. Author manuscript; available in PMC: 2012 Oct 3.

Published in final edited form as: Proteomics. 2011 Nov 23;11(24):4660–4676. doi: 10.1002/pmic.201100058

Table 2.

Template evaluation using BLAST PDB search (E value) and RMSD of homology models from PyMOL. Homology models were constructed in MODELLER. Secondary and tertiary structure comparison.

Template	RMSD (Å)	E value
Collagen IX NC4 (2UUR)	0.828	5.0 × 10⁻¹⁰
Bovine Neurexin 1α LNS (21R6)	2.506	0.65
N-terminal Lg-domain Shbg (1LHN)	8.619	1.3
Thrombospondin (1Z78)	7.482	1.5

Basic Alignment Search Tool (BLAST) Protein Database (PDB), root mean square deviation (RMSD). Smaller values indicate better match between template structure and generated model. Expected value (E value) refers to the number of hits expected when searching a database. Smaller value indicates a more accurate match.