Structures of proteins and their complexes modeled by BIOmodeling group available for downloading.
S. Yuan, U. Ghoshdastider, B. Trzaskowski, D. Latek, A. Debinski, W.
Pulawski, R. Wu, V. Gerke, S. Filipek, The role of water in
activation mechanism of human N formyl Peptide Receptor 1 (FPR1) based
on molecular dynamics simulations, PLOS ONE (2012) 7, e47114. doi: 10.1371/journal.pone.0047114.
Formyl Peptide Receptor 1 (FPR1)
with agonist fMLF
with antagonist tBocMLF.
The models contain water molecules within a distance < 3 Å from the complex.
Agonist fMLF located deep in binding site of FPR1.
T.M. Stepniewski, S. Filipek, Non-peptide ligand binding to the formyl peptide receptor FPR2 - a comparison to peptide ligand binding modes, Bioorg. Med. Chem. (2015) 23, 4072-4081. doi: 10.1016/j.bmc.2015.03.062.
Our service GPCRM is completely reshaped, much faster, and user friendly. Now, it contains 3 main routes: Quick path (default), Long path, and High similarity (the fastest) for homology modeling of GPCRs. Currently, the service contains over 90 template structures. The updated version was recently published in NAR 2018, W1.
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.