MAE File

What are MAE files and how to open them

Are you having problems opening a MAE file or are you simply curious about its contents? We're here to explain the properties of these files and provide you with software that can open or handle your MAE files.

What is a MAE file?

A .MAE file is a Maestro Molecular Model file.

Maestro molecular model (.mae) files are created and used by the Maestro environment from Schrödinger. These files store fully prepared molecular structures including three-dimensional coordinates, atomic connectivity, atom types, formal charges, protonation states, residue and chain identifiers, and other metadata necessary for molecular modelling workflows. These files are what Maestro imports or exports when you save a structure, run simulations, or prepare a protein or small molecule for downstream tasks.

Maestro writes .mae files as human-readable, block-based text using a native structural data notation. The format supports both compressed (.maegz or .mae.gz) and uncompressed forms. It is used to store not only molecular geometries but also associated properties and workflow states, such as title, entry names, protonation assignments and preparation metadata. Maestro also reads its own .mae files when loading projects or importing structures.

Internally, a .mae file begins with a version block, then a structure table block ("CT" block) which defines properties and then lists values for atoms, residues and bonds. The file uses labels such as "s_m_title", "i_m_residue_number", "r_m_x_coord", "i_m_atomic_number", "f_m_ct" and similar tags.

How to open MAE files

We have identified one MAE opener that is compatible with this specific type of MAE file.

Programs that open Maestro Molecular Model files

Last updated: August 9, 2026

Various apps that use files with this extension

These apps are known to open certain types of MAE files. Remember, different programs may use MAE files for different purposes, so you may need to try out a few of them to be able to open your specific file.

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File.org helps thousands of users every day, and we would love to hear from you if you have additional information about MAE file formats, example files, or compatible programs. Please use the links below or email us at submit@file.org to discuss further.