ProMod3-A versatile homology modelling toolbox

PLoS Comput Biol. 2021 Jan 28;17(1):e1008667. doi: 10.1371/journal.pcbi.1008667. eCollection 2021 Jan.


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. The most accurate methods today are based on homology modelling, i.e. detecting a homologue to the desired target sequence that can be used as a template for modelling. Here we present a versatile open source homology modelling toolbox as foundation for flexible and computationally efficient modelling workflows. ProMod3 is a fully scriptable software platform that can perform all steps required to generate a protein model by homology. Its modular design aims at fast prototyping of novel algorithms and implementing flexible modelling pipelines. 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. ProMod3 is the central software component of the widely used SWISS-MODEL web-server.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Computational Biology / methods*
  • Databases, Protein
  • Internet
  • Models, Molecular*
  • Protein Conformation
  • Proteins / chemistry*
  • Software*
  • Structural Homology, Protein*


  • Proteins

Grants and funding

This work was supported by funding from the SIB - Swiss Institute of Bioinformatics ( and the Biozentrum, University of Basel ( GS was supported by a PhD fellowship funded by the Swiss Foundation for Excellence and Talent in Biomedical Research. Computational resources have been provided by the sciCORE center for scientific computing ( at the University of Basel. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.