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
The latest news
The post-doc position in Biomodellab in molecular modeling for realization of the project: "Novel ligands of histamine receptor H4 as potential anti-allergic and anti-inflammatory drugs".
Temat 27: Modelowanie struktury mitochondrialnego kanału potasowego oraz identyfikacja miejsc wiążących ATP i hem. Projekt będzie realizowany z Instytutem Biologii Doświadczalnej im. M.Nenckiego zatem umiejętności z zakresu biologii/biotechnologii jak również modelowania molekularnego mile widziane. Aplikowanie online do 18.05.2018 poprzez stronę TRI-BIO-CHEM. Zapytania w sprawie projektu proszę kierować na adres sfilipek.lab|gmail.com.
A development of cryo-EM (cryo-electron microscopy) was the subject of the Nobel Prize in Chemistry 2017. Recently, this method became so precise that it is possible to obtain the structures of large biomolecular complexes with very high, atomic resolution. This article [»»»] describes in short the cryo-EM method and the Nobel laureates (including YouTube movie).
Currently, our group works on the γ-secretase, the very large complex of 4 membrane proteins. This complex produces β-amyloid being a hallmark of Alzheimer's disease. The determination of structure of this complex was possible only using the cryo-EM method.
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.