Table 1.

Tiam1-PDZ:peptide complexes and free energies used for model fitting.

Complex	Exp.a	Comp.	Error	PB	VdW	SA	Rest.b	Corr.c
Sdc1d	0.00	0.00 (0.1)	0.00	0.00	0.00	0.00	0.00	0.00
Sdc1.A0F	0.43	0.16 (0.1)	−0.27	0.19	−4.21	−47.95	0.00	0.00
Sdc1.E4K	0.81	0.98 (0.2)	0.17	2.62	−0.17	−12.94	0.28	0.00
Sdc1.E4L	0.56e	0.49 (0.2)	−0.07	1.95	−1.30	−8.08	0.00	0.00
Sdc1.E3D, Y1T	0.87e	0.41 (0.1)	−0.46	1.67	2.08	12.05	0.00	0.00
Sdc1.E3T, Y1K	1.33e	0.38 (0.1)	−0.95	1.49	3.49	15.64	0.00	0.00
Sdc1.F2I	0.80e	0.26 (0.1)	−0.54	0.38	−0.44	−42.27	0.00	0.00
Sdc1.A0mA	0.04f	0.62 (0.1)	0.58	2.06	2.46	−13.51	0.00	0.00
Sdc3	0.13	0.21 (0.1)	0.08	0.38	1.38	−23.06	0.00	0.00
Consensus	0.84	0.48 (0.1)	−0.36	2.72	3.35	67.97	0.00	0.00
YAAEKYWA	0.72	0.36 (0.1)	−0.36	2.10	4.73	64.29	0.00	0.00
YAAKAFRF	1.17	1.35 (0.1)	0.18	4.70	5.02	53.73	0.29	0.00
YAAYRYRA	1.32g	1.26 (0.1)	−0.06	4.07	1.66	−18.18	0.14	0.00
YAARKFAK	1.32g	1.30 (0.1)	−0.02	3.81	7.13	5.44	0.23	0.00
YAAKRTYV	1.32g	1.14 (0.1)	−0.18	3.72	8.01	49.20	0.25	0.00
YAAGRKHF	1.32g	1.52 (0.2)	0.20	3.49	2.11	14.15	0.66	0.00
YAALIHKF	1.32g	0.98 (0.1)	−0.34	2.70	1.16	−2.87	0.27	0.00
YAAQKHFH	1.32g	0.92 (0.2)	−0.40	2.59	−1.74	−34.81	0.17	0.00
QM:CADM1	0.87	1.43 (0.2)	0.56	5.74	4.77	24.95	0.00	0.00
L911M:Sdc1	0.15	0.32 (0.2)	0.17	0.62	−1.03	−45.29	0.00	0.00
K912E:Sdc1	0.97	0.58 (0.2)	−0.39	2.27	−0.99	−8.66	0.00	0.00
L911M,K912E:Sdc1	1.21	0.54 (0.1)	−0.67	1.71	−1.52	−35.42	0.00	0.00
L915F:Sdc1	0.65	0.05 (0.2)	−0.60	0.04	−0.98	−13.78	0.00	0.00
L920V:Sdc1	0.31	−0.07 (0.2)	−0.38	−1.10	0.17	−48.56	0.01	0.00
L915F,L920V:Sdc1	1.32	0.19 (0.2)	−1.13	−0.24	1.03	−27.04	0.12	0.00
QM:Sdc1	0.89	0.27 (0.1)	−0.62	−0.02	−0.83	−71.82	0.00	0.00
QM:Sdc1.A0F	0.22	0.20 (0.2)	−0.02	0.26	1.50	−26.96	0.00	0.00
QM:Caspd	−0.23	−0.23 (0.1)	0.00	3.35	1.86	10.98	0.00	−1.06
WT:Casp	−0.21	−0.37 (0.1)	−0.16	2.04	2.77	32.77	0.26	−1.06
WT:Caspr.F0A	0.52	−0.57 (0.1)	−1.09	2.90	3.61	77.81	0.00	−1.06
L911M:Casp	−0.39	0.00 (0.1)	0.39	2.81	3.49	24.68	0.39	−1.06
K912E:Casp	0.46	0.09 (0.1)	−0.37	2.70	−0.44	−50.13	0.28	−1.06
L911M,K912E:Casp	0.04	−0.01 (0.1)	−0.05	3.41	2.57	22.74	0.24	−1.06
L915F:Casp	0.48	−0.45 (0.1)	−0.93	2.33	0.78	−2.68	0.00	−1.06
L920V:Casp	−0.54	−0.51 (0.1)	0.03	2.29	−0.28	4.82	0.00	−1.06
L915F,L920V:Casp	0.62	−0.37 (0.1)	−0.99	2.49	−0.07	−17.92	0.00	−1.06
QM:Caspr.F0A	1.09	−0.22 (0.1)	−1.31	4.59	3.78	95.58	0.00	−1.06

Experimental and computed (PB/LIE) binding free energies, their deviation, and the computed components (PB, van der Waals, SA terms). Energies in kcal/mol; SA in Ų. Protein is WT unless otherwise mentioned. Peptide positions are numbered backwards from the C-terminus (position 0).

^aFrom earlier work (Shepherd et al., 2011; Liu et al., 2013) unless otherwise mentioned.

^bRestraint energy.

^cFree energy correction (Equation 6).

^dThe Sdc1 sequence is TKQEEFYA. The Caspr4 sequence is ENQKEYFF.

^eThis work.

^fFrom alchemical FEP simulations, this work.

^gLower bound.