Table VI.

Comparison of H3 Loop Predictions with Homology Modeling and the Prime Ab Initio Method

H3 RMSD (Å)	H3 length	Best in database	Using crystal structure		Using homology model
			Homology prediction	Prime prediction	Homology prediction	Prime prediction
AM2	11	1.69	4.35	2.78	6.49	2.29
AM3	8	0.88	1.48	0.37	1.41	1.49
AM4	8	0.72	2.20	0.65	3.31	2.04
AM5	8	1.00	2.35	2.37	1.80	1.78
AM6	14	2.60	3.12	3.11	3.04	4.69
AM7	8	1.46	2.33	0.45	1.88	1.50
AM8	11	1.68	3.30	1.25	3.34	3.99
AM9	10	0.73	1.89	0.54	2.50	3.78
AM10	11	1.53	2.79	0.85	2.27	2.05
AM11	10	0.37	2.56	0.40	3.10	3.10
Average		1.26	2.64	1.28	2.91	2.67

Best in database: The H3 loop in the PDB database with the best backbone RMSD to the crystallographic conformation of the target H3 loop. Using crystal structure: H3 loops built in the context of the remainder of the antibody structure taken from crystallographic coordinates. Using homology model: H3 loops built in the context of the remainder of the antibody structure taken from our “Model #1” submission from the first part of this assessment.