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


Chikalov et al. BMC Bioinformatics 2011 12(Suppl 1):S34   doi:10.1186/1471-2105-12-S1-S34

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