rust_pdbloader

A bunch of Rust snippet to play with data in PDB (https://www.rcsb.org/).

These commits were created as a pointer to the state used in CASP14.

A large update is planned.

Note: This software has its own matrix calculation module. It (coding original module for matrix calculation) is HIGHLY DISCOURAGED. I recommend you to prepare other software for validating this software's output.

Requirement

Rust https://www.rust-lang.org/

Usage (Template Based Modeling)

git clone /~https://github.com/yamule/rust_pdbloader.git
cd rust_pdbloader
cargo run --release --  residue_mapping -sidechains "./resources/pepbuilderj/resources/sampledresidues/" -backbones "./resources/pepbuilderj/resources/sampledresidues/" -in "./example_files/T1094.1IW7_C.fas" -out "./example_files/results/T1094.1IW7_C.fas.mapped.pdb"
cargo run --release --  refinement -resource "./resources/" -angle "./resources/angle_distribution_energy.dat" -steps_checkpoint 1 -out "./example_files/results/T1094.1IW7_C.fas.refined1.pdb" -param_file "example_files/param_refine.txt"  -in "./example_files/results/T1094.1IW7_C.fas.mapped.pdb"  -flag "./example_files/results/T1094.1IW7_C.fas.mapped.pdb.flag" -build_missing_param1 "./example_files/param_build_missing.txt"  -build_missing_param2 "./example_files/param_build_missing2.txt"  -num_structurs_step1 5 -num_structurs_step2 1

Usage (Secondary Structure Assignment)

git clone /~https://github.com/yamule/rust_pdbloader.git
cd rust_pdbloader
cargo run --release --  ss_assign -in "example_files/1EFH_A.pdb"

Usage (Structural Alignment)

git clone /~https://github.com/yamule/rust_pdbloader.git
cd rust_pdbloader
cargo run --release --  structural_alignment -query ./example_files/1EFH_A.pdb -template ./example_files/2OV8_A.pdb -out_pdb ./example_files/1EFH_A_aligned.pdb
# Use "-type max" when you align unrelated or distantly related proteins (very slow)
# cargo run --release --  structural_alignment -type max -query ./example_files/1EFH_A.pdb -template ./example_files/2OV8_A.pdb -out_pdb ./example_files/1EFH_A_aligned.pdb

Energy functions or terms used in this software

solvation_parameters.dat

Lazaridis, Themis, and Martin Karplus. "Effective energy function for proteins in solution." Proteins: Structure, Function, and Bioinformatics 35.2 (1999): 133-152.

opt_nov15_lj_param.dat opt_nov15_partial_charge.dat

Park, Hahnbeom, et al. "Simultaneous optimization of biomolecular energy functions on features from small molecules and macromolecules." Journal of chemical theory and computation 12.12 (2016): 6201-6212.

CHARMM

Brooks, Bernard R., et al. "CHARMM: a program for macromolecular energy, minimization, and dynamics calculations." Journal of computational chemistry 4.2 (1983): 187-217.

EvoEF2

Huang, Xiaoqiang, Robin Pearce, and Yang Zhang. "EvoEF2: accurate and fast energy function for computational protein design." Bioinformatics 36.4 (2020): 1135-1142.