Collaborative projects
NOTE:
Due to a change in job location by JVF, currently director of the Superior Polytechnical School at University of Vic, this site is currently on hold for the length of such assignment. The site will be kept up to date with respect to academic and research activity, but will not represent the current work by JVF
Irrespective of the funding behind them, this is a list of current collaborative projects of the lab (to the extend they can be made public).
Active collaborations
- Luis Agulló and David García-Dorado, Hospital Vall d’Hebrón, Barcelona. We are interested in understanding the interaction of different types of small molecules with soluble guanylate cyclase. The project involves a combination of homology modelling, docking calculations and molecular simulations.
- Lluís Espinosa, Ana Bigas, IMIM Hospital del Mar, Barcelona. The goal is to understand particular interactions of certain proteins involved in the NF-KB pathway. As in the previous collaboration, the tools we use are homology modelling, docking and molecular simulations with Adun.
- Miquel Llobera, Universitat de Barcelona. Modelling of the properties of a lipase. Its interaction substrates and with other proteins. Homology modelling, docking and molecular dynamics with Adun.
- Janusz Bujnicki, International Institute of Molecular and Cell Biology, Warsaw. RNA folding with knowledge based potentials and multiscale simulations with Adun.
- Berta Alsina, Universitat Pompeu Fabra. Development of mathematical models to understand early events in the inner ear development in vertebrates. Deterministic and stochastic anaysis with ByoDyn.
- Francisco Muñoz, Universitat Pompeu Fabra, Rosana Chehin, Universidad de Tucumán, and Gian Pietro Miscione, Università di Bologna. Study of nitrotyrosination effect on different proteins involved in Alzheimer disease. Using quantum chemistry and hybrid QM/MM calculations, as well as molecular dynamics simulations.
- Chritopher Fennell and Ken Dill, UCSF. Implementation and further development of solvation models for biomolecular simulations.
- Gonzao Jaña, Eduardo Delgado and Joel Alderete, Universidad de Concepción. Quantum mechanical analysis of acetohidroxyacid synthase. QM/MM, molecular dynamics.
- Ozlem Keskin, Koc University. Protein-Protein interactions. PDLD/S-LRA calculations of protein interactions.
- Cedric Notredame, Center for Genomic Regulation. Protein evolution. Molecular dynamics and related methods.
- Baldo Oliva, UPF. Statistical potentials. FFML, molecular dynamics.
In addition, the CBBL shares space and many research interests with the MultiScale lab at the GRIB
