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Table 3 RMSD values (in Å) obtained after matching the optimized and initial structures (A) and the optimized and X-ray structures (B)

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

A

AMMOS

MMFF94s

Tff

raloxifene

0.80

0.84

1.34

FDI

0.14

0.49

1.13

thymidine

0.15

0.26

0.51

PR2

0.40

1.13

1.23

B

AMMOS

MMFF94s

Tff

raloxifene

2.12

2.39

1.51

FDI

1.88

1.90

1.52

thymidine

1.03

1.01

1.17

PR2

1.69

1.68

1.57

  1. The minimization with AMMOS is performed with 2×500 iterations and sp4 force field.
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BMC Bioinformatics

ISSN: 1471-2105

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