Repetitive folder assembly
Docking projects often require the same directory structure, scripts, receptor files, ligand folders, and result paths to be rebuilt for every new target or screen.
The hardest part of a docking screen is often the setup around the docking run.
AutoDock Vina workflows depend on careful preparation of receptor files, ligand inputs, docking boxes, and run folders. Small setup mistakes can propagate into wasted compute time, confusing results, or docking packages that are difficult to reproduce later.
Problem map
Most failures are small, practical mismatches that compound.
A docking package can look complete while still hiding a missing center, a receptor that did not convert to PDBQT, a ligand CSV with the wrong column selected, or a folder structure that no longer matches the runner script.
PrepServer helps by turning those assumptions into visible workflow states. That does not make the scientific choices automatic, but it does make the preparation trail easier to review, repeat, and hand off.
Coordinate tracking
Docking centers are easy to lose when they live in notes, screenshots, or one-off command lines. PrepServer records centers in a structured CSV-based workflow.
File-format friction
Receptors and ligands often move between PDB, CIF, PDBQT, SDF, SMILES, SMI, CSV, ZIP, and folder-based inputs. The app organizes these transitions into staged steps.
Hidden assumptions
Manual cleanup choices such as heteroatom removal, chain selection, or ligand column mapping should be visible and repeatable, not buried in a local shell history.
Before you start a new docking package
Confirm the receptor source, chain or biological assembly choice, ligand input format, desired docking box center, box size, and downstream environment where Vina will actually run.
Before you trust a generated package
Inspect the receptor PDBQT files, center CSV, ligand provenance, package README, and runner scripts. Preparation consistency is not the same thing as scientific validity.
When collaborating
Share the generated package together with notes about receptor cleanup, docking box rationale, ligand source, and any environment-specific settings used downstream.
When scaling up
Use the API and package artifacts to reduce manual repetition, but keep review checkpoints for failed conversions, ambiguous centers, malformed ligands, and scheduler-specific assumptions.
Start with a workspace
Each job begins with a workspace so receptors, centers, ligands, logs, and generated packages stay grouped together.
Make preparation visible
The interface marks receptor status as new, centered, or prepared so users know what still needs attention before package generation.
Export instead of hand-assembling
Once the required inputs are complete, PrepServer builds a downloadable ZIP package for downstream docking execution.
Use the guided workflow instead of rebuilding every docking folder by hand.
Prepare receptor, ligand, center, and package assets from one browser-guided flow.
FAQ
Docking preparation problem FAQ
Why do docking packages fail even when the receptor and ligand files exist?
A package also depends on saved docking box coordinates, successful receptor preparation, ligand format or CSV column handling, expected folder names, and downstream runner assumptions.
Can PrepServer choose the correct docking box for me?
PrepServer can help save and package center coordinates, including supported selector-based workflows. Choosing an appropriate biological search space still requires user review.
What should I preserve for reproducibility?
Preserve the original receptor source, cleanup choices, center coordinates and size, ligand source, package mode, generated ZIP, and notes about downstream docking parameters.