> For the complete documentation index, see [llms.txt](https://docs.virtual-flow.org/documentation-vf1/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.virtual-flow.org/documentation-vf1/vfvs/principles-and-theory/input-and-output-databases.md). # Input & Output Databases The input and output ligand database are in the standard VirtualFlow format as described [here](/documentation-vf1/principles-and-theory/naming-conventions.md). ## Input Ligand Databases In VFVS, the ligands (fourth hierarchical level) in the input databases are stored as plain text files a ready-do-dock format. All docking programs supported so far by VirtualFlow support the PDBQT format, thus the PDBQT format is at the moment the only supported. The filename ending of each file has to be `.pdbqt`. Each ligand in the PDBQT format only contains the SMILES, and no additional information. The output ligand databases of VFLP can directly be used with VFVS for the virtual screening procedures, provided that VFLP was set up to generate the output ligand database in the PDBQT format. ### REAL Database of Enamine We provide on the VirtualFlow the REAL database of Enamine in a ready-to-dock format, ready for direct employment with VFVS. It contains over 1.4 billion distinct molecules. It was prepared with VFLP, and can be downloaded here on the VirtualFlow homepage: * Specific subsets can be easily chosen on the website via an interactive interface. ## Output Databases In VFVS, the output databases contain for each ligand a tar-archive, which contains all the docking output files for each ligand. --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://docs.virtual-flow.org/documentation-vf1/vfvs/principles-and-theory/input-and-output-databases.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.