Table 1.

Comparison of different protein structure evaluation programs and servers

	ProCheck	ProCheck NMR	WhatCheck (Whatif)	MolProbity	VADAR	OOPS	PROSESS
Program or Server	Program	Program	Program & Server	Server & Program	Server & Program	Program	Server
Protein evaluation	Yes	Yes	Yes	Yes	Yes	Yes	Yes
DNA/RNA evaluation	No	No	Partial	Yes	No	No	No
Handles NMR (NOE/δ) data	No	Yes	No	No	No	No	Yes
Secondary structure calc.	Yes	Yes	Yes	No	Yes	No	Yes
Bond length check	Yes	Yes	Yes	Yes	No	No	Yes
Bond angle check	Yes	Yes	Yes	Yes	No	No	Yes
Planarity and Chiral check	Yes	Yes	Yes	No	No	Yes	No
H-bond check	Yes	Yes	Yes	Yes	Yes	No	Yes
Volume check & calculation	No	No	No	No	Yes	No	Yes
Surface area check & calc	No	No	Yes	No	Yes	No	Yes
Heavy atom bump check	No	No	Yes	Yes	No	No	Yes
H-atom bump check (clash)	No	No	No	Yes	No	No	Yes
His/Asn/Gln flip check	No	No	No	Yes	No	No	Yes
VDW energy calculation	No	No	No	No	No	No	Yes
Threading energy calc.	No	No	No	No	Yes	No	Yes
B-factor check or correlation	No	No	Yes	Yes	No	Yes	Yes
Ramachandran check (global)	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Ramachandran check (res spc)	No	No	No	Yes	No	Yes/No	Yes
Side chain torsion check	Yes	Yes	Yes	Yes	Yes	Yes	Yes
NOE statistics calculations	No	Yes	No	No	No	No	Yes
NOE violation check	No	Yes	No	No	No	No	Yes
Chemical shift check	No	No	No	No	No	No	Yes
Ensemble RMSF check	No	No	No	No	No	No	Yes
Graphs & plots	Yes	Yes	Yes	No	Yes	Yes	Yes
Structure images/maps	No	No	Yes	Yes	No	No	Yes