Knowledge of a protein’s structure permits key insights in its molecular function and supports scientists in the design of targeted and efficient experiments. ProMod3 is the central software component of the widely used SWISS-MODEL web-server. Common modelling tasks, such as loop modelling, sidechain modelling or generating a full protein model by homology, are provided as production ready pipelines, forming the starting point for own developments and enhancements. Its modular design aims at fast prototyping of novel algorithms and implementing flexible modelling pipelines. ProMod3 is a fully scriptable software platform that can perform all steps required to generate a protein model by homology. Here we present a versatile open source homology modelling toolbox as foundation for flexible and computationally efficient modelling workflows. detecting a homologue to the desired target sequence that can be used as a template for modelling. The most accurate methods today are based on homology modelling, i.e. Computational methods for protein structure modelling are routinely used to complement experimental structure determination, thus they help to address a broad spectrum of scientific questions in biomedical research.
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