NeuroPep 2.0: an updated database dedicated to neuropeptide and its receptor annotations

New prediction tools

• NeuroPred-PLM: an interpretable and robust model for prediction of neuropeptides by protein language model
  • Source code: https://github.com/ISYSLAB-HUST/NeuroPred-PLM
  • Web server: https://huggingface.co/spaces/isyslab/NeuroPred-PLM
  • Dataset: https://github.com/ISYSLAB-HUST/NeuroPred-PLM/tree/main/dataset
• DeepNeuropePred: a robust tool to predict cleavage sites in neuropeptide precursors
  • Source code: https://github.com/ISYSLAB-HUST/DeepNeuropePred
  • Web server: http://isyslab.info/NeuroPepV2/deepNeuropePred.jsp
  • Dataset: https://github.com/ISYSLAB-HUST/DeepNeuropePred/tree/main/data

Neuropeptide structure prediction

• AlphaFold: https://github.com/deepmind/alphafold
• APPTEST: https://research.timmons.eu/apptest

Data Source:

• UniProtKB: https://www.uniprot.org
• PubMed: https://pubmed.ncbi.nlm.nih.gov
• GPCRdb: https://gpcrdb.org
• IUPHAR: https://www.guidetopharmacology.org
• STRING: https://string-db.org
• NeuroPep 1.0: http://isyslab.info/NeuroPep/
• RCSB Protein Data Bank: https://www.rcsb.org

Physicochemical properties

• EMBOSS Pepinfo: https://www.ebi.ac.uk/Tools/seqstats/emboss_pepinfo/
• Compute pI/Mw tool: https://web.expasy.org/compute_pi/

Web server

The front-end of NeuroPep 2.0 server were build via HTML, JSP and Ajax, and the web services and data management were based Java and JDBC.

License

Released under the Apache License.

Contact

If you have any questions, comments, or would like to report a bug, please file a Github issue or contact me at wanglei94@hust.edu.cn.