Building Confidence in Deep Generative Protein Design

Protein Structures Data

BLDB:   Beta-lactamases
CYTC:   Cytochrom c
GFP:    GFP
Ras:    Ras GTPase

Metadata of protein structures used for training can be found in /data/*.csv.

Generated Structures

B:      Backbone only
BQ:     Backbone + Optimal predicted sequences
BQS:    Backbone + Optimal preidcted sequences + homology modeled side-chains
BQSH:   Backbone + Optimal preidcted sequences + homology modeled side-chains + hydrogen atoms added
C:      Conserved residues
Q:      Optimal predicted sequences

Dependencies

Python Packages

TODO

TM-align

Forked from https://zhanggroup.org/TM-align/ ¹.

cd tmalign
g++ -static -O3 -ffast-math -lm -o TMalign TMalign.cpp
chmod +x ./TMalign

GROMACS

https://manual.gromacs.org/current/download.html ²

cd gromacs
tar xfz gromacs-2024.2.tar.gz
cd gromacs-2024.2
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC

For cuda users,

cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA -DCMAKE_CUDA_COMPILER=/usr/local/cuda/bin/nvcc

min_sd.mdp, nvt_heat.mdp, npt_prod.mdp, npt_eq.mdp, to_origin.tcl, del_wat_inside.tcl are derived from https://github.com/allison-group/structural-phylogenetics-bootstrap/blob/master/MD/GMX/.

CHARMM36 Force Field for GROMACS

https://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

charmm36-jul2022.ff.tgz (July 2022, ver.) https://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jul2022.ff.tgz

cd gromacs
tar xfz charmm36-jul2022.ff.tgz

VMD

Download VMD (e.g., vmd-1.9.4a57.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185.opengl.tar.gz) from https://www.ks.uiuc.edu/Research/vmd/ to ./vmd.

cd vmd
tar xfz vmd-1.9.4a57.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185.opengl.tar.gz
cd vmd-1.9.4a57
./configure
cd src
sudo make install

Autodock Vina

https://vina.scripps.edu/

conda install conda-forge::vina

ADFR Suite

https://ccsb.scripps.edu/adfr/downloads/

conda install hcc::adfr-suite

Reduce

conda install bioconda::reduce

ClustalW

conda install bioconda::clustalw

Modeller

conda install salilab::modeller

Emboss

conda install bioconda::emboss

conda install bioconda::mgltools

Footnotes

1. Zhang, Y. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Research 33, 2302–2309. issn: 1362-4962. http://dx.doi.org/10.1093/nar/gki524 (Apr. 2005). ↩

2. Abraham, M. J. et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25. issn: 2352-7110. http://dx.doi.org/10.1016/j.softx.2015.06.001 (Sept. 2015). ↩