Mapping GPCR contacts and their stability – a web-based analysis tool

2019 edition

David Aranda

G-protein coupled receptors (GPCRs) constitute one of the main targets for the pharmaceutical industry. For drug discovery programs, molecular dynamics (MD) techniques are increasingly gaining importance  (Borhani & Shaw, 2012)⁠ as they provide a way to analyze the behavior of macromolecules such as GPCRs through time. For this reason, we are developing GPCRmd ( a database to store and display MD simulations of GPCRs from all over the world. This database will be linked to the highly renowned GPCRdb database (

In particular, this project is centered on the creation of an online tool for the analysis of intra- and intermolecular interactions and their stability derived from GPCR dynamics. The analysis tool will be based on GetContacts ( scripts, which offers a way to precisely calculate different types of interactions (hydrogen bonds, water bridges, …) formed between the residues of a molecular system in a MD simulation. It will be designed as an easy, user-friendly web tool allowing researchers with different expertise (e.g. biologists, medicinal chemists, pharmacologists) to browse and exploit simulation data.

Once the tool is completed, we will study how inter- and intramolecular interaction networks are affected by (i) evolution and (ii) polymorphism across different GPCRs, which could be ultimately useful for drug design studies.


Borhani, D. W., & Shaw, D. E. (2012). The future of molecular dynamics simulations in drug discovery. Journal of Computer-Aided Molecular Design, 26(1), 15–26.

Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., … Zhu, X. (2001). The Sequence of the Human Genome. Science, 291(5507), 1304–1351.

Authors and affiliation:
David Aranda-Garcia, Mariona Torrens-Fontanals, Ismael Rodriguez-Espigares and Jana Selent
GPCR drug discovery group, Research Programme on Biomedical Informatics (GRIB), Universitat Pompeu Fabra (UPF) – Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain