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Fill out the form below to analyze your PDB structure
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Structure Source
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Upload your own file or fetch a structure from the RCSB PDB database
PDB File
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RCSB PDB ID
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Enter a 4-character PDB ID from
RCSB.org
Email Address
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Job Name
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A descriptive name for this analysis
Structure Type
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Experimental (PDB)
AlphaFold (AF)
Select whether the structure is experimental or AlphaFold predicted (affects slipknot removal model)
Organism
*
E. coli (cutoff: 57)
Human (cutoff: 52)
Yeast (cutoff: 49)
Custom
Select the organism for clustering analysis (cutoff values shown for known organisms)
Custom Organism Name
*
Enter the organism name for your structure
Custom Clustering Cutoff
*
Enter the distance cutoff for clustering (typical range: 45-60)
Model Resolution
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All-Atom
C-alpha Coarse-Grained
For C-alpha CG models, PDB must have atom names "A" and residue names "G1", "G2", etc.
Contact Type
*
Heavy Atom Contacts
C-alpha Contacts
Select the type of contacts to use for analysis
Entanglement Detection Method
Method 1:
GLN-based (any nonzero Gaussian linking)
Method 2:
TLN-based (any nonzero topological linking)
Method 3:
Consensus (both GLN and TLN must agree) - Recommended
Method used to determine if a non-covalent lasso entanglement is present
Generate Entanglement Features
If enabled, additional entanglement features will be calculated and included in results. Requires UniProt Accession ID (must be provided below).
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UniProt Accession ID
*
Optional UniProt accession for your protein (e.g., P12345).
Required
if generating entanglement features.
Description (optional)
Any additional information about this analysis
Email Address
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You'll receive a notification when all jobs are complete
Batch Name
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A descriptive name for this batch submission
PDB Files
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Select multiple .pdb files at once. You can select up to 100 files per batch.
Per-File Analysis Options
Customize analysis parameters for each file. All options must be specified per-file.
Batch Description (optional)
Any additional information about this batch
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