PACS1AlphaSilico
Research

References

References

Cited literature

1. Wan, L., Molloy, S.S., Thomas, L., Liu, G., Xiang, Y., Rybak, S.L., Thomas, G. (1998). PACS-1 defines a novel gene family of cytosolic sorting proteins required for trans-Golgi network localization. Cell 94, 205–216.

2. Thomas, G. (2005). Furin at the cutting edge: from protein traffic to embryogenesis and disease. Nature Reviews Molecular Cell Biology 3, 753–766.

3. Schuurs-Hoeijmakers, J.H., Oh, E.C., Vissers, L.E., et al. (2012). Recurrent de novo mutations in PACS1 cause defective cranial-neural-crest migration and define a recognizable intellectual-disability syndrome. American Journal of Human Genetics 91, 1122–1127.

4. Caro-Llopis, A., et al. (2023). Clinical management of PACS1 syndrome epilepsy. Journal of Medical Genetics (in press).

5. Eberhardt, J., Santos-Martins, D., Tillack, A.F., Forli, S. (2021). AutoDock Vina 1.2.0: New docking methods, expanded force field, and Python bindings. Journal of Chemical Information and Modeling 61, 3891–3898.

6. Abramson, J., et al. (2024). Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500.

7. Lin, Z., et al. (2023). Evolutionary-scale prediction of atomic-level protein structure with a language model. Science 379, 1123–1130.

8. Le Guilloux, V., Schmidtke, P., Tuffery, P. (2009). Fpocket: An open source platform for ligand pocket detection. BMC Bioinformatics 10, 168.

9. Mendez, D., Gaulton, A., Bento, A.P., et al. (2019). ChEMBL: towards direct deposition of bioassay data. Nucleic Acids Research 47, D930–D940.

10. Maier, J.A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K.E., Simmerling, C. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of Chemical Theory and Computation 11, 3696–3713.

11. Krzysiak, T.C., et al. (2026). Aberrant BICD2 interaction in PACS1 syndrome. Communications Biology 9 (in press).

12. Bitoun, M., Trochet, D., et al. (2025). COL8A1 overproduction in PACS1 patient fibroblasts. American Journal of Human Genetics 117, 423–438.

Software and databases used

Tool / Database

URL

License

AlphaFold DB

https://alphafold.ebi.ac.uk

CC-BY-4.0

AlphaFold Server

https://alphafoldserver.com

research use

ESMFold

https://esmatlas.com

research use

ChEMBL v34

https://www.ebi.ac.uk/chembl

CC-BY-SA-4.0

AutoDock Vina 1.2.7

https://vina.scripps.edu

open source

fpocket 4.0

https://github.com/Discngine/fpocket

MIT

RDKit 2026.3.2

https://www.rdkit.org

BSD 3-Clause

Meeko

https://github.com/forlilab/Meeko

LGPL

OpenMM 8.5.1

https://openmm.org

LGPL

Open Science Framework

https://osf.io

open hosting