BLDB: Beta-lactamases
CYTC: Cytochrom c
GFP: GFP
Ras: Ras GTPase
Metadata of protein structures used for training can be found in /data/*.csv
.
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
environment
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- alsa-lib=1.2.8=h166bdaf_0
- argon2-cffi=23.1.0=pyhd8ed1ab_1
- argon2-cffi-bindings=21.2.0=py310ha75aee5_5
- argtable2=2.13=hd590300_1004
- arrow=1.3.0=pyhd8ed1ab_1
- attr=2.5.1=h166bdaf_1
- attrs=25.3.0=pyh71513ae_0
- autodock-vina=1.1.2=h9ee0642_3
- blas=1.0=openblas
- bleach-with-css=6.2.0=h82add2a_4
- blosc=1.21.5=hc2324a3_1
- bottleneck=1.3.7=py310ha9d4c09_0
- brotli-bin=1.0.9=h5eee18b_8
- brotli-python=1.0.9=py310hd8f1fbe_8
- bzip2=1.0.8=h5eee18b_6
- c-ares=1.19.1=h5eee18b_0
- ca-certificates=2025.1.31=hbcca054_0
- cached-property=1.5.2=hd8ed1ab_1
- cached_property=1.5.2=pyha770c72_1
- cairo=1.18.0=h3faef2a_0
- cffi=1.17.1=py310h8deb56e_0
- chardet=5.2.0=pyhd8ed1ab_3
- clustalo=1.2.4=h503566f_9
- colorama=0.4.6=py310h06a4308_0
- comm=0.2.2=pyhd8ed1ab_1
- contourpy=1.2.0=py310hdb19cb5_0
- curl=8.12.1=h251f7ec_0
- custom-inherit=2.4.1=pyhd8ed1ab_0
- cycler=0.11.0=pyhd3eb1b0_0
- cyrus-sasl=2.1.28=h52b45da_1
- dbus=1.13.18=hb2f20db_0
- defusedxml=0.7.1=pyhd8ed1ab_0
- dendropy=5.0.6=pyhdfd78af_0
- emboss=6.6.0=hfb8fa87_10
- ete3=3.1.3=pyhd8ed1ab_0
- exceptiongroup=1.2.2=pyhd8ed1ab_1
- executing=2.1.0=pyhd8ed1ab_1
- expat=2.6.3=h6a678d5_0
- fasttree=2.1.11=h7b50bb2_5
- fftw=3.3.10=nompi_hf1063bd_110
- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- font-ttf-inconsolata=3.000=h77eed37_0
- font-ttf-source-code-pro=2.038=h77eed37_0
- font-ttf-ubuntu=0.83=h77eed37_3
- fontconfig=2.14.2=h14ed4e7_0
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- fonttools=4.51.0=py310h5eee18b_0
- fqdn=1.5.1=pyhd8ed1ab_1
- freetype=2.12.1=h267a509_2
- freetype-py=2.3.0=pyhd8ed1ab_0
- future=1.0.0=pyhd8ed1ab_2
- gettext=0.23.1=h5888daf_0
- gettext-tools=0.23.1=h5888daf_0
- glew=2.1.0=h295c915_3
- glib=2.78.4=hfc55251_0
- glib-tools=2.78.4=hfc55251_0
- glm=0.9.9.8=h00ab1b0_0
- graphite2=1.3.13=h59595ed_1003
- gst-plugins-base=1.18.4=h29181c9_0
- gstreamer=1.22.0=h25f0c4b_2
- gstreamer-orc=0.4.41=h17648ed_0
- h11=0.14.0=pyhd8ed1ab_1
- h2=4.2.0=pyhd8ed1ab_0
- harfbuzz=8.3.0=h3d44ed6_0
- hdf4=4.2.15=h9772cbc_5
- hdf5=1.12.2=nompi_h4df4325_101
- hdf5-1107=1.10.7=0
- hpack=4.1.0=pyhd8ed1ab_0
- hyperframe=6.1.0=pyhd8ed1ab_0
- icu=73.2=h59595ed_0
- idna=3.10=pyhd8ed1ab_1
- importlib-metadata=8.6.1=pyha770c72_0
- importlib_resources=6.5.2=pyhd8ed1ab_0
- ipykernel=6.29.5=pyh3099207_0
- ipywidgets=8.1.5=pyhd8ed1ab_1
- isoduration=20.11.0=pyhd8ed1ab_1
- jack=1.9.22=h11f4161_0
- joblib=1.4.2=py310h06a4308_0
- jpeg=9e=h5eee18b_3
- jsonpointer=3.0.0=py310hff52083_1
- jsonschema=4.23.0=pyhd8ed1ab_1
- jsonschema-specifications=2024.10.1=pyhd8ed1ab_1
- jsonschema-with-format-nongpl=4.23.0=hd8ed1ab_1
- jupyter=1.1.1=pyhd8ed1ab_1
- jupyter-lsp=2.2.5=pyhd8ed1ab_1
- jupyter_client=8.6.3=pyhd8ed1ab_1
- jupyter_console=6.6.3=pyhd8ed1ab_1
- jupyter_core=5.7.2=pyh31011fe_1
- jupyter_events=0.12.0=pyh29332c3_0
- jupyter_server=2.15.0=pyhd8ed1ab_0
- jupyter_server_terminals=0.5.3=pyhd8ed1ab_1
- jupyterlab=4.3.6=pyhd8ed1ab_0
- jupyterlab_pygments=0.3.0=pyhd8ed1ab_2
- jupyterlab_server=2.27.3=pyhd8ed1ab_1
- jupyterlab_widgets=3.0.13=pyhd8ed1ab_1
- kiwisolver=1.4.4=py310h6a678d5_0
- krb5=1.20.1=h143b758_1
- lame=3.100=h166bdaf_1003
- lcms2=2.12=h3be6417_0
- ld_impl_linux-64=2.40=h12ee557_0
- lerc=3.0=h295c915_0
- libabseil=20250127.0=cxx17_hbbce691_0
- libaec=1.1.3=h59595ed_0
- libasprintf=0.23.1=h8e693c7_0
- libasprintf-devel=0.23.1=h8e693c7_0
- libbrotlicommon=1.0.9=h5eee18b_8
- libbrotlidec=1.0.9=h5eee18b_8
- libbrotlienc=1.0.9=h5eee18b_8
- libcap=2.67=he9d0100_0
- libclang=15.0.7=default_h127d8a8_5
- libclang13=15.0.7=default_h5d6823c_5
- libcups=2.3.3=h36d4200_3
- libcurl=8.12.1=hc9e6f67_0
- libdb=6.2.32=h9c3ff4c_0
- libdeflate=1.12=h166bdaf_0
- libedit=3.1.20230828=h5eee18b_0
- libev=4.33=h7f8727e_1
- libevent=2.1.10=h28343ad_4
- libexpat=2.6.3=h5888daf_0
- libffi=3.4.4=h6a678d5_1
- libflac=1.4.3=h59595ed_0
- libgcc=14.1.0=h77fa898_1
- libgcc-ng=14.1.0=h69a702a_1
- libgcrypt=1.11.0=ha770c72_2
- libgcrypt-devel=1.11.0=hb9d3cd8_2
- libgcrypt-lib=1.11.0=hb9d3cd8_2
- libgcrypt-tools=1.11.0=hb9d3cd8_2
- libgd=2.3.3=h695aa2c_1
- libgettextpo=0.23.1=h5888daf_0
- libgettextpo-devel=0.23.1=h5888daf_0
- libgfortran-ng=8.2.0=hdf63c60_1
- libgfortran5=14.1.0=hc5f4f2c_1
- libglib=2.78.4=h783c2da_0
- libglu=9.0.0=hf484d3e_1
- libgomp=14.1.0=h77fa898_1
- libgpg-error=1.51=hbd13f7d_1
- libharu=2.4.4=h267a509_0
- libiconv=1.18=h4ce23a2_1
- libidn2=2.3.8=ha4ef2c3_0
- libllvm14=14.0.6=hcd5def8_4
- libllvm15=15.0.7=hadd5161_1
- libltdl=2.4.3a=h5888daf_0
- libnetcdf=4.9.1=nompi_h34a3ff0_101
- libnghttp2=1.57.0=h2d74bed_0
- libnsl=2.0.1=hd590300_0
- libogg=1.3.5=h4ab18f5_0
- libopenblas=0.3.21=h043d6bf_0
- libopus=1.3.1=h7f98852_1
- libpng=1.6.43=h2797004_0
- libpq=17.4=hdbd6064_0
- libprotobuf=5.29.3=hc99497a_0
- libsndfile=1.2.2=hc60ed4a_1
- libsodium=1.0.18=h36c2ea0_1
- libsqlite=3.45.2=h2797004_0
- libssh2=1.11.1=h251f7ec_0
- libstdcxx=14.1.0=hc0a3c3a_1
- libstdcxx-ng=14.1.0=h4852527_1
- libsystemd0=253=h8c4010b_1
- libtiff=4.4.0=hc85c160_1
- libtool=2.5.4=h5888daf_0
- libudev1=253=h0b41bf4_1
- libunistring=0.9.10=h7f98852_0
- libuuid=2.38.1=h0b41bf4_0
- libvorbis=1.3.7=h9c3ff4c_0
- libwebp-base=1.3.2=h5eee18b_0
- libxcb=1.15=h0b41bf4_0
- libxkbcommon=1.7.0=h662e7e4_0
- libxml2=2.12.7=hc051c1a_1
- libxslt=1.1.39=h76b75d6_0
- libzip=1.10.1=h2629f0a_3
- libzlib=1.2.13=h4ab18f5_6
- lxml=5.2.2=py310h6a33d3d_0
- lz4-c=1.9.4=h6a678d5_1
- matplotlib=3.9.2=py310h06a4308_0
- matplotlib-base=3.9.2=py310hbfdbfaf_0
- matplotlib-inline=0.1.7=pyhd8ed1ab_1
- modeller=10.6=py310h9bf148f_0
- mpg123=1.32.9=hc50e24c_0
- multipledispatch=0.6.0=pyhd8ed1ab_1
- mysql=8.4.0=h721767e_2
- mysql-common=8.0.33=hf1915f5_6
- mysql-libs=8.0.33=hca2cd23_6
- nbconvert-core=7.16.6=pyh29332c3_0
- nbformat=5.10.4=pyhd8ed1ab_1
- ncurses=6.4=h6a678d5_0
- nest-asyncio=1.6.0=pyhd8ed1ab_1
- notebook-shim=0.2.4=pyhd8ed1ab_1
- nspr=4.36=h5888daf_0
- nss=3.98=h1d7d5a4_0
- numexpr=2.8.7=py310h286c3b5_0
- numpy=1.26.4=py310heeff2f4_0
- numpy-base=1.26.4=py310h8a23956_0
- openjpeg=2.5.0=h7d73246_1
- openldap=2.6.5=h389dcaa_0
- openssl=3.4.1=h7b32b05_0
- outcome=1.3.0.post0=pyhd8ed1ab_1
- overrides=7.7.0=pyhd8ed1ab_1
- packaging=24.1=py310h06a4308_0
- pandas=2.2.2=py310h6a678d5_0
- parso=0.8.4=pyhd8ed1ab_1
- pcre2=10.42=hcad00b1_0
- pexpect=4.9.0=pyhd8ed1ab_1
- pickleshare=0.7.5=pyhd8ed1ab_1004
- pillow=11.0.0=py310hfdbf927_0
- pip=24.2=py310h06a4308_0
- pixman=0.44.2=h29eaf8c_0
- pkgutil-resolve-name=1.3.10=pyhd8ed1ab_2
- ply=3.11=py310h06a4308_0
- pmw=2.0.1=py310hff52083_1008
- prometheus_client=0.21.1=pyhd8ed1ab_0
- prompt_toolkit=3.0.50=hd8ed1ab_0
- pthread-stubs=0.4=hb9d3cd8_1002
- ptyprocess=0.7.0=pyhd8ed1ab_1
- pulseaudio=16.1=hcb278e6_3
- pulseaudio-client=16.1=h5195f5e_3
- pulseaudio-daemon=16.1=ha8d29e2_3
- pure_eval=0.2.3=pyhd8ed1ab_1
- pybind11-abi=4=hd3eb1b0_1
- pycairo=1.27.0=py310h25ff670_0
- pycparser=2.22=pyh29332c3_1
- pymol-open-source=2.5.0=py310h5b21ba0_6
- pyparsing=3.1.2=py310h06a4308_0
- pypng=0.20220715.0=pyhd8ed1ab_1
- pyqt=6.7.1=py310h6a678d5_0
- pyqt5-sip=12.13.0=py310h5eee18b_0
- pyqt6-sip=13.9.1=py310h5eee18b_0
- pysocks=1.7.1=pyha55dd90_7
- python=3.10.13=hd12c33a_0_cpython
- python-dateutil=2.9.0post0=py310h06a4308_2
- python-fastjsonschema=2.21.1=pyhd8ed1ab_0
- python-json-logger=2.0.7=pyhd8ed1ab_0
- python-tzdata=2023.3=pyhd3eb1b0_0
- python_abi=3.10=2_cp310
- pytz=2024.1=py310h06a4308_0
- pyyaml=6.0.2=py310h89163eb_2
- pyzmq=26.2.0=py310h71f11fc_1
- qt-main=6.7.2=h06a4308_0
- qt5compat=6.7.2=h0902c3e_0
- qtbase=6.7.2=hdaa5aa8_1
- qtdeclarative=6.7.2=h6a678d5_0
- qtimageformats=6.7.2=h7fa0f6f_0
- qtshadertools=6.7.2=h6a678d5_0
- qtsvg=6.7.2=he621ea3_0
- qttools=6.7.2=h80c7b02_0
- qttranslations=6.7.2=h6a678d5_0
- qtwebchannel=6.7.2=h6a678d5_0
- qtwebsockets=6.7.2=h6a678d5_0
- readline=8.2=h5eee18b_0
- reportlab=4.3.1=py310ha75aee5_0
- requests=2.32.3=pyhd8ed1ab_1
- rfc3339-validator=0.1.4=pyhd8ed1ab_1
- rfc3986-validator=0.1.1=pyh9f0ad1d_0
- rlpycairo=0.2.0=pyhd8ed1ab_0
- scipy=1.13.1=py310heeff2f4_0
- seaborn=0.13.2=py310h06a4308_0
- selenium=4.30.0=pyh29332c3_0
- selenium-manager=4.30.0=h6c30b3d_0
- send2trash=1.8.3=pyh0d859eb_1
- setuptools=75.1.0=py310h06a4308_0
- sip=6.10.0=py310h6a678d5_0
- six=1.16.0=pyhd3eb1b0_1
- snappy=1.2.1=h6a678d5_0
- sniffio=1.3.1=pyhd8ed1ab_1
- sortedcontainers=2.4.0=pyhd8ed1ab_1
- sqlite=3.45.3=h5eee18b_0
- stack_data=0.6.3=pyhd8ed1ab_1
- terminado=0.18.1=pyh0d859eb_0
- tk=8.6.13=noxft_h4845f30_101
- tomli=2.0.1=py310h06a4308_0
- tornado=6.4.1=py310h5eee18b_0
- toyplot=1.0.3=pyhd8ed1ab_0
- toytree=2.0.1=pyh9f0ad1d_0
- tqdm=4.67.1=pyhd8ed1ab_1
- traitlets=5.14.3=pyhd8ed1ab_1
- trio=0.29.0=py310hff52083_0
- trio-websocket=0.12.2=pyh29332c3_0
- typing_extensions=4.13.0=pyh29332c3_1
- typing_utils=0.1.0=pyhd8ed1ab_1
- tzdata=2024b=h04d1e81_0
- unicodedata2=15.1.0=py310h5eee18b_0
- uri-template=1.3.0=pyhd8ed1ab_1
- wcwidth=0.2.13=pyhd8ed1ab_1
- webencodings=0.5.1=pyhd8ed1ab_3
- websocket-client=1.8.0=pyhd8ed1ab_1
- wheel=0.44.0=py310h06a4308_0
- widgetsnbextension=4.0.13=pyhd8ed1ab_1
- wsproto=1.2.0=pyhd8ed1ab_1
- xcb-util=0.4.0=h516909a_0
- xcb-util-cursor=0.1.4=hd590300_1
- xcb-util-image=0.4.0=h8ee46fc_1
- xcb-util-keysyms=0.4.0=h516909a_0
- xcb-util-renderutil=0.3.9=hd590300_1
- xcb-util-wm=0.4.1=h516909a_0
- xkeyboard-config=2.38=h0b41bf4_0
- xorg-kbproto=1.0.7=hb9d3cd8_1003
- xorg-libice=1.1.2=hb9d3cd8_0
- xorg-libsm=1.2.6=he73a12e_0
- xorg-libx11=1.8.9=h8ee46fc_0
- xorg-libxau=1.0.12=hb9d3cd8_0
- xorg-libxdmcp=1.1.5=hb9d3cd8_0
- xorg-libxext=1.3.4=h0b41bf4_2
- xorg-libxrender=0.9.11=hd590300_0
- xorg-renderproto=0.11.1=hb9d3cd8_1003
- xorg-xextproto=7.3.0=hb9d3cd8_1004
- xorg-xproto=7.0.31=hb9d3cd8_1008
- xz=5.4.6=h5eee18b_1
- yaml=0.2.5=h7f98852_2
- zeromq=4.3.5=h59595ed_1
- zipp=3.21.0=pyhd8ed1ab_1
- zlib=1.2.13=h4ab18f5_6
- zstandard=0.23.0=py310ha75aee5_1
- zstd=1.5.6=ha6fb4c9_0
- pip:
- anyio==4.6.0
- asttokens==2.4.1
- async-lru==2.0.4
- babel==2.16.0
- beautifulsoup4==4.12.3
- biopython==1.85
- bleach==6.1.0
- bottle==0.13.2
- brotli==1.1.0
- certifi==2024.8.30
- charset-normalizer==3.4.0
- debugpy==1.8.7
- decorator==5.1.1
- ete4==4.0.0b2
- fastjsonschema==2.20.0
- httpcore==1.0.6
- httpx==0.27.2
- ipython==8.28.0
- jedi==0.19.1
- jinja2==3.1.4
- json5==0.9.25
- jupyter-events==0.10.0
- jupyter-server==2.14.2
- markupsafe==3.0.1
- mistune==3.0.2
- nbclient==0.10.0
- nbconvert==7.16.4
- notebook==7.2.2
- pandocfilters==1.5.1
- platformdirs==4.3.6
- prometheus-client==0.21.0
- prompt-toolkit==3.0.48
- psutil==6.0.0
- pygments==2.18.0
- python-dotenv==1.1.0
- ramachandraw==1.0.1
- referencing==0.35.1
- rpds-py==0.20.0
- soupsieve==2.6
- tinycss2==1.3.0
- types-python-dateutil==2.9.0.20241003
- typing-extensions==4.12.2
- urllib3==2.2.3
- webcolors==24.8.0
- webdriver-manager==4.0.2
- wget==3.2
Forked from https://zhanggroup.org/TM-align/ 1.
cd tmalign
g++ -static -O3 -ffast-math -lm -o TMalign TMalign.cpp
chmod +x ./TMalign
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/.
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
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
conda install conda-forge::vina
https://ccsb.scripps.edu/adfr/downloads/
conda install hcc::adfr-suite
conda install bioconda::reduce
conda install bioconda::clustalw
conda install bioconda::clustalo
conda install salilab::modeller
conda install bioconda::emboss
conda install bioconda::mgltools
Footnotes
-
Zhang, Y. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Research 33, 2302–2309. issn: 1362-4962. https://dx.doi.org/10.1093/nar/gki524 (Apr. 2005). ↩
-
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. https://dx.doi.org/10.1016/j.softx.2015.06.001 (Sept. 2015). ↩