Features

Different options to customize the search:

• sites with a minimum of coordinating amino acids

• sites with a custom combination of coordinating amino acids

• taking into account coordinations with backbone oxygen atoms (or only with the side chains)

• scanning the whole protein or only a region of interest

Search for a structural motif and propose mutations:

• scan the structure to search a specific motif (e.g. HIS,HIS,ASP/GLU)

• propose mutations to complete the motif (e.g. having a HIS,HIS motif, search for mutations to complete with either a GLU or an ASP)

Possible applications

• screening of a pool of .pdb structures

• identification of conformational changes that alter the formation of metal-binding sites

• metalloenzyme design

A more complete overview of the capabilities of the program, illustrated with several case studies, is available in our ChemRxiv preprint.

Documentation and support

Documentation is available at this link.

Installation instructions are available at this webpage.

If you need help with BioMetAll, please use the issues page of this GitHub repository. You can drop me a message at joseemilio.sanchez@uab.cat too.

License

BioMetAll is an open-source software licensed under the BSD-3 Clause License. Check the details in the LICENSE file.

History of versions

• v1.0: Release version used in the preparation of the JCIM article.

• v0.2: New backbone_clashes and sidechain_clashes parameters, which allow to customize the filtering of probes with clashes.

• v0.1: Release version used in the preparation of the ChemRxiv preprint.

OS Compatibility

BioMetAll is compatible with Linux, macOS and Windows.

If you find some dificulties when installing it in a concrete distribution, please use the issues page to report them.

How to cite this software

Sánchez-Aparicio, J.-E.; Tiessler-Sala, L.; Velasco-Carneros, L.; Roldán-Martín, L.; Sciortino, G.; Maréchal, J.-D.. Biometall: Identifying Metal-binding Sites in Proteins from Backbone Preorganization, J. Chem. Inf. Model., 2020, https://dx.doi.org/10.1021/acs.jcim.0c00827.

Acknowledgements

Project template based on the Computational Molecular Science Python Cookiecutter version 1.2.

Standalone executables have been created with PyInstaller