VZV_ORF14

VZV_ORF14
P09256

The model was generated using Colabfold with 3x recycles

Sequence coverage

pLDDT

Predicted Alignment Error (PAE)


Model rank 1


Model without the signal peptide rank 1

Using DeepTMHMM, this protein was identified to contain a signal peptide and a transmembrane domain.
The transmembrane domain spans residues: 534-556


Download files:
VZV_ORF14_rank_001.pdb
VZV_ORF14_rank_002.pdb
VZV_ORF14_rank_003.pdb
VZV_ORF14_rank_004.pdb
VZV_ORF14_rank_005.pdb
VZV_ORF14_coverage.png
VZV_ORF14_plddt.png
VZV_ORF14_pae.png

VZV_ORF14-nosignal_rank_001.pdb
VZV_ORF14-nosignal_rank_002.pdb
VZV_ORF14-nosignal_rank_003.pdb
VZV_ORF14-nosignal_rank_004.pdb
VZV_ORF14-nosignal_rank_005.pdb

Search for similar structures using Foldseek:




This page uses 3Dmol.js: Molecular visualization with WebGL by Nicholas Rego and David Koes.
Bioinformatics (2015) doi: 10.1093/bioinformatics/btu829

Predictions were run with Colabfold by the Steinegger lab:
Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M. “ColabFold: Making protein folding accessible to all”.
Nature Methods (2022) doi: 10.1038/s41592-022-01488-1

Foldseek is developed by the Steinegger lab:
van Kempen M, Kim S, Tumescheit C, Mirdita M, Söding J, and Steinegger M. “Foldseek: fast and accurate protein structure search”.
bioRxiv (2022) doi: 10.1101/2022.02.07.479398

Alphafold2 was developed by Deepmind:
Jumper et al. “Highly accurate protein structure prediction with AlphaFold.”
Nature (2021) doi: 10.1038/s41586-021-03819-2

Signal peptide predictions were performed with DeepTMHMM
Jeppe Hallgren, Konstantinos D. Tsirigos, Mads Damgaard Pedersen, José Juan Almagro Armenteros, Paolo Marcatili, Henrik Nielsen, Anders Krogh, Ole Winther. “DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks.”
bioRxiv (2022) doi: 10.1101/2022.04.08.487609

AlphaFold3 models were generated through the Alphafold Server, which uses Google DeepMind’s AlphaFold technology
Abramson, J et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature (2024).
Nature (2021) doi: 10.1038/s41586-024-07487-w

Leave a Reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.