|
Id. |
PDB |
Type |
SubType |
ForceField |
Solvent |
Description |
Time (ns) |
Sequence |
|
NAFlex_GC-rich_crowd_Lys_500mM |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked TIP3P AddedSalt |
5,000 |
CACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGC |
|
NAFlex_GC-rich_crowd_Arg_500mM |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked TIP3P AddedSalt |
5,000 |
CACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGC |
|
NAFlex_GC-rich_crowd_neut_500mM |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked TIP3P AddedSalt |
5,000 |
CACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGC |
|
NAFlex_GC-rich_crowd_Na_500mM |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked TIP3P AddedSalt |
5,000 |
CACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGCGCACCGGGCGTGCACGCCCGGTGC |
|
NAFlex_ProtDNA_1zgw |
1ZGW |
Prot-Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral |
2,000 |
GCAAATTAAAGCGCAAGA |
|
NAFlex_BSC1-C36 |
1NAJ |
Dna |
B |
Charmm36 |
TIP3P |
DNA-B Duplex Naked Charmm36 TIP3P Electroneutral |
1,500 |
CGCGAATTCGCGCGCGAATTCGCG |
|
NAFlex_437d |
437D |
Rna |
A |
parmBSC0 |
TIP3P |
RNA-A Single Stranded Naked ParmBSC0 TIP3P Electroneutral Pseudoknot Flipout-bases Overhanging-bases Loops |
1,015 |
GGCGCGGCACCGUCCGCGGAACAAACGG |
|
NAFlex_2y95 |
2Y95 |
Rna |
A |
parmBSC1 |
TIP3P |
RNA-A Single-Stranded Naked ParmBSC1 TIP3P AddedSalt Hairpin-loop |
1,000 |
GGCGCAUCGGCGCC |
|
NAFlex_GGGC |
NONE |
Dna |
B |
parmBSC1 |
SPCE |
DNA-B Duplex Naked ParmBSC1 SPC/E AddedSalt |
1,000 |
GCGCGGGCGGGCGGGCGC |
|
NAFlex_lks4 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral |
1,000 |
GGCGCGCACCACGCGCGG |
|
NAFlex_1zgw |
1ZGW |
Dna |
B |
parmBSC1 |
SPCE |
DNA-B Duplex ParmBSC1 SPC/E AddedSalt |
1,000 |
GCAAATTAAAGCGCAAGA |
|
NAFlex_muAGGC |
NONE |
Dna |
B |
parmBSC0 |
SPCE |
DNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt |
1,000 |
GCGCAGGCAGGCAGGCGC |
|
NAFlex_muATGC |
NONE |
Dna |
B |
parmBSC0 |
SPCE |
DNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt |
1,000 |
GCGCATGCATGCATGCGC |
|
NAFlex_muCGCG |
NONE |
Dna |
B |
parmBSC0 |
SPCE |
DNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt |
1,000 |
GCCGCGCGCGCGCGCGGC |
|
NAFlex_muCGGC |
NONE |
Dna |
B |
parmBSC0 |
SPCE |
DNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt |
1,000 |
GCGCCGGCCGGCCGGCGC |
|
NAFlex_muGGGC |
NONE |
Dna |
B |
parmBSC0 |
SPCE |
DNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt |
1,000 |
GCGCGGGCGGGCGGGCGC |
|
NAFlex_muTGGC |
NONE |
Dna |
B |
parmBSC0 |
SPCE |
DNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt |
1,000 |
GCGCTGGCTGGCTGGCGC |
|
NAFlex_miniABC_K_3 |
NONE |
Dna |
B |
parmBSC1 |
SPC/E |
B-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol KCl |
1,000 |
GCAGAAACAGCTCTGCGC |
|
NAFlex_miniABC_K_4 |
NONE |
Dna |
B |
parmBSC1 |
SPC/E |
B-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol KCl |
1,000 |
GCAGGCGCAAGACTGAGC |
|
NAFlex_miniABC_Na_3 |
NONE |
Dna |
B |
parmBSC1 |
SPC/E |
B-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol NaCl |
1,000 |
GCAGAAACAGCTCTGCGC |
|
NAFlex_miniABC_Na_4 |
NONE |
Dna |
B |
parmBSC1 |
SPC/E |
B-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol NaCl |
1,000 |
GCAGGCGCAAGACTGAGC |
|
NAFlex_miniABC_NaK_3 |
NONE |
Dna |
B |
parmBSC1 |
SPC/E |
B-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol NaCl/KCl 50%/50% |
1,000 |
GCAGAAACAGCTCTGCGC |
|
NAFlex_miniABC_NaK_4 |
NONE |
Dna |
B |
parmBSC1 |
SPC/E |
B-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol NaCl/KCl 50%/50% |
1,000 |
GCAGGCGCAAGACTGAGC |
|
NAFlex_RNA_miniABC_KCl_4 |
NONE |
Rna |
A |
parmBSC0+OL3 |
TIP3P |
RNA-A Duplex Naked TIP3P AddedSalt |
1,000 |
GCAGGCGCAAGACUGAGC |
|
NAFlex_Z-DNA-4M |
1I0T |
Dna |
Z |
parmBSC1 |
TIP3P |
DNA-Z Duplex Naked ParmBSC1 TIP3P AddedSalt |
946 |
CGCGCGCGCG |
|
NAFlex_2hkb |
2HKB |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral |
590 |
CTCGGCGCCATC |
|
NAFlex_2m2c |
2M2C |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral |
590 |
GCGCATGCTACGCG |
|
NAFlex_56merL |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGCCGGCAGTAGCCGAAAAAATAGGCGCGCGCTCAAAAAAATGCCCCATGCCGCGC |
|
NAFlex_CTAG_10 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGCGCGCTAGCGCGGC |
|
NAFlex_CTAG_9 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGGCGCCTAGGCGCGC |
|
NAFlex_56merB |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
440 |
CGCCGGCAGTAGCCGAAAAAATAGGCGCGCGCTCAAAAAAATGCCCCATGCCGCGC |
|
NAFlex_PYR |
NONE |
Dna |
DNA unfolding |
parmBSC1 |
TIP3P |
DNA Duplex Naked ParmBSC1 TIP3P Electroneutral |
400 |
GGCGCC |
|
NAFlex_Z-DNA-0M |
1I0T |
Dna |
Z |
parmBSC1 |
TIP3P |
DNA-Z Duplex Naked ParmBSC1 TIP3P Electroneutral |
385 |
CGCGCGCGCG |
|
NAFlex_56merA |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
360 |
CGCCGGCAGTAGCCGAAAAAATAGGCGCGCGCTCAAAAAAATGCCCCATGCCGCGC |
|
NAFlex_56merSeq2 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked Parm99 TIP3P Electroneutral |
300 |
CGTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGCG |
|
NAFlex_ZDNA |
NONE |
Dna |
Z |
parmBSC1 |
TIP3P |
DNA-Z Duplex Naked ParmBSC1 TIP3P Electroneutral |
240 |
CGCGCGCGCG |
|
NAFlex_rna4 |
NONE |
Rna |
A |
parmBSC0 |
TIP3P |
RNA-A Duplex Naked ParmBSC0 TIP3P Electroneutral |
201 |
GGCGCGCACCACGCGCGG |
|
NAFlex_CG_OG1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTCXAACGCACGCXCGCGCTGTCCXCCGCGTTTCXACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_CG_OG2 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACXGCTTAAACCXACGTACGCGCXGTCCCCCGCXTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_CG_5hmC1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXGAACGCACGXGCGCGCTGTCXGCCGCGTTTXGACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_CG_5mC1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXGAACGCACGXGCGCGCTGTCXGCCGCGTTTXGACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_CG_noalch1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTCGAACGCACGCGCGCGCTGTCCGCCGCGTTTCGACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_CG_noalch2 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACGGCTTAAACCGACGTACGCGCGGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_TT_DZ1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXTAACGCACGXTCGCGCTGTCXTCCGCGTTTXTACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_TT_PP1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXXAACGCACGXXCGCGCTGTCXXCCGCGTTTXXACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_TT_SSB1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXTAACGCACGXTCGCGCTGTCXTCCGCGTTTXTACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_TT_TG1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXTAACGCACGXTCGCGCTGTCXTCCGCGTTTXTACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_TT_TT1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXXAACGCACGXXCGCGCTGTCXXCCGCGTTTXXACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_TT_noalch1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXTAACGCACGXTCGCGCTGTCXTCCGCGTTTXTACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_TF_6f57_14_dna_wholeA |
- |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked TIP3P Electroneutral |
200 |
AGAGCGCATG |
|
NAFlex_TF_6f57_14_dna_wholeB |
- |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked TIP3P Electroneutral |
200 |
AGAGCGCATG |
|
NAFlex_TF_6f57_16_dna_wholeA |
- |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked TIP3P Electroneutral |
200 |
AGAGCGCATG |
|
NAFlex_TF_6f57_16_dna_wholeB |
- |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked TIP3P Electroneutral |
200 |
AGAGCGCATG |
|
NAFlex_TF_6f57_14_wholeA |
- |
Prot |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
AGAGCGCATG |
|
NAFlex_TF_6f57_14_wholeB |
- |
Prot |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
AGAGCGCATG |
|
NAFlex_TF_6f57_16_wholeA |
- |
Prot |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
AGAGCGCATG |
|
NAFlex_TF_6f57_16_wholeB |
- |
Prot |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
AGAGCGCATG |
|
NAFlex_RNA_miniABC_KCl_3 |
|
Rna |
|
parmBSC0+OL3 |
|
|
- |
GCAGAAACAGCUCUGCGC |
|
NAFlex_TEST_HOSP |
|
Rna |
|
parmBSC0+OL3 |
|
|
- |
GCAGAAACAGCUCUGCGC |
