Standalone local browser tools grouped by purpose. Open a tool directly from its card or use the documentation link for inputs, outputs, workflow notes, and citation text.
Tools for Oroboros/O2k trace inspection, Mark-based summaries, and export-ready figures.
Load Oroboros DatLab 7 DLD files, inspect Chamber A/B traces, use Events/Marks, normalize O2 flux, compare Marks, and export figures.
Build, clean, and prepare ligand and receptor files before PDBQT conversion.
Create or import a ligand structure and export a MOL2-style starting point for downstream docking preparation.
Inspect and clean ligand inputs, keep preparation notes, and prepare MOL2/PDBQT-related files for docking.
Clean receptor PDB files, keep desired chains/heteroatoms, remove unwanted records, and prepare receptor input.
Guide receptor protonation/charge-assignment handoff through external PDB2PQR-style workflows and record settings.
Convert receptor and ligand material into approximate PDBQT-style files with validation notes.
Prepare docking boxes/configuration files and inspect docking run output.
Define docking boxes and generate Vina-style configuration files from receptor and ligand inputs.
Run or emulate a browser-assisted Vina workflow and inspect poses, scores, and run notes.
Build nucleic-acid and membrane starting structures, then inspect AMBER topology and trajectory material.
Generate an idealized B-form double-stranded DNA PDB from a sequence and export Amber-oriented setup notes.
Build a rectangular Lipid21-style bilayer PDB from curated lipid templates and export a LEaP input draft.
Load AMBER prmtop topology files with multi-frame XYZ trajectories, inspect frames, filter residues, and export PNG snapshots.
Figure/mesh utilities plus the external structural biology software overview.
Visualize structures with 3Dmol-style views and export molecular surfaces or mesh-oriented outputs.
Purpose-first survey of structural biology software: docking, MD simulation, QM/QM-MM computation, visualization, preparation, and analysis.
For the full package, cite using the author form Weiss AKH:
For a single tool, use the citation shown on its card and documentation page.
Copyright © 2026 Alexander Weiss, akhw.at. All rights reserved.
These tools are provided as local research helpers. They are not substitutes for validated scientific packages, official vendor software, or expert review. Check generated files, warnings, units, versions, and assumptions before using results in publications or decisions.