This repository contains all experimental validated ensemble from Al-Hashimi lab
TAR
This is the folder including all the HIV-1-TAR Ensembles
The Measured RDCs and PALES predicted RDCs for the TAR ensembles were also supplied as a csv file. The measured RDCs is in "rdc" column, the PALES predicted value (after scaling) is in "rdc_pred" column and the scaling factor used for scaling predicted RDC to measured RDC for each alignment are in "scaling" column
For FARFAR-NMR ensemble, we also supply the structure after in silico elongation in order to reproduce the results
Anton_TAR_Ens_N20.pdb
Selected by NMR RDC
Anton-MD-NMR Ensemble (N=20)
Citation: Salmon L. et al. 2013 JACS
FARFAR_TAR_Ens_N20.pdb (PDBID: 7JU1)
Selected by NMR RDC
FARFAR-NMR Ensemble (N=20)
Citation: Shi H. et al. 2020 Nat Commun
A6-DNA
This is the folder including all the A6-DNA duplex Ensemble
A6-DNA_Ens_N10.pdb
Selected by NMR RDC
Amber MD Ensemble (N=10)
Citation: Sathyamoorthy B. et al. 2017 NAR
A6-DNAm1A16
This is the folder including all the A6-DNAm1A16 duplex Ensemble
A6-DNAm1A16_Ens_N15.pdb
Selected by NMR RDC
Amber MD Ensemble (N=15)
Citation: Sathyamoorthy B. et al. 2017 NAR
A2-DNA
This is the folder including all the A2-DNA duplex Ensemble
A2-DNA_Ens_N6.pdb
Selected by NMR RDC
Amber MD Ensemble (N=6)
Citation: Sathyamoorthy B. et al. 2017 NAR
A2-DNAm1A16
This is the folder including all the A2-DNAm1A16 duplex Ensemble
A2-DNAm1A16_Ens_N10.pdb
Selected by NMR RDC
Amber MD Ensemble (N=10)
Citation: Sathyamoorthy B. et al. 2017 NAR
Elongation
This is the folder including all the helices used for TAR in-silico elongation
The Python Code for elongate TAR helix was put in the same "Elongation" folder: elongate.py and we supply a dummy test case for HIV-1 TAR and do in silico elongation of EI22, EI3, EII22
tar_stem1_el_v3.pdb
For elongate TAR Helix I
Citation: Salmon L. et al. 2013 JACS
tar_stem2_el_v2.pdb
For elongate TAR Helix II
Citation: Salmon L. et al. 2013 JACS
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All experimentally determined dynamic ensembles from Al-Hashimi lab