locuaz 0.2.0

Antibody optimization protocol

Looping Uniquely Catered Amino Acid Sequences

• Free software: MIT license

• Documentation: https://locuaz.readthedocs.io.

Install

Mambaforge is recommended instead of pure conda. Download Mambaforge from:

https://github.com/conda-forge/miniforge

Clone this repo and, optionally, get the DLPacker submodule as well:

git clone https://github.com/pgbarletta/locuaz
git submodule int
git submodule update

You’ll also have to get DLPacker’s weights.

Post-Install

If on MDAnalysis 2.4.3 or older, edit the file MDAnalysis/topology/tpr/utils.py line 330:

segid = f"seg_{i}_{molblock}"

replace it with:

segid = molblock[14:] if molblock[:14] == "Protein_chain_" else molblock

On scoring

All scoring functions (SFs) should be inside the ['paths']['scoring_functions'] (see input config yaml) directory. Their folder names should match the exact SF names used in the config file and their binaries should be on the top level of their folders and also be named with the exact SF name. Some scoring functions have additional requirements, like parameter files, or the case of gmxmmpbsa which is included with the protocol and only needs an input text file.

Additional requirements for specific SFs

Assuming a scoring functions folder set to: ['paths']['scoring_functions']=home/user/my_SFs.

gmxmmpbsa

gmxmmpbsa directory: home/user/my_SFs/gmxmmpbsa

This is the only scoring function that comes bundled with the protocol. Inside the gmxmmpbsa folder, a gmxmmpbsa input text file is needed. The contents are up to the user. For example, for a simple MM-GBSA:

&general
sys_name="Prot-Prot",
startframe=51,
endframe=250,
/
&gb
igb=2, saltcon=0.150,
/

And if residue decomposition is needed (for a mmpbsa generator):

&general
sys_name="Prot-Prot",
startframe=51,
endframe=250,
/
&gb
igb=2, saltcon=0.150,
/
&decomp
idecomp=2, dec_verbose=0,
print_res="within 4"
/

pisa

pisa directory: home/user/my_SFs/pisa

pisa binary: home/user/my_SFs/pisa/pisa

pisa parameters: home/user/my_SFs/pisa/pisa.params

rosetta

rosetta directory: home/user/my_SFs/rosetta

Symbolic links on the top rosetta folder should be added, pointing to files in the rosetta installation Eg: inside the main rosetta folder, with the rosetta directory called sources:

ln -s sources/rosetta_source/bin/InterfaceAnalyzer.linuxgccrelease rosetta
ln -s sources/rosetta_database/ rosetta_database
ln -s sources/rosetta_source/build/src/release/linux/4.14/64/ppc64le/gcc/8.4/ parameters
ln -s sources/rosetta_source/build/external/release/linux/4.14/64/ppc64le/gcc/8.4/ external_parameters

haddock

haddock directory: home/user/my_SFs/haddock

As with all the scoring functions, all the necessary files have to be at the top level. The template_scoring.inp file has to be at the top level of the haddock, as the rescoring-scripts folder (included with the protocol insed the sample_bin folder). Then, the following smybolic links have to be created. Version number and specific folder names and locations may change:

ln -s ./cns_solve_1.3/ibm-ppc64le-linux/bin/cns haddock
ln -s haddock/protocols/ protocols
ln -s haddock/toppar/ toppar
ln -s cns_solve_1.3/cns_solve_env cns_solve_env
ln -s haddock/haddock_configure.csh haddock_configure.csh

piepisa

piepisa directory: home/user/my_SFs/piepisa

Download pie. If you can run the binary, good, if you can’t, then you probably won’t be able to run it, since compiling and running it in a modern PC is quite cumbersome. Then, normalize the directory to the scoring functions standard:

• rename the pie folder to piepisa

• be sure to also have the pisa scoring function

• Inside the piepisa folder, make symbolic links to the binaries and parameters so they have proper names:

  ln -s bin/pie_score pie
  ln -s bin/pie.params pie.params
  ln -s ../pisa/pisaEnergy_linux pisa
  ln -s ../pisa/pisa.params pisa.params

evoef2

evoef2 directory: home/user/my_SFs/evoef2

Download and compile evoef2.

• rename the EvoEF2 folder to evoef2

• Inside the evoef2 folder, make a symbolic link to the binary so it has a proper name:

  ln -s bin/evoef2 evoef2

bluues

bluues directory: home/user/my_SFs/bluues

• Inside the bluues folder, make symbolic links to the binaries so it has a proper name:

  ln -s bin/bluues_new_2 bluues

bluuesbmf

bluuesbmf directory: home/user/my_SFs/bluuesbmf

• Inside the bluuesbmf folder, make symbolic links to the binary so it has a proper name:

  ln -s bin/bluues_new_2 bluues
  ln -s bin/score_bmf_3 bmf

autodockvina

autodockvina directory: home/user/my_SFs/autodockvina

Download autodockvina. Then, normalize the directory to the scoring functions standard: * create a folder named autodockvina with the downloaded binary * Inside the autodockvina folder, make symbolic links to the binary so it has a proper name:

ln -s vina_1.2.3_linux_x86_64 autodockvina

Mutators

• DLPacker is included as a submodule. To download it:

  git submodule init
  git submodule update

Then, in a dlpacker directory, the following files have to be present:

1. charges.rtp

2. library.npz

3. DLPacker_weights.h5

The first 2 can be copied from the recently downloaded directory (locuaz/DLPacker). The weights have to be downloaded. Then, the path to the dlpacker directory has to be specified in the input config under the paths key, on the mutator option.

Generators

• gmxmmpbsa based generators like SPM4gmxmmpbsa need a residue decomposition file from gmxmmpbsa, so the gmxmmpbsa script needs to include something along the lines of:

  /
  &decomp
  idecomp=2, dec_verbose=0,
  print_res="within 4"
  /

Credits

• Biobb

• MDAnalysis

• FreeSASA

MIT License

Copyright (c) [year] [fullname]

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.