Table 2. Output of the CovCys module for test case 1(PDB ID: 3GCD) and test case 2 (PDB ID: 2OU7).

PDB ID	ResID	CavID	Cov	Probability	pKa	QSASA	pKdAve
3GCD	CYS_A_140	cavity_1	Yes	0.90	7.70	0.23	6.81
	CYS_A_140	cavity_3	No	0.17	7.70	0.23	5.37
2OU7	CYS_A_67	cavity_1	Yes	0.91	9.24	0.16	6.92
	CYS_A_67	cavity_8	No	0.19	9.24	0.16	4.89
	CYS_A_133	cavity_1	Yes	0.92	11.33	0.16	6.92
	CYS_A_133	cavity_9	No	0.09	11.33	0.16	4.84
	CYS_A_212	cavity_1	No	0.28	7.34	0.59	6.92
	CYS_A_212	cavity_2	No	0.49	7.34	0.59	6.57
	CYS_A_212	cavity_4	No	0.29	7.34	0.59	5.55
	CYS_A_239	cavity_3	No	0.21	11.15	0.06	5.66
	CYS_A_239	cavity_5	No	0.38	11.15	0.06	5.49
	CYS_A_164	None	undetermined	0.00	7.84	0.09	None
	CYS_A_255	None	undetermined	0.00	5.15	0.30	None
	CYS_A_318	None	undetermined	0.00	10.68	0.09	None

Note. ResID: cysteine residues ID of the protein; CavID: the cavity ID detected by the CAVITY; Cov: the predicted annotation of being a covalent targetable cysteine; Probability: the probability of being a covalent targetable cysteine. pKa: the pKa value predicted by the PROPKA program (30); QSASA: the exposure degree of the cysteine, which is calculated by dividing the solvent accessible surface area (SASA) of this cysteine with the theoretical SASA, which is calculated by the Pops program (31). pKdAve: the average binding affinity of the associated pocket, which is calculated by CAVITY.