GPCRM - The GPCR structure Modeling server.
GPCRM provides 3D homology models of GPCR. The modeling procedure is based on profile-profile comparison and multiple structural templates. Loops are refined with two different methods: Modeller and Rosetta.
D. Latek, P. Pasznik, T. Carlomagno, S. Filipek (2013) Towards improved quality of GPCR models by usage of multiple templates and profile-profile comparison.
PLOS ONE 8(2): e56742, DOI
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Oferta dwóch stypendiów doktoranckich w dziedzinie modelowania molekularnego w projekcie badawczym OPUS „Badanie mechanizmu proteolizy oraz selektywnego wiązania ligandów do kompleksu gamma-sekretazy” finansowanym przez NCN. Kierownik projektu: prof. dr hab. Sławomir Filipek. Termin przesyłania dokumentów upływa 15 sierpnia 2017 roku. Więcej informacji.
We revealed how the hydrophobic ligands entry to and exit from CB1 cannabinoid receptor directly from the membrane, Published in J. Chem. Inf. Model. (2016) (DOI).
New papers linking the activation of GPCRs with water flows inside receptor: in Nature Communication (2014) (DOI) and in Angew. Chem. Int. Ed. (2015) (DOI).
The web server GPCRM, built by BIOmodeling group for construction of homology models of GPCRs based on multiple templates, proved to be one of the best among other services of this type so it was recently selected to be implemented into GPCRDB platform. Employing this service we participated in GPCR Dock competition for docking of ligands to unknown structures of serotonin receptors 5-HT1B and 5-HT2B where we obtained 2nd and 1st place, respectively.
The Nobel prize in Chemistry for 2013 was awarded to three computer scientists. They created foundations of methods for molecular modeling and molecular dynamics to study both small molecules and large systems composed of DNA and proteins enabling docking of ligands to molecular targets for drug design. They developed a concept of force-field and also combined these methods with quantum chemistry to simulate enzymatic reactions.