UCSF Laboratory of Andrej Sali QB3



MDT prepares a raw frequency table, given information from MODELLER alignments and/or PDB files. More precisely, MDT uses a sample of sequences, structures, and/or alignments to construct a table N(a,b,c,...,d) for features a, b, c, ..., d. The sample for generating the frequencies N is obtained depending on the type of features a, b, c, ..., d. The sample can contain individual proteins, pairs of proteins, pairs of residues in proteins, pairs of aligned residues, pairs of aligned pairs of residues, chemical bonds, angles, dihedral angles, and pairs of tuples of atoms. Some features work with triple alignments, too. All the needed features a, b, c, ..., d are calculated automatically from the sequences, alignments, and/or PDB files. The feature bins are defined by the user when each feature is created.

MDT is Copyright 1989-2020 Andrej Sali. MDT is free software: you can redistribute it and/or modify it under the terms of version 2 of the GNU General Public License as published by the Free Software Foundation. MDT is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. For further details, please consult the Copyright and license section of the documentation.


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MDT 5.5

Source code [GPG signature]

Binary RPM package for 64-bit Fedora 31 Linux (requires Modeller 9.15 or later)

Source RPM package

Mac users: install homebrew, then run "brew tap salilab/salilab; brew install mdt"

Anaconda Python users (Linux or Mac): run "conda install -c salilab mdt"


All packages are signed with this GPG key.


Development version

MDT development is hosted at GitHub.

Andrej Sali, PhD, Professor, Department of Bioengineering and Therapeutic Sciences; Department of Pharmaceutical Chemistry; School of Pharmacy, University of California at San Francisco, UCSF MC 2552, Mission Bay, Byers Hall, 1700 4th Street, Suite 503B, San Francisco, CA 94143, Tel +1 (415) 514-4227, Fax +1 (415) 514-4231, , Web https://salilab.org