We have just updated our HerpesFold interactive table. The table, which previously contained predictions for HSV-1 strain 17 (UP000009294), HCMV strain Merlin (UP000000938), and KSHV strain GK18 (UP000000942), now also provides predictions for EBV strain B95-8 (UP000153037). This new version is also using an overall better annotation.
Sequence coverage 
pLDDT 
Predicted Alignment Error (PAE) 
Model rank 1
Download files:
KSHV_ORF73_rank_001.pdb
KSHV_ORF73_rank_002.pdb
KSHV_ORF73_rank_003.pdb
KSHV_ORF73_rank_004.pdb
KSHV_ORF73_rank_005.pdb
KSHV_ORF73_coverage.png
KSHV_ORF73_plDDT.png
KSHV_ORF73_pae.png
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 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:Âxa010.1038/s41586-021-03819-2
n’
Sequence coverage 
pLDDT 
Predicted Alignment Error (PAE) 
Model rank 1
Download files:
KSHV_ORF6_rank_001.pdb
KSHV_ORF6_rank_002.pdb
KSHV_ORF6_rank_003.pdb
KSHV_ORF6_rank_004.pdb
KSHV_ORF6_rank_005.pdb
KSHV_ORF6_coverage.png
KSHV_ORF6_plDDT.png
KSHV_ORF6_pae.png
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 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:Âxa010.1038/s41586-021-03819-2
n’
Sequence coverage 
pLDDT 
Predicted Alignment Error (PAE) 
Model rank 1
Download files:
KSHV_ORF75_rank_001.pdb
KSHV_ORF75_rank_002.pdb
KSHV_ORF75_rank_003.pdb
KSHV_ORF75_rank_004.pdb
KSHV_ORF75_rank_005.pdb
KSHV_ORF75_coverage.png
KSHV_ORF75_plDDT.png
KSHV_ORF75_pae.png
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 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:Âxa010.1038/s41586-021-03819-2
n’
Sequence coverage 
pLDDT 
Predicted Alignment Error (PAE) 
Model rank 1
Download files:
KSHV_ORF25_rank_001.pdb
KSHV_ORF25_rank_002.pdb
KSHV_ORF25_rank_003.pdb
KSHV_ORF25_rank_004.pdb
KSHV_ORF25_rank_005.pdb
KSHV_ORF25_coverage.png
KSHV_ORF25_plDDT.png
KSHV_ORF25_pae.png
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 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:Âxa010.1038/s41586-021-03819-2
n’
Sequence coverage 
pLDDT 
Predicted Alignment Error (PAE) 
Model rank 1
Download files:
KSHV_ORF64_rank_001.pdb
KSHV_ORF64_rank_002.pdb
KSHV_ORF64_rank_003.pdb
KSHV_ORF64_rank_004.pdb
KSHV_ORF64_rank_005.pdb
KSHV_ORF64_coverage.png
KSHV_ORF64_plDDT.png
KSHV_ORF64_pae.png
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 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:Âxa010.1038/s41586-021-03819-2
n’
Sequence coverage 
pLDDT 
Predicted Alignment Error (PAE) 
Model rank 1
Download files:
KSHV_ORF17_rank_001.pdb
KSHV_ORF17_rank_002.pdb
KSHV_ORF17_rank_003.pdb
KSHV_ORF17_rank_004.pdb
KSHV_ORF17_rank_005.pdb
KSHV_ORF17_coverage.png
KSHV_ORF17_plDDT.png
KSHV_ORF17_pae.png
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 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:Âxa010.1038/s41586-021-03819-2
n’
Sequence coverage 
pLDDT 
Predicted Alignment Error (PAE) 
Model rank 1
Download files:
KSHV_ORF8_rank_001.pdb
KSHV_ORF8_rank_002.pdb
KSHV_ORF8_rank_003.pdb
KSHV_ORF8_rank_004.pdb
KSHV_ORF8_rank_005.pdb
KSHV_ORF8_coverage.png
KSHV_ORF8_plDDT.png
KSHV_ORF8_pae.png
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 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:Âxa010.1038/s41586-021-03819-2
n’
Sequence coverage 
pLDDT 
Predicted Alignment Error (PAE) 
Model rank 1
Download files:
KSHV_ORF19_rank_001.pdb
KSHV_ORF19_rank_002.pdb
KSHV_ORF19_rank_003.pdb
KSHV_ORF19_rank_004.pdb
KSHV_ORF19_rank_005.pdb
KSHV_ORF19_coverage.png
KSHV_ORF19_plDDT.png
KSHV_ORF19_pae.png
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 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:Âxa010.1038/s41586-021-03819-2
n’
Sequence coverage 
pLDDT 
Predicted Alignment Error (PAE) 
Model rank 1
Download files:
KSHV_vIRF-4_rank_001.pdb
KSHV_vIRF-4_rank_002.pdb
KSHV_vIRF-4_rank_003.pdb
KSHV_vIRF-4_rank_004.pdb
KSHV_vIRF-4_rank_005.pdb
KSHV_vIRF-4_coverage.png
KSHV_vIRF-4_plDDT.png
KSHV_vIRF-4_pae.png
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 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:Âxa010.1038/s41586-021-03819-2
n’
