MAIDEN (Model quality Assessment for Intramembrane Domains using an ENergy criterion) is a statistical potential optimized on native alpha-helica and beta-sheet membrane protein structures. MAIDEN computes pseudo-energies for transmembrane domains of native or predicted protein structures, in order to evaluate their quality.
The set of structures used for the calculation of MAIDEN contains 66 representative structures (41 alpha and 25 beta) from the PDBTM database (Tusnady, et al., 2005) determined by crystallography at <2.5 A resolution and with an R-factor <0.3 (see below):
1JB0 2F93 2VDF 3EMN 3SZV 4AL0 1KQF 2FGQ 2W2E 3GIA 3TDS 4AMJ 1OKC 2GR7 2WJR 3GP6 3TIJ 4DVE 1QD5 2HDI 2WSW 3HD6 3TX3 4DX5 1QJP 2J58 2X27 3KVN 3V5U 4E1S 1U19 2J7A 2X55 3M73 3VY8 4EIY 1UUN 2MPR 2X9K 3N5K 3W54 4ENE 1XKW 2O4V 2XOV 3PCV 3WBN 4EZC 1YC9 2Q67 2YEV 3PGU 3ZUX 4HFI 2A65 2QTS 3ARC 3QRA 4A01 4IKW 2BL2 2R9R 3DH4 3RLF 4AFK 7AHL
To benchmark MAIDEN and others methods, we have generated 700 predicted structures (alpha and beta) by homology modelling and used the 15340 membrane protein models of EVfold_membrane (Hopf et al., 2012).
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