
molecular dynamics force field	28
other	31

Atomic Displacement (B) and Occupancy

single overall B value applied to entire model	2
grouped B (per residue)	6
individual B for each atom	23
neigbor restraints	11
occupancy refinement or occupancy reduced for specific atoms/residues	6
other	3
none	29

Final model optimization software

Chimera	7
COOT	3
CDMD	4
MDFF	10
phenix	20
refmac	3
rosetta	10
Schrodinger	1
VMD	3

Did you modify the map?

yes	4
no	57

EMDR information release

yes

61