HSV-1

HSV-1 UL40

Predicted structure model: ColabFold (3x recycles).

The model was generated using ColabFold with 3 recycles.

Predicted Structure (ColabFold (3x recycles))
Predicted Aligned Error (PAE) Click image to open full size
Predicted Aligned Error (PAE)
Structural Homologs
Virus Protein Uniprot pTM
HSV-1 UL40 P10224 0.83
HSV-2 UL40 P69521 0.83
VZV ORF18 P09247 0.86
MDV MDV053 Q77MS0 n/a
PrV UL40 G3G964 n/a
EBV BaRF1-RIR2 P0CAP6 0.86
KSHV ORF60 F5HAW0 0.86
MHV68 ORF60 P88997 n/a

This page uses Mol* for molecular visualization, with JSmol as a fallback when WebGL is unavailable.

Predictions were run with Colabfold by the Steinegger lab:
Mirdita M, Schutze 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, Soding J, and Steinegger M. "Fast and accurate protein structure search with Foldseek". Nature Biotechnology (2023) doi: 10.1038/s41587-023-01773-0

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, Jose 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). doi: 10.1038/s41586-024-07487-w