BMC Bioinformatics

Table 1 Comparison of AMMP optimization methods for small molecules minimized with sp4 and sp5 force fields

From: AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening

			Optimization methods
Compound		Initial Energy	Steepest descent		Conjugate gradient		BFGS		Simplex		GA
			N_iter	E_min	N_iter	E_min	N_iter	E_min	N_iter	E_min	N_iter	E_min
raloxifene	sp4	121.08	20	86.72	1600	66.71	1500	75.89	80	102.24	300	69.97
	sp5	117.41	20	88.46	1000	71.65	1200	77.62	100	107.03	300	70.89
	RMSD			0.01		1.23		0.05		0.14		0.42
FDI	sp4	119.61	30	74.02	200	66.14	1200	64.38	10	268.07	300	48.95
	sp5	116.89	30	75.48	300	67.94	1000	67.96	10	283.08	200	51.83
	RMSD			0.01		0.12		0.02		0.14		1.14
thymidine	sp4	99.64	30	64.82	400	60.52	500	61.17	20	114.81	300	61.40
	sp5	95.78	20	68.49	200	64.29	1000	64.57	10	99.78	200	65.85
	RMSD			0.01		0.09		0.03		0.06		0.63
PR2	sp4	156.55	50	-5.22	300	-14.57	700	-13.58	10	78.01	200	-5.77
	sp5	155.04	50	1.11	300	-13.01	600	-11.77	20	72.18	200	-12.73
	RMSD			0.07		0.02		0.01		0.02		0.61

The number of iterations needed to reach convergence (Niter) and the minimized energy (Emin in kcal/mol) and the RMSD values (in Å) between the optimized structures with sp4 and sp5 force fields are given.

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