Sequence similarity searches, multiple sequence-structure alignments, and homology modelling within PyMOL



A simple and intuitive interface, PyMod, between the popular molecular graphics system PyMOL and several other tools (i.e., BLAST, ClustalW, Muscle, CEalign and MODELLER) has been developed, to show how the integration of the individual steps required for homology modelling and sequence/structure analysis within the PyMOL framework can hugely simplify these tasks. Sequence similarity searches, multiple sequence and structural alignments generation and editing, and even the possibility to merge 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.