PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL
2016; Oxford University Press; Volume: 33; Issue: 3 Linguagem: Inglês
10.1093/bioinformatics/btw638
ISSN1367-4811
AutoresGiacomo Janson, Chengxin Zhang, Maria G. Prado, Alessandro Paiardini,
Tópico(s)Bioinformatics and Genomic Networks
ResumoThe 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.PyMod 2.0 installer packages for Windows, Linux and Mac OS X and user guides are available at http://schubert.bio.uniroma1.it/pymod/index.html. The open source code of the project is hosted at https://github.com/pymodproject/pymod.alessandro.paiardini@uniroma1.it or giacomo.janson@uniroma1.it
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