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PDBspheres.README_INSTALLATION.txt
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PDBspheres.README_INSTALLATION.txt
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PDBspheres software
Adam T. Zemla, Jonathan E. Allen, Dan Kirshner, Felice C. Lightstone. (2022) "PDBspheres - a method for finding 3D similarities
in local regions in proteins", bioRxiv preprint https://doi.org/10.1101/2022.01.04.474934
PDBspheres is a structure-based method for finding and evaluating structural similarities in protein regions relevant to
ligand binding. PDBspheres comprises an exhaustive library of protein structure regions (“spheres”) adjacent to complexed
ligands derived from the Protein Data Bank (PDB), along with methods to find and evaluate structural matches between a protein
of interest and spheres in the library. PDBspheres uses the LGA structure alignment algorithm as the main engine for detecting
structure similarities between the protein of interest and template spheres from the library, which currently contains more
than 2 million spheres. To assess confidence in structural matches an all-atom-based similarity metric takes sidechain placement
into account.
Correspondence should be addressed to:
Adam T. Zemla
Global Security Computing Applications
Lawrence Livermore National Laboratory
Livermore, CA, 94550, USA
Tel: US +1 (925) 423-5571;
Fax: US +1 (925) 423-6437;
Email: zemla1@llnl.gov
AVAILABILITY
The PDBspheres library and scripts how to use the LGA program are made publicly available for download at
https://github.com/LLNL/PDBspheres
# Library of PDBspheres compound binding sites:
Library.Pdb_HET.at_least_1_HETATM_and_5_CA.list.txt.zip size 147M
# Library of PDBspheres short-peptide binding sites:
Library.Pdb_PEP.peptide_25_and_sphere_5_CA.list.txt.zip size 7.6M
# A summary table of predicted pocket-ligands for a structural model of papain-like proteinase (PL2pro model: nCoV_nsp3.6w9c_A.pdb).
PDBspheres.COVID19_PL2pro.protein_ligand_summary.txt.zip size 7.4K
# Results from PDBspheres analysis of pairwise similarities in binding sites between proteins from PDBbind v.2019.
PDBspheres.PDBbind_Binding_sites_similarities.GDC_and_affinities.txt.zip size 21M
# Specifics of assigned EC annotations for each member of created clusters of PDBbind.
PDBspheres.PDBbind_Clusters.EC_included.txt.zip size 37K
# Specifics of assigned GO annotations for each member of created clusters of PDBbind.
PDBspheres.PDBbind_Clusters.GO_included.txt.zip size 76K
# Specifics of assigned SCOP annotations for each member of created clusters of PDBbind.
PDBspheres.PDBbind_Clusters.SCOP_included.txt.zip size 38K
# HTML file allowing interactive overview of predicted clusters of proteins from PDBbind.
PDBspheres.PDBbind_Clusters.interactive_plot.html.zip size 4.0M
SOFTWARE INSTALLATION
1. Download "Library.Pdb_HET.at_least_1_HETATM_and_5_CA.list.txt.zip" from: https://github.com/LLNL/PDBspheres
2. unzip Library.Pdb_HET.at_least_1_HETATM_and_5_CA.list.txt.zip
3. Download "Library.Pdb_PEP.peptide_25_and_sphere_5_CA.list.txt.zip" from: https://github.com/LLNL/PDBspheres
4. unzip Library.Pdb_PEP.peptide_25_and_sphere_5_CA.list.txt.zip
5. Download LGA package (LGA_package_src.tar.gz) from: http://proteinmodel.org/AS2TS/LGA
6. tar -zxvf LGA_package_src.tar.gz
7. mv Library.Pdb_HET.at_least_1_HETATM_and_5_CA.list.txt LGA_package_src/PDBspheres/
8. mv Library.Pdb_PEP.peptide_25_and_sphere_5_CA.list.txt LGA_package_src/PDBspheres/
9. Install local version of the PDB database. For example, the "pdbnxyz.ent" files should be made accessible in the folder "LGA_package_src/PDB_local".
USAGE
cd LGA_package_src
./runlga.model_sphere_library.pl model sphere library
EXAMPLES OF USAGE
1. Running simple similarity check between PL2pro model ("PDBspheres/nCoV_nsp3.6w9c_A.pdb") and a single
compound (HET: Sphere.Y97.35.7los_B.404_B.12.pdb) binding site sphere from preselected PDBspheres.HET_compound_library.txt
cd LGA_package_src
./runlga.model_sphere_library.pl PDBspheres/nCoV_nsp3.6w9c_A.pdb Sphere.Y97.35.7los_B.404_B.12.pdb PDBspheres/PDBspheres.HET_compound_library.txt
./runlga.model_sphere_library.pl PDBspheres/nCoV_nsp3.6w9c_A.pdb Sphere.ZN.1.7kol_A.505_A.12.pdb PDBspheres/Pdb_HET.at_least_1_HETATM_and_5_CA.list.txt
./runlga.model_sphere_library.pl PDBspheres/nCoV_nsp3.6w9c_A.pdb Sphere.GOL.14.6bi8_B.1906_B.12.pdb PDBspheres/Pdb_HET.at_least_1_HETATM_and_5_CA.list.txt
2. Running simple similarity check between PL2pro model ("PDBspheres/nCoV_nsp3.6w9c_A.pdb") and a single
short-peptide (PEP: Sphere.6wx4.6wx4_D.6wx4_I.5_3_4_30.12.pdb) binding site sphere from preselected PDBspheres.PEP_peptides_library.txt
cd LGA_package_src
./runlga.model_sphere_library.pl PDBspheres/nCoV_nsp3.6w9c_A.pdb Sphere.6wx4.6wx4_D.6wx4_I.5_3_4_30.12.pdb PDBspheres/PDBspheres.PEP_peptides_library.txt
3. Running similarity check between PL2pro model ("PDBspheres/nCoV_nsp3.6w9c_A.pdb") and 20 compound (HET) sphere binding sites
from preselected PDBspheres.HET_compound_library.txt
cd LGA_package_src
for s in `cut -f15 -d' ' PDBspheres/PDBspheres.HET_compound_library.txt | cut -f3 -d'/' | sort -n -r -k 3 -t. | head -n 20`; do \
./runlga.model_sphere_library.pl PDBspheres/nCoV_nsp3.6w9c_A.pdb $s PDBspheres/PDBspheres.HET_compound_library.txt; \
done >> TEST.reproduce_results_reported_in_PDBspheres.COVID19_PL2pro.protein_ligand_summary.txt
4. Running similarity check between PL2pro model ("PDBspheres/nCoV_nsp3.6w9c_A.pdb") and short-peptide (PEP) sphere binding sites
from preselected PDBspheres.PEP_peptide_library.txt
cd LGA_package_src
for s in `cut -f15 -d' ' PDBspheres/PDBspheres.PEP_peptides_library.txt | cut -f3 -d'/'`; do \
./runlga.model_sphere_library.pl PDBspheres/nCoV_nsp3.6w9c_A.pdb $s PDBspheres/PDBspheres.PEP_peptides_library.txt; \
done >> TEST.reproduce_results_reported_in_PDBspheres.COVID19_PL2pro.protein_ligand_summary.txt
5. Results collected in the file: TEST.reproduce_results_reported_in_PDBspheres.COVID19_PL2pro.protein_ligand_summary.txt
correspond to the subset of results reported in the PDBspheres manuscript (Fig.4): https://www.biorxiv.org/content/10.1101/2022.01.04.474934v2
Please compare with PDBspheres.COVID19_PL2pro.protein_ligand_summary.txt