How StructSure Works
From raw PDB file to clean, validated structure in under a minute. StructSure automates the preprocessing steps that computational biologists spend hours doing manually — and doesn't retain a single file.
Choose Your Workflow & Configure Cleanup Operations
Select the preprocessing steps your workflow requires — or use the recommended preset for your use case (docking, simulation, or structure analysis). Every option is explained in plain language with a note on which downstream tools it affects.
You don't need to know what a HETATM record is to use StructSure — but if you do, the underlying logic is fully transparent.
Common options: remove waters · strip HETATM · resolve alt conformations · extract chains · renumber residues · convert to PDBQT · merge binding partners
Upload a PDB File or Search by ID
Provide your structure by uploading a PDB file directly from your computer, or let StructSure fetch it by searching the RCSB Protein Data Bank or AlphaFold database by accession ID.
StructSure accepts standard .pdb files up to 50 MB. Structures containing multiple models, assembly files, and NMR ensembles are all supported. If you're working with an unpublished or in-house structure, uploading a local file keeps your data completely off any external network — it goes directly from your browser to the processing server.
Supported sources: RCSB PDB · AlphaFold DB · Local file upload
Processing & AI Validation
StructSure applies your selected operations in the correct order — the sequence of preprocessing steps matters, and StructSure handles the dependency graph automatically. After cleanup, the structure passes through a validation stage that checks bond geometry, Ramachandran outliers, and steric clashes.
Validation results are summarized in a report delivered alongside your cleaned structure. For longer jobs requiring intensive structure validation, users may provide an email address for job results.
Validation: MolProbity geometry · DeepAccNet accuracy estimation
Download & Verified Deletion
Your cleaned structure is packaged and a time-limited download link is generated. Download your file and StructSure permanently deletes all associated data — the uploaded file, the processed output, and any intermediate files — from the server.
There is no recovery mechanism and no archive. This is not a policy statement; it is the architecture. StructSure is designed as a stateless processing service: it has no database for user files, no backup bucket, and no logging that captures structure content.
Deletion is immediate and permanent. Download links expire after 15 minutes.
Why PDB Preprocessing Matters
Most molecular docking failures aren't caused by bad docking algorithms — they're caused by bad input structures. A PDB file downloaded directly from RCSB contains crystallographic artifacts that were never meant to be part of a simulation: water molecules that fill crystal packing voids, alternate conformations of flexible side chains, missing atoms in terminal residues, and HETATM records for buffer molecules and cryoprotectants.
For antibody-antigen docking specifically, the problem is compounded by inconsistent chain naming and CDR loop numbering schemes across different PDB depositions. AutoDock Vina, HADDOCK, ClusPro, and Rosetta each have their own quirks about what they'll accept, and debugging a failed docking run back to a misformatted PDB file is a significant time sink.
StructSure treats preprocessing as a first-class problem rather than an afterthought. The preprocessing pipeline was built by reading the documentation of downstream tools and encoding their input requirements directly — so what StructSure outputs actually works.
The Privacy Architecture
Most structural bioinformatics work involves proprietary data. An antibody sequence against a novel target, a binding pose for a lead compound, a predicted structure for an unpublished protein — these are competitive assets that researchers understandably protect.
The existing open-source tools (PDB-Tools, PDBrestore, OpenBabel) require local installation and often depend on complex dependency stacks. Web services that accept PDB uploads typically retain files for debugging, analytics, or training data — sometimes for months.
StructSure takes the opposite approach: every architectural decision is optimized to minimize data retention. Files are processed in ephemeral compute, results are handed back immediately, and deletion is automatic. The goal is a service where using it leaves no trace.
Try it now — no account required
Submit your first PDB cleanup job. No signup, no credit card, no file retention.