Introducing Pep McConst — A user-friendly peptide modeler for biophysical applications
Journal of Computational Chemistry
We are introducing Pep McConst — a software that employs a Monte-Carlo algorithm to construct 3D structures of polypeptidechains which could subsequently be studied as stand-alone macromolecules or complement the structure of known proteins. Using an approach toavoid steric clashes, Pep McConst allows to create multiple structures for a predefined primary sequence of amino acids. These structures couldthen effectively be used for further structural analysis and investigations. The article introduces the algorithm and describes its user-friendlyapproach that was made possible through the VIKING online platform. Finally, the manuscript provides several highlight examples where Pep McConst was used to predict the structure of the C-terminal of a known protein, generate a missing bit of already crystallized protein structures and simply generate short polypeptide chains.