PyMod: a tool for the analysis of protein structures and sequences in PyMOL

In recent years, an exponential growing number of tools for protein sequence analysis, editing and modelling tasks have been put at the disposal of the scientific community. Despite the vast majority of these tools have been released as open source software, their deep learning curves often discourages even the most experienced users. For example, in the earlier stages of protein modeling by homology means, the lack of user-friendly Graphical User Interfaces (GUIs), the need to make use of many programs in an integrated way, Input and Output file format problems, and platform-dependent installation dependencies, often lead to submition of homology modelling tasks to automatic online servers, with no or poor chances to apply human knowledge and experience in the key-steps required to yield a good model.In order to tackle this issue, a simple and intuitive interface, PyMOD, between the popular molecular graphics system PyMOL and several other tools (i.e., BLAST, ClustalW, CEalign and Modeller) has been developed, to show how the integration of the individual steps required for homology modelling and sequence/structure analysis inside PyMOL can hugely simplify these tasks. PyMOD was developed with an emphasis on ease of use and full customization of the parameters of all the algorithms used for analysis. Database searches, multiple sequence and structural alignments generation and editing, and even the possibility to mix sequence and structure alignments have been implemented in PyMod, with the aim of creating a simple, yet powerful tool for preliminary analysis and building of homology models.