Antibody optimization protocol
Project description
Looping Uniquely Catered Amino Acid Sequences
Free software: MIT license
Documentation: https://locuaz.readthedocs.io.
Install
Check the Installation section on the docs..
Mambaforge is recommended instead of pure conda. Download Mambaforge from:
https://github.com/conda-forge/miniforge
Why there’s no straight pip or conda install
Being this a high-level protocol, there are many dependencies to it and, unfortunately, python packaging has its quirks so different developers have solved their issues in different ways. A straight pip install is out of the question given the tensorflow (for DLPacker) and ambertools (for tleap) dependencies. On the other hand, not all packages have a conda recipe (freesasa), and while the biobb packages do show up on the bioconda channel, when installed in this manner, they bring over many unwanted, heavy dependencies, like GROMACS itself. So, in summary, a mix of pip and conda is needed.
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
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
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
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
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
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
Inside the bluues folder, make symbolic links to the binaries so it has a proper name:
ln -s bin/bluues_new_2 bluues
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
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:
charges.rtp
library.npz
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
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.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.