ProCare: Unexpected binding site similarity between HIV-1 reverse transcriptase and tumor necrosis factor revealed by computer vision

Prospective application of ProCare to identify subpocket similarities between structurally and functionally remote proteins.
Source data for:
Eguida, M., Rognan, D. Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision. J Cheminform 13, 90 (2021). https://doi.org/10.1186/s13321-021-00567-3

Contacts:
Merveille Eguida, keguida(at)unistra[dot]fr
Didier Rognan, rognan(at)unistra[dot]fr

Content

.
|-- input_data.tgz ---> prepared input structures for binding sites and ligands comparisons
|-- binding_sites_comparisons ---> pockets similarity/distance scores
|-------- fuzcav_scores.tsv
|-------- glosa_scores.tsv
|-------- kripo_scores.tsv
|-------- probis_scores.tsv
|-------- procare_scores.tsv
|-------- shaper_scores.tsv
|-------- sitealign_scores.tsv
|-- ligands_comparisons ---> ligands similarity scores
|-------- chembl_ligand_2d_similarity.tsv
|-------- rocs.tsv
|-------- tnf_hiv1rt_ligand_2D_similarity.tsv
|-- amino_acids_standard.txt ---> standard amino acid list used by SiteAlign
|-- hiv1_rt_chembl_potent_inhibitors.tsv ---> ChEMBL HIV-1 RT ligands for 2D comparisons
|-- hiv1_rt_chembl_targets.txt
|-- pdb_1vrt_query_results.txt ---> PDB query to retrieve HIV-1 RT structures + visual filtering
|-- pdb_1vrt_query_results_uniprot.txt ---> PDB query to retrieve HIV-1 RT structures + visual filtering
|-- pdb_1vrt_query.txt ---> PDB query to retrieve HIV-1 RT structures + visual filtering
|-- scpdb_hiv1_rt.tsv ---> final list of HIV-1 RT structures
`-- videoS1.mp4 ---> ProCare-aligned HIV-1 RT cavity (purple point cloud) onto TNF-a cavity cloud (white points) showing bound RT ligand (NVP)

License

Apache License 2.0
Copyright 2022 LIT

For academic use only.
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software and data.

THE SOFTWARE AND DATA ARE 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 AND DATA OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE AND DATA.

References

If you use these data, please cite the references below:

• Eguida, M., Rognan, D. Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision. J. Cheminf. 2021 13, 90.
• Eguida, M.; Rognan, D. A Computer Vision Approach to Align and Compare Protein Cavities: Application to Fragment-Based Drug Design. J. Med. Chem. 2020, 63, 7127–7142.
• Weill, N.; Rognan, D. Alignment-Free Ultra-High-Throughput Comparison of Druggable Protein-Ligand Binding Sites. J. Chem. Inf. Model. 2010, 50, 123–135.
• Lee, H. S.; Im, W. G-LoSA: An Efficient Computational Tool for Local Structure-Centric Biological Studies and Drug Design. Protein Sci. 2016, 25, 865–876.
• Wood, D. J.; Vlieg, J. De; Wagener, M.; Ritschel, T. Pharmacophore Fingerprint-Based Approach to Binding Site Subpocket Similarity and Its Application to Bioisostere Replacement. J. Chem. Inf. Model. 2012, 52, 2031–2043.
• Konc, J.; Janežič, D. ProBiS Algorithm for Detection of Structurally Similar Protein Binding Sites by Local Structural Alignment. Bioinformatics 2010, 26, 1160–1168.
• Schalon, C.; Surgand, J. S.; Kellenberger, E.; Rognan, D. A Simple and Fuzzy Method to Align and Compare Druggable Ligand-Binding Sites. Proteins Struct. Funct. Genet. 2008, 71, 1755–1778.
• Desaphy, J.; Bret, G.; Rognan, D.; Kellenberger, E. Sc-PDB: A 3D-Database of Ligandable Binding Sites—10 Years On. Nucleic Acids Res. 2014, 43, D399–D404.
• Bietz, S.; Urbaczek, S.; Schulz, B.; Rarey, M. Protoss: A Holistic Approach to Predict Tautomers and Protonation States in Protein-Ligand Complexes. J. Cheminform. 2014, 6, 12.
• OpenEye Toolkits 2020.2.0. OpenEye Scientific Software, Santa Fe, N. M., U.S.A., http://www. eyesopen. com (accessed Mar 30, 2021).
• RDKit: Open-source cheminformatics. http://www.rdkit.org (accessed Mar 30, 2021).
• Burley, S. K.; Bhikadiya, C.; Bi, C.; Bittrich, S.; Chen, L.; Crichlow, G. V.; Christie, C. H.; Dalenberg, K.; Di Costanzo, L.; Duarte, J. M.; Dutta, S.; Feng, Z.; Ganesan, S.; Goodsell, D. S.; Ghosh, S.; Green, R. K.; Guranović, V.; Guzenko, D.; Hudson, B. P.; Lawson, C. L.; Liang, Y.; Lowe, R.; Namkoong, H.; Peisach, E.; Persikova, I.; Randle, C.; Rose, A.; Rose, Y.; Sali, A.; Segura, J.; Sekharan, M.; Shao, C.; Tao, Y.-P.; Voigt, M.; Westbrook, J. D.; Young, J. Y.; Zardecki, C.; Zhuravleva, M. RCSB Protein Data Bank: Powerful New Tools for Exploring 3D Structures of Biological Macromolecules for Basic and Applied Research and Education in Fundamental Biology, Biomedicine, Biotechnology, Bioengineering and Energy Sciences. Nucleic Acids Res. 2021, 49, D437–D451.
• Gaulton, A.; Bellis, L. J.; Bento, A. P.; Chambers, J.; Davies, M.; Hersey, A.; Light, Y.; McGlinchey, S.; Michalovich, D.; Al-Lazikani, B.; Overington, J. P. ChEMBL: A Large-Scale Bioactivity Database for Drug Discovery. Nucleic Acids Res. 2012, 40, D1100–D1107.