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#1. MolDesign (Windows) Oleh: amezcua-dev.com
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#3. MolDesign (Windows) Oleh: amezcua-dev.com
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Deskripsi

MolDesign
MolDesign is a desktop application to produce, organize and communicate structural computational evidence in early-stage drug research. It does not answer "will this molecule be a good drug?". It answers a narrower, more useful question: what evidence did this run produce, with which structure and configuration, which checks did it pass and what uncertainty remains.

All computation happens on your computer. The core works offline, and the app only uses the network when you ask it to: optional downloads or external services you configure.

WHAT YOU CAN DO
• Evaluation: dock a molecule with AutoDock Vina 1.2.7, included in the installation, and gather the pose, interactions, properties and run conditions in one dossier.
• Batch: evaluate a series of molecules under one configuration and declare its coverage.
• Preparation: audit the structural system (receptor, ligand, site and decisions) and see what is ready, what needs review and what blocks it. Download the complete run as a .zip, with the recipe to repeat it and the SHA-256 of every file, ready to share.
• Moldex: a library of saved evaluations, with a 3D viewer and a PDF report.
• History: all your runs, each with its provenance.
• Molcy (Beta): videos and photos of a run, made with Blender.

YOUR RECEPTORS OR DEMO ONES
Upload your own receptors as a raw structure (PDB, mmCIF or predicted), as a structure already prepared by your team, or as a Vina-ready PDBQT. The catalog includes 381 demo receptors to explore the app; none has yet passed the pose verification and calibration protocol, and everything produced from them says so.

A TOOL THAT ABSTAINS
When something cannot be checked, MolDesign declares it instead of filling it in: a site with gaps, a removed metal, an ambiguous tautomer or a doubtful chemical species shows up as a warning with its reason. ADMET and rescoring layers are presented as experimental.

WHAT IT IS NOT
• It does not predict biological activity or replace experimental validation.
• It does not run molecular dynamics or free-energy (FEP) calculations. Preparation is an FEP readiness auditor in development and does not certify compatibility with any provider.
• It is not a cloud service.

OPTIONAL DOWNLOADS AND CONNECTIONS
• ESMFold (8.4 GB), to fold peptides that Vina then docks. This route is experimental.
• Blender and Molecular Nodes, third-party programs Molcy uses for videos and photos. Video needs a GPU; photos can also be taken on the CPU. Photos carry the MolDesign mark and every video ends with the MolDesign closing.
• MolChat, the AI interpreter, works with a local model or an external provider; that provider only receives data if you configure it and authorize its destination.

Interface, dossier and PDF in English and Spanish.

LICENSE
Free for noncommercial use (PolyForm Noncommercial 1.0.0). Commercial use requires a separate license.

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