Frequently Asked Questions

What is PDB file cleanup?

PDB file cleanup (also called PDB preprocessing or structure preparation) refers to the process of removing and correcting artifacts in raw PDB files before use in molecular docking, MD simulation, or structure analysis. Raw PDB files downloaded from RCSB or AlphaFold often contain crystallographic water molecules, alternate conformations, missing atoms, non-standard residue names, and HETATM records that interfere with downstream computational tools like AutoDock, HADDOCK, GROMACS, and Rosetta.

Why do I need to clean my PDB files?

Most molecular docking and simulation software requires carefully prepared input structures. Common issues in raw PDB files include:

• ✗Crystallographic water molecules filling crystal packing voids (not biologically relevant)
• ✗Alternate location indicators (altLoc A/B) causing atom ambiguity that breaks parsers
• ✗Missing hydrogen atoms or side chain atoms that force fields can't handle
• ✗Non-standard residue codes (e.g. MSE, HID, HIE) that force fields don't recognize
• ✗Inconsistent chain naming or non-sequential residue numbering in antibody structures

These issues cause silent errors or outright failures in docking software, and are often not readily visible in modeling software. Proper preprocessing dramatically improves docking accuracy and simulation stability.

What cleanup operations does StructSure support?

For longer jobs requiring intensive structure validation, users may provide an email address for job results. See the features page for detailed descriptions of each operation.

Is StructSure suitable for antibody structure preparation?

Yes — antibody-antigen docking preparation is a primary use case. StructSure handles antibody-specific issues including inconsistent CDR loop numbering across PDB depositions, chain renaming to match HADDOCK or ClusPro conventions, and heavy/light chain extraction. Residue renumbering supports preparation for tools that require clean sequential numbering regardless of the original Chothia, Kabat, or IMGT scheme in the deposited structure.

Are my PDB files kept private?

Yes. StructSure uses a use-and-delete architecture: your files are processed in ephemeral compute and permanently deleted the moment your download link is generated. There is no persistent file storage, no backup system, and no logging that captures structure content. Your data is never used to train any model.

How long are my files stored?

Your uploaded files and processed outputs are deleted immediately after your download link is generated. Download links expire after 15 minutes. There is no archive, no recovery mechanism, and no way to retrieve files after deletion. This is an architectural property of the system, not just a policy.

What file formats does StructSure accept?

StructSure accepts .pdb files as input. Structures up to 50 MB are supported, including multi-model PDB files, NMR ensembles, and biological assembly files.

What output formats are available?

Output formats include: .pdb (legacy PDB format for broad tool compatibility) and .pdbqt (for AutoDock Vina and AutoDock4, with polar hydrogens and Gasteiger charges pre-applied).

Can I fetch structures from RCSB or AlphaFold?

Yes. StructSure connects to the RCSB Protein Data Bank and the AlphaFold Protein Structure Database. Search by PDB ID for any of the 227,000+ experimentally determined structures, or by UniProt accession for AlphaFold computed models — without downloading the file yourself first.

Is StructSure free?

Yes, for single file processing. All recipes — Quality Screen, Renumber & Normalize, Docking-Ready Export, SnugDock Export, and MD Simulation Prep — are free when run against a single file. Credits (1 credit = $1.00) are only required for batch jobs. See the pricing page for per-recipe batch rates.

What counts as a batch job?

A batch job submits multiple PDB files to the same recipe in one request. You are charged the recipe's base rate per file successfully processed — failed files are never charged. Running one file through several recipes is still a single-file job and is free.

Do you offer institutional pricing?

Not yet — pricing is the same for all users at the moment. However, if you are interested in group access for a lab or research organization, please reach out via the feedback link in the app.

How does StructSure compare to PDB-Tools, PDBrestore, or AutoDock Tools?

PDB-Tools (Bonvin Lab) and PDBrestore are excellent open-source tools that require local installation or run on academic servers. AutoDock Tools is a standalone desktop application. StructSure is a commercial service optimized for three things those tools don't prioritize:

1. Pipeline integration — select multiple cleanup operations to run in a single reproducible job, directly in the browser or via batch processing, without managing local dependencies.
2. AI-assisted validation — deep learning accuracy estimation integrated directly into the processing step, not a separate tool to install and run.
3. Strict privacy — files are deleted immediately after download, not retained for debugging, analytics, or training data. Academic web servers typically log requests and may retain files indefinitely.

For quick one-off jobs on non-sensitive data, open-source tools are great choices. For teams running large screening campaigns with proprietary structures, StructSure offers meaningful advantages.