neksa / PDBspheres

PDBspheres

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.

Manuscript submitted to bioRxiv:
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

LLNL-JRNL-829772

Correspondence should be addressed to:
Adam T. Zemla
Global Security Computing Applications
Lawrence Livermore National Laboratory
Livermore, CA, 94550, USA
Tel: US [phone]
Mobile1: [phone]
Mobile2: [phone]
Fax: US [phone]
Email: [e-mail]

Supplemental Data:
The PDBspheres library and instructions how to use the LGA program are made publicly available for download at https://github.com/LLNL/PDBspheres

1. Library of PDBspheres compound binding sites divided into 11 subsets in the folder PDBspheres-Libraries:

• Pdb_HET.at_least_1_HETATM_and_5_CA.list.Subset_01.zip size 22M
• Pdb_HET.at_least_1_HETATM_and_5_CA.list.Subset_02.zip size 22M
• Pdb_HET.at_least_1_HETATM_and_5_CA.list.Subset_03.zip size 22M
• Pdb_HET.at_least_1_HETATM_and_5_CA.list.Subset_04.zip size 22M
• Pdb_HET.at_least_1_HETATM_and_5_CA.list.Subset_05.zip size 22M
• Pdb_HET.at_least_1_HETATM_and_5_CA.list.Subset_06.zip size 22M
• Pdb_HET.at_least_1_HETATM_and_5_CA.list.Subset_07.zip size 22M
• Pdb_HET.at_least_1_HETATM_and_5_CA.list.Subset_08.zip size 22M
• Pdb_HET.at_least_1_HETATM_and_5_CA.list.Subset_09.zip size 22M
• Pdb_HET.at_least_1_HETATM_and_5_CA.list.Subset_10.zip size 22M
• Pdb_HET.at_least_1_HETATM_and_5_CA.list.Subset_11.zip size 22M

2. Library of PDBspheres short-peptide binding sites in the folder PDBspheres-Libraries:

• Library.Pdb_PEP.peptide_25_and_sphere_5_CA.list.txt.zip size 7.6M

3. 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

4. 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

5. Specifics of assigned EC annotations for each member of created clusters of PDBbind:

• PDBspheres.PDBbind_Clusters.EC_included.txt.zip size 37K

6. Specifics of assigned GO annotations for each member of created clusters of PDBbind:

• PDBspheres.PDBbind_Clusters.GO_included.txt.zip size 76K

7. Specifics of assigned SCOP annotations for each member of created clusters of PDBbind:

• PDBspheres.PDBbind_Clusters.SCOP_included.txt.zip size 38K

8. HTML file allowing interactive overview of predicted clusters of proteins from PDBbind:

• PDBspheres.PDBbind_Clusters.interactive_plot.html.zip size 4.0M