Learning probabilistic models of hydrogen bond stability from molecular dynamics simulation trajectories

BMC Bioinformatics

Table 1 Characteristics of the MD simulation trajectories used to create the 6 datasets

Trajectory	Protein	# res.	Force field	Duration	# H-bonds	# occurrences
*1c9oA*	Cold shock protein	66	ENCAD [12] with F3C explicit water model	10ns	263	363463
*1e85A*	Cytochrome C	124	Same as above	10ns	525	1253879
*1g9oA_1*	PDZ1 domain of human Na(+)/H(+) exchanger regulatory factor	91	Same as above	10ns	374	558761
*1g9oA_2*	Same as above	91	Same as above	10ns	397	544491
*complex*	Efb-C/C3d complex formed by the C3d domain of human Complement Component C3 and one of its bacterial inhibitors	362	Amber 2003 with implicit solvent using the General Born solvation method [13]	2ns	1825	348943
*1eia*	EIAV capsid protein P26	207	Amber 2003 with SPC/E water model	2ns	757	379573

ISSN: 1471-2105