PepFun: Open Source Protocols for Peptide-Related Computational Analysis |
| |
Authors: | Rodrigo Ochoa Pilar Cossio |
| |
Affiliation: | 1.Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellin 050010, Colombia;2.Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60348 Frankfurt am Main, Germany |
| |
Abstract: | Peptide research has increased during the last years due to their applications as biomarkers, therapeutic alternatives or as antigenic sub-units in vaccines. The implementation of computational resources have facilitated the identification of novel sequences, the prediction of properties, and the modelling of structures. However, there is still a lack of open source protocols that enable their straightforward analysis. Here, we present PepFun, a compilation of bioinformatics and cheminformatics functionalities that are easy to implement and customize for studying peptides at different levels: sequence, structure and their interactions with proteins. PepFun enables calculating multiple characteristics for massive sets of peptide sequences, and obtaining different structural observables derived from protein-peptide complexes. In addition, random or guided library design of peptide sequences can be customized for screening campaigns. The package has been created under the python language based on built-in functions and methods available in the open source projects BioPython and RDKit. We present two tutorials where we tested peptide binders of the MHC class II and the Granzyme B protease. |
| |
Keywords: | peptide python bioinformatics cheminformatics |
|
|