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Bioinformatics. 2017 Feb 1;33(3):444-446. doi: 10.1093/bioinformatics/btw638.

PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL.

Author information

Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza Università di Roma, Rome, Italy.
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
Department of Biology and Biotechnology "Charles Darwin", Sapienza Università di Roma, Rome, Italy.



The recently released PyMod GUI integrates many of the individual steps required for protein sequence-structure analysis and homology modeling within the interactive visualization capabilities of PyMOL. Here we describe the improvements introduced into the version 2.0 of PyMod.


The original code of PyMod has been completely rewritten and improved in version 2.0 to extend PyMOL with packages such as Clustal Omega, PSIPRED and CAMPO. Integration with the popular web services ESPript and WebLogo is also provided. Finally, a number of new MODELLER functionalities have also been implemented, including SALIGN, modeling of quaternary structures, DOPE scores, disulfide bond modeling and choice of heteroatoms to be included in the final model.

Availability and Implementation:

PyMod 2.0 installer packages for Windows, Linux and Mac OS X and user guides are available at The open source code of the project is hosted at

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[Indexed for MEDLINE]

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