Beginner path
Start at the browser build workflow, then read the workflow guide to understand how receptor intake, centers, ligand upload, and package generation depend on each other.
Practical references for using and extending the PrepServer.
Use this page as a starting point for the public workflow, accepted input types, generated package modes, setup expectations, API endpoints, GitHub repository, and common troubleshooting paths.
What the documentation covers
This documentation hub points users to the browser workflow, accepted receptor and ligand inputs, portable and scheduler-oriented package modes, the staged headless API, troubleshooting guidance, open-source repository context, and responsible public-deployment notes.
What this page covers
Use the docs as a map, not a single wall of instructions.
The documentation hub groups public resources by task: starting a browser workflow, understanding why docking setup fails, checking accepted file types, scripting with the API, diagnosing package errors, and reviewing the open-source repository.
If you are new to the server, begin with the workflow guide. If you are automating package creation, use the API page. If an existing job is stuck, start with troubleshooting before rerunning every step.
Researcher path
Review docking preparation problems, data cautions, receptor cleanup assumptions, and generated package contents before moving files into downstream docking runs.
Developer path
Use the API reference, GitHub repository, and open-source page to understand the Flask routes, templates, helper modules, and extension points.
Deployment path
Check public/private data boundaries, external conversion dependencies, package-mode configuration, and operational controls before exposing an instance to users.
Quick start
Create a workspace, add receptors, save docking centers, prepare proteins, upload ligands, choose package mode, then build the ZIP.
Start the build workflowWhy docking prep fails
Learn why repeated manual setup, file naming, coordinate tracking, and folder assembly can make docking workflows fragile.
Read docking-prep problemsWorkflow guide
Beginner-friendly explanation of receptor intake, docking boxes, receptor preparation, ligand intake, and package generation.
Read the workflow guideAccepted input types
Receptors: PDB, CIF, mmCIF, ENT, PDBQT, ZIP, and folder uploads. Ligands: SDF, SMILES, SMI, CSV, ZIP, and folder uploads where enabled.
Generated package modes
Portable mode creates generic local runner assets. LSF mode adds scheduler-oriented files when enabled by the deployment.
Headless API
PrepServer includes a versioned API for scripted workspace creation, coordinate-based box generation, receptor preparation, ligand upload, and package generation.
View API overviewTroubleshooting
Check workspace creation, external executables such as Open Babel, CSV column mapping, and package-mode settings before running long workflows.
Troubleshoot workflow issuesOpen source / GitHub
The project source code is available for inspection, issue reporting, extension, and deployment adaptation.
Open GitHub repository
FAQ
Documentation FAQ
Where should I start if I only want to build a package?
Use the Build page first. The documentation hub is here when you need explanations, API references, troubleshooting, or deployment context.
Where are the programmatic API instructions?
The Headless API page documents the staged JSON workflow for workspace creation, receptor intake, center saving, receptor preparation, ligand upload, package generation, artifact listing, and download.
Does the documentation describe scientific validation?
No. These pages explain preparation and packaging behavior. Docking parameters, pose review, controls, and scientific interpretation require separate validation by the research team.