Author Archives: jens.bosse

HSV-1_US8_HSV-1_US9

HSV-1_US8_HSV-1_US9
Monomer Prediction HSV-1_US8
Monomer Prediction HSV-1_US9

Sequence coverage

pLDDT

Predicted Alignment Error (PAE)


Model rank 1, ipTM = 0.2

 

Model rank 2, ipTM = 0.18

 

Model rank 3, ipTM = 0.17

 

Model rank 4, ipTM = 0.16

 

Model rank 5, ipTM = 0.15

 

Download files:
HSV-1_US8_HSV-1_US9_rank_001.pdb
HSV-1_US8_HSV-1_US9_rank_002.pdb
HSV-1_US8_HSV-1_US9_rank_003.pdb
HSV-1_US8_HSV-1_US9_rank_004.pdb
HSV-1_US8_HSV-1_US9_rank_005.pdb
HSV-1_US8_HSV-1_US9_coverage.png
HSV-1_US8_HSV-1_US9_plddt.png
HSV-1_US8_HSV-1_US9_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 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

HSV-1_US9_HSV-1_US9

HSV-1_US9_HSV-1_US9
Monomer Prediction HSV-1_US9
Monomer Prediction HSV-1_US9

Sequence coverage

pLDDT

Predicted Alignment Error (PAE)


Model rank 1, ipTM = 0.25

 

Model rank 2, ipTM = 0.21

 

Model rank 3, ipTM = 0.18

 

Model rank 4, ipTM = 0.18

 

Model rank 5, ipTM = 0.17

 

Download files:
HSV-1_US9_HSV-1_US9_rank_001.pdb
HSV-1_US9_HSV-1_US9_rank_002.pdb
HSV-1_US9_HSV-1_US9_rank_003.pdb
HSV-1_US9_HSV-1_US9_rank_004.pdb
HSV-1_US9_HSV-1_US9_rank_005.pdb
HSV-1_US9_HSV-1_US9_coverage.png
HSV-1_US9_HSV-1_US9_plddt.png
HSV-1_US9_HSV-1_US9_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 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

HSV-1_UL36_HSV-1_UL36

HSV-1_UL36_HSV-1_UL36
Monomer Prediction HSV-1_UL36
Monomer Prediction HSV-1_UL36

Sequence coverage

pLDDT

Predicted Alignment Error (PAE)


Model rank 1, ipTM = 0.33

 

Model rank 2, ipTM = 0.33

 

Model rank 3, ipTM = 0.33

 

Model rank 4, ipTM = 0.33

 

Model rank 5, ipTM = 0.32

 

Download files:
HSV-1_UL36_HSV-1_UL36_rank_001.pdb
HSV-1_UL36_HSV-1_UL36_rank_002.pdb
HSV-1_UL36_HSV-1_UL36_rank_003.pdb
HSV-1_UL36_HSV-1_UL36_rank_004.pdb
HSV-1_UL36_HSV-1_UL36_rank_005.pdb
HSV-1_UL36_HSV-1_UL36_coverage.png
HSV-1_UL36_HSV-1_UL36_plddt.png
HSV-1_UL36_HSV-1_UL36_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 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

HSV-1_US6_HSV-1_US8

HSV-1_US6_HSV-1_US8
Monomer Prediction HSV-1_US6
Monomer Prediction HSV-1_US8

Sequence coverage

pLDDT

Predicted Alignment Error (PAE)


Model rank 1, ipTM = 0.2

 

Model rank 2, ipTM = 0.17

 

Model rank 3, ipTM = 0.15

 

Model rank 4, ipTM = 0.15

 

Model rank 5, ipTM = 0.14

 

Download files:
HSV-1_US6_HSV-1_US8_rank_001.pdb
HSV-1_US6_HSV-1_US8_rank_002.pdb
HSV-1_US6_HSV-1_US8_rank_003.pdb
HSV-1_US6_HSV-1_US8_rank_004.pdb
HSV-1_US6_HSV-1_US8_rank_005.pdb
HSV-1_US6_HSV-1_US8_coverage.png
HSV-1_US6_HSV-1_US8_plddt.png
HSV-1_US6_HSV-1_US8_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 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

HSV-1_US6_HSV-1_US9

HSV-1_US6_HSV-1_US9
Monomer Prediction HSV-1_US6
Monomer Prediction HSV-1_US9

Sequence coverage

pLDDT

Predicted Alignment Error (PAE)


Model rank 1, ipTM = 0.2

 

Model rank 2, ipTM = 0.16

 

Model rank 3, ipTM = 0.15

 

Model rank 4, ipTM = 0.15

 

Model rank 5, ipTM = 0.11

 

Download files:
HSV-1_US6_HSV-1_US9_rank_001.pdb
HSV-1_US6_HSV-1_US9_rank_002.pdb
HSV-1_US6_HSV-1_US9_rank_003.pdb
HSV-1_US6_HSV-1_US9_rank_004.pdb
HSV-1_US6_HSV-1_US9_rank_005.pdb
HSV-1_US6_HSV-1_US9_coverage.png
HSV-1_US6_HSV-1_US9_plddt.png
HSV-1_US6_HSV-1_US9_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 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

HSV-1_US7_HSV-1_US7

HSV-1_US7_HSV-1_US7
Monomer Prediction HSV-1_US7
Monomer Prediction HSV-1_US7

Sequence coverage

pLDDT

Predicted Alignment Error (PAE)


Model rank 1, ipTM = 0.27

 

Model rank 2, ipTM = 0.21

 

Model rank 3, ipTM = 0.2

 

Model rank 4, ipTM = 0.2

 

Model rank 5, ipTM = 0.2

 

Download files:
HSV-1_US7_HSV-1_US7_rank_001.pdb
HSV-1_US7_HSV-1_US7_rank_002.pdb
HSV-1_US7_HSV-1_US7_rank_003.pdb
HSV-1_US7_HSV-1_US7_rank_004.pdb
HSV-1_US7_HSV-1_US7_rank_005.pdb
HSV-1_US7_HSV-1_US7_coverage.png
HSV-1_US7_HSV-1_US7_plddt.png
HSV-1_US7_HSV-1_US7_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 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

HSV-1_US7_HSV-1_US8.5

HSV-1_US7_HSV-1_US8.5
Monomer Prediction HSV-1_US7
Monomer Prediction HSV-1_US8.5

Sequence coverage

pLDDT

Predicted Alignment Error (PAE)


Model rank 1, ipTM = 0.22

 

Model rank 2, ipTM = 0.21

 

Model rank 3, ipTM = 0.18

 

Model rank 4, ipTM = 0.18

 

Model rank 5, ipTM = 0.17

 

Download files:
HSV-1_US7_HSV-1_US8.5_rank_001.pdb
HSV-1_US7_HSV-1_US8.5_rank_002.pdb
HSV-1_US7_HSV-1_US8.5_rank_003.pdb
HSV-1_US7_HSV-1_US8.5_rank_004.pdb
HSV-1_US7_HSV-1_US8.5_rank_005.pdb
HSV-1_US7_HSV-1_US8.5_coverage.png
HSV-1_US7_HSV-1_US8.5_plddt.png
HSV-1_US7_HSV-1_US8.5_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 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

HSV-1_US7_HSV-1_US8

HSV-1_US7_HSV-1_US8
Monomer Prediction HSV-1_US7
Monomer Prediction HSV-1_US8

Sequence coverage

pLDDT

Predicted Alignment Error (PAE)


Model rank 1, ipTM = 0.59

 

Model rank 2, ipTM = 0.59

 

Model rank 3, ipTM = 0.58

 

Model rank 4, ipTM = 0.51

 

Model rank 5, ipTM = 0.5

 

Download files:
HSV-1_US7_HSV-1_US8_rank_001.pdb
HSV-1_US7_HSV-1_US8_rank_002.pdb
HSV-1_US7_HSV-1_US8_rank_003.pdb
HSV-1_US7_HSV-1_US8_rank_004.pdb
HSV-1_US7_HSV-1_US8_rank_005.pdb
HSV-1_US7_HSV-1_US8_coverage.png
HSV-1_US7_HSV-1_US8_plddt.png
HSV-1_US7_HSV-1_US8_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 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

HSV-1_US7_HSV-1_US9

HSV-1_US7_HSV-1_US9
Monomer Prediction HSV-1_US7
Monomer Prediction HSV-1_US9

Sequence coverage

pLDDT

Predicted Alignment Error (PAE)


Model rank 1, ipTM = 0.21

 

Model rank 2, ipTM = 0.2

 

Model rank 3, ipTM = 0.2

 

Model rank 4, ipTM = 0.19

 

Model rank 5, ipTM = 0.16

 

Download files:
HSV-1_US7_HSV-1_US9_rank_001.pdb
HSV-1_US7_HSV-1_US9_rank_002.pdb
HSV-1_US7_HSV-1_US9_rank_003.pdb
HSV-1_US7_HSV-1_US9_rank_004.pdb
HSV-1_US7_HSV-1_US9_rank_005.pdb
HSV-1_US7_HSV-1_US9_coverage.png
HSV-1_US7_HSV-1_US9_plddt.png
HSV-1_US7_HSV-1_US9_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 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

HSV-1_US4_HSV-1_US9

HSV-1_US4_HSV-1_US9
Monomer Prediction HSV-1_US4
Monomer Prediction HSV-1_US9

Sequence coverage

pLDDT

Predicted Alignment Error (PAE)


Model rank 1, ipTM = 0.25

 

Model rank 2, ipTM = 0.24

 

Model rank 3, ipTM = 0.21

 

Model rank 4, ipTM = 0.2

 

Model rank 5, ipTM = 0.21

 

Download files:
HSV-1_US4_HSV-1_US9_rank_001.pdb
HSV-1_US4_HSV-1_US9_rank_002.pdb
HSV-1_US4_HSV-1_US9_rank_003.pdb
HSV-1_US4_HSV-1_US9_rank_004.pdb
HSV-1_US4_HSV-1_US9_rank_005.pdb
HSV-1_US4_HSV-1_US9_coverage.png
HSV-1_US4_HSV-1_US9_plddt.png
HSV-1_US4_HSV-1_US9_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 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