What do we do?
At the Molecular Modelling Group (MMG) we study mechanisms of molecular recognition in particular protein-protein or protein-small ligand interactions, using molecular modelling techniques such as homology modelling, molecular dynamics, docking and free energy simulations. Our main activity consists of the development and application of state-of-the-art methods in computer-aided protein engineering and drug design. Most efforts are concentrated on the development of new small molecule inhibitors of important targets for cancer therapy, as well as the design of optimized proteins like T cell receptor (TCR), for cancer immunotherapy. We develop and maintain several web tools for drug design, such as SwissDock, SwissBioisostere and SwissTargetPrediction.
We also act as the Protein Modeling Facility (PMF) of the University of Lausanne.
Highlights 2016In 2016, the group officially released SwissSimilarity, a new web tool for rapid ligand-based virtual screening. SwissSimilarity is part of a large SIB initiative to provide online tools for drug design – such as SwissDock, SwissBioisostere and SwissTargetPrediction, with which it can interoperate.
In addition, the group designed the BOILED-Egg classification model, which provides an intuitive graph prediction of passive intestinal absorption and brain penetration. The group also developed a new on-the-fly QM/MM docking algorithm within the in-house docking tool Attracting Cavities.
The group finished the development of SwissADME, a new web tool to compute the physicochemistry and estimate the pharmacokinetics, druglikeness and medicinal chemistry friendliness of small molecules. Among others, SwissADME provides an exclusive access to our in-house models iLogP and BOILED-Egg. The SwissADME interface is designed to allow both experts and non-experts to use it. Official release is planned for 2017.
Main publications 2016
- Daina A, Zoete V. A BOILED-Egg To Predict Gastrointestinal Absorption and Brain Penetration of Small Molecules. Chemmedchem, 2016;11(11):1117–1121.
- Zoete V, Daina A, Bovigny C, Michielin O. SwissSimilarity: A Web Tool for Low to Ultra High Throughput Ligand-Based Virtual Screening. J. Chem. Inf. Model., 2016; 56(8):1399–1404.
- Zoete V, Schuepbach T, Bovigny C, Chaskar P, Daina A, Röhrig UF, Michielin O. Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape. J. Comput. Chem., Journal of Computational Chemistry, 2016;37(4):437–447.
- Chaskar P, Zoete V, Röhrig UF. On-the-fly QM/MM Docking with Attracting Cavities. J. Chem. Inf. Model., 2017;57(1):73–84
- Daina A, Michielin O, Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci. Rep., 2017, in press