StructSure Features
StructSure is a structural bioinformatics service built for computational biologists who need clean, validated PDB files — fast, privately, and without friction. Every file you upload is processed and permanently deleted. No data retention. No hidden storage.
PDB File Cleanup & Preprocessing
Raw PDB files downloaded from RCSB or AlphaFold are rarely ready for molecular docking or simulation workflows. They contain crystallographic waters, HETATM records, alternate conformations, and non-standard residues that break downstream tools like AutoDock, HADDOCK, and Rosetta. StructSure handles all of it automatically.
Water & Solvent Removal
Strips HOH records, crystallographic water molecules, and bound solvents that interfere with docking pocket calculations.
HETATM Filtering
Selectively remove or retain heteroatom records — cofactors, ligands, metal ions — with per-record control.
Alternate Conformation Handling
Resolves alternate location indicators (altLoc A/B) by keeping the highest-occupancy conformer and removing ambiguity.
Non-Standard Residue Correction
Detects and standardizes modified residues, selenomethionine (MSE → MET), and other non-canonical amino acids to ensure force field compatibility.
Chain Extraction & Renaming
Extract specific chains (heavy/light antibody chains, antigen) and rename them to match pipeline requirements.
Residue Renumbering
Renumber residues sequentially — critical for antibody structures where CDR loop numbering schemes (Chothia, Kabat, IMGT) can vary.
Geometry Validation
Catch Ramachandran outliers or steric clashes before docking or measuring affinity, to prevent incorrect calculations in downstream applications.
Merge Binding Partner Models for Docking
Quickly merge antibody and antigen files into one model for docking — works as 1-to-1 or 1-to-many to test variations.
CDR Loop QC Check
Read-only CDR geometry screen for antibody structures. Detects steric clashes and Ramachandran outliers per CDR loop and returns a safe_for_docking flag before you commit to a docking run.
Structure Search & Format Conversion
StructSure connects directly to RCSB PDB and the AlphaFold Protein Structure Database, so you can fetch any structure by accession ID rather than uploading a local file. Once processed, download your cleaned structure in the format your workflow requires.
- ✓ RCSB PDB search — fetch any of the 227,000+ experimentally determined structures by PDB ID
- ✓ AlphaFold database — retrieve computed structure models by UniProt accession
- ✓ PDBQT conversion — output AutoDock-ready files with polar hydrogens and Gasteiger charges for immediate use in AutoDock Vina or AutoDock4
- ✓ PDB format output — clean legacy .pdb files compatible with all major downstream tools
AI-Assisted Structure Validation
Before delivery, validated structures pass through a multi-stage validation pipeline that checks for geometry errors, steric clashes, and model quality — the kinds of issues that silently corrupt docking results and simulation trajectories.
Dual-Tier Validation
- Geometry validation — checks bond lengths, angles, and Ramachandran outliers using MolProbity-based scoring
- Deep learning quality assessment — DeepAccNet-based per-residue local accuracy estimation to flag regions of structural uncertainty
For longer jobs requiring intensive structure validation, users may provide an email address for job results. See pricing for details.
Antibody CDR Loop Validation
CDR loop geometry is a common failure point for antibody docking. Steric clashes or Ramachandran outliers in the CDR H3 loop, for example, can silently corrupt predicted binding poses. The CDR QC Check recipe screens your antibody structure before any docking run and reports whether it is safe to proceed.
What CDR QC Check reports
- Per-CDR clashscore — detects steric overlaps in each of the six CDR loops (H1, H2, H3, L1, L2, L3)
- Per-CDR Ramachandran outliers — flags backbone dihedral angles outside allowed regions on a loop-by-loop basis
- Auto-detected numbering scheme — automatically identifies Chothia or IMGT residue numbering; no manual configuration needed
safe_for_dockingflag — a single pass/fail signal you can use to gate downstream docking or simulation jobs
The check is read-only — it never modifies the input structure. It runs as a standalone recipe or automatically as part of Docking-Ready Export and SnugDock Export pipelines, so structures are screened before format conversion. It also runs gracefully on non-antibody PDB files, reporting zero CDR residues rather than failing.
Works with ABB3 and IgFold output
If you are modelling antibody structures with ABB3 or IgFold, you can pipe the resulting PDB directly into a CDR QC Check job to verify loop geometry before downstream use. This is especially useful for CDR H3, which homology modellers can misplace, and for confirming that energy-minimised variants have not introduced new clashes.
Privacy-First by Design
Structural bioinformatics often involves proprietary research data — unpublished antibody sequences, pre-publication binding targets, or confidential lead compounds. StructSure was designed from the ground up with a use-and-delete architecture that keeps your data out of our systems.
- ✓ Uploaded files are processed in memory and deleted immediately after your download link is generated — no persistent storage, ever
- ✓ No training data collection — your structures are never used to train or fine-tune any model
- ✓ No account required — anonymous job submission for quick one-off cleanups
Ready to clean your first structure?
Upload a PDB file or search by ID and get a cleaned structure in seconds.