Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?

BMC Bioinformatics

Table 9 Criteria used to discriminate the models at 300 K

Class	Model	RMSd mean	RMSd fluct.	Clusters	SSEs	Satisfaction score
all-α	NS0	+	+	++	++	+++
	ST1	+	+	++	++	+++
	ST2	+	+	++	++	+++
	ST3	+	+	-	+	- -
	DT1	+	++	++	++	+++
	DT2	- -	-	++	++	+++
all-β	NS0	+	+	++	+	+++
	ST1	+	+	++	+	+++
	ST2	+	+	++	-	+++
	DT1b	-	-	- -	- -	+++
	DT1a	+	+	++	+	+++
	DT2	-	+	- -	- -	+++
αβ	NS0	+	+	++	++	+++
	ST1	+	+	++	++	+++
	ST2	+	+	+	+	- -
	ST3	+	+	+	+	- -
	DT1	+	+	++	-	+++
	DT2	- -	+	+	-	+++

RMSd mean, RMSd uctuations, number of clusters along the trajectory, evolution of the secondary structures, hydrophobic and polar satisfaction score. The number of '+' symbolises the confidence in the criterion result. For instance the hydrophobic/polar satisfaction score provides a quantitative answer that is easy to interpret whereas results provided by the RMSd mean are more difficult to judge. The '-' indicates false positives or negatives.

ISSN: 1471-2105