An Automated Pipeline for HIV-1 Envelope Glycoprotein Sequence Design To Achieve Prefusion-Closed Trimers
ADROITrimer has been successfully tested on Mac and Linux systems
- MUSCLE alignment software (https://www.drive5.com/muscle/). Please download and install.
- The R Project for Statistical Computing (https://www.r-project.org/).
Please download and install
- Mac: Go to https://cran.r-project.org/bin/macosx/ , download and install latest version.
- Linux: For instance in Ubuntu type into command line: sudo apt-get install r-base
- R library bio3d: In command line type
- R
- In R console type: install.packages("bio3d")
- Exit R console with CRTL-D
ADROITrimer can be run in the command line
3 files are required to be placed in current work directory (please download them from this repository from the required_files sub-directory)
- HIV1_FLT_2016_env_PRO_cleanLastCol_final.fasta
- 5fyl_trimer.pdb
- 5fyl_trimer.rsa
- HIV-1 Env target sequence (sequence you would like to be optimized) in FASTA format
- Clade/Subtype of target sequence (Clade can be for instance determined using RIP from LANL: https://www.hiv.lanl.gov/content/sequence/RIP/RIP.html)
- Path to installed MUCLE software (e.g. "/usr/local/bin/muscle")
R --no-save < ADROITrimer1.0-3.R target.fasta A /usr/bin/muscle
Multiple analysis and output files will be provided. The critical DS-SOSIP-RnS stabilized sequences are provided in FASTA format. In particular,
- With N- and C-terminal tags (N-terminal - Prolactin leader sequence, C-terminal - D7324-tag): output_xxx_DS-SOSIP-RnS_NtCt-tags.fasta (with xxx being a numeric value - time stamp)
- Without N- and C-terminal tags: output_xxx_DS-SOSIP-RnS.fasta (with xxx being a numeric value - time stamp) You would have to add signal peptide and any desired C-terminal tag.
Clade A Strain BG505 testing sequence (please find BG505.W6M.C2.fasta example sequence in example sub-directory)
R --no-save < ADROITrimer1.0-1.R BG505.W6M.C2.fasta A /usr/bin/muscle
Reda Rawi: reda.rawi@nih.gov