This toolkit was developed as a parasitology analysis protocol. The goal is to try to explain how certain protein mutations on the parasite affect antibody binding.
This is largely undocumented and disorganized, currently work in progress.
This README is also incomplete.
If someone is doing this type of research and is interested in using the software,
contact me over gabriel_scf@hotmail.com.
.aln files, such as those generated by Clustal when fed with a multifasta protein sequence file with many sequences of the same protein, one for each strain.
.csv files, such as those generated at iedb.org with the "export search" function.
.pdb files, such as those found at rcsb.org.
A docking protocol that creates an antibody based on heavy and light variable chain sequences, and dock them to a protein. Then it mutates the protein and tries again, checking how the mutation affected the protein.
This uses the Rosetta software suite and GROMACS md system.
You'll probably need to modify the pipeline to suit your needs.
This is best used with Rosetta MPI, enabling multicore runs.
To compile it with MPI just add extras=mpito your scons compile flags.
./scons.py -j 4 mode=release bin cxx=clang extras=mpi
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Each executable can be called with --help to see how its arguments work.
Shows, for each residue in the selected chain in the protein structure, the minimum distance from that residue from residues located in another chain, in the same .pdb file.
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