Since PyMOL supports several commonly used file formats for electron density maps it is also the preferred tool for crystallographers. Additionally it provides exceptional 3D-viewing functionalities which can be very useful in structure-based drug design. PyMOL is the most frequently used program for generating publication quality pictures of molecular structures and offers multiple advanced rendering options. The PyMOL plugin described here is developed specifically to make use of PyMOL’s exceptional molecular viewing capabilities. The APBS plugin is an interface to the popular adaptive Poisson-Boltzmann solver (APBS ) program and provides easy access to electrostatics calculations and the visualization of potential energy surfaces and charge densities on protein surfaces. In the field of molecular interactions there have been several (plugin)-extensions developed that gain great popularity. Extensions can either make use of the wizard-interface or the plugin-interface, the latter of which is the more commonly utilized. Over the last years the PyMOL molecular graphics system has evolved from being a powerful molecular viewer with exceptional 3D-capabilities into a platform for several programs and applications which make use of PyMOL’s versatile visualization properties.Through its multi-layer architecture and the use of the powerful object-oriented scripting language Python at the top-level, PyMOL is relatively easy to extend and customize without re-compiling the source code.

Visual examination of predicted binding geometries (docking poses) thereby contributes crucially to the further development of a lead compound either towards enhanced binding affinity, towards reduced side effects or towards reduced susceptibility to drug resistance related mutations. If a suitable structure of the target is available molecular docking can be used to discriminate between putative binders and non-binders in large databases of chemicals and to reduce the number of compounds to be subjected to experimental testing substantially.

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