alhashimilab / Ensemble

All experimentally determined dynamic ensembles from Al-Hashimi lab

Ensemble

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