BIOmodeling

Conferences

The final GLISTEN
conference:
GLISTEN spring meeting in Porto, Portugal. 29-31.03.2017
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GLISTEN
conference:
Allschwil(Basel)/Actelion Pharm. Ltd., Switzerland.
April 1-2, 2015
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GLISTEN - GPCR-Ligand Interactions, Structures, and Transmembrane Signalling: a European Research Network,
7-9 October 2013,
Warsaw, Poland
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The Modern Techniques for Drug Design Purposes,
4-5 October 2011,
Warsaw, Poland
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The relationship of numerical simulations and experimental methods,
26-28 May 2011,
Warsaw, Poland
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Home

Drug design
Modeling of structure and dynamics of membrane proteins
Action of molecular switches on activation pathway of GPCRs, agonist/antagonist sensors
Development of new methods for coarse-grain dynamics
Oligomerization processes of proteins and peptides
Interactions of proteins with graphene, carbon nanotubes and other electrode materials
Simulated mechanical unfolding of proteins

Graphics created by Shuguang Yuan

Membrane receptor with a membrane and water in a periodic box.

G-protein-coupled receptors - GPCRs (rhodopsin, adrenergic / opioid / cannabinoid / chemokine / … receptors)
Bacteriorhodopsin, halorhodopsin
Membrane proteases including the γ-secretase complex (Alzheimer disease)
Glucose oxidase (for biosensors)

May 2018.

GPCRM

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.

October 2017.

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.

November 2016.

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).

January 2015.

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).

August 2014.

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-HT_1B and 5-HT_2B where we obtained 2^nd and 1^st place, respectively.

October 2013.

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.

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