MSCS Key Lab Home | NeuroDrug Design Home | Bioinformatics and Computational biology tools
The NeuroDrug Design web portal is dedicated to collect, categorize, model, and simulation of brain-related proteins. The portal is developed together in collaboration with the group of Profs. Paolo Carloni from Computational Biomedicine Institutes (IAS-5/INM-9), Forschungszentrum Juelich GmbH, 52425 Juelich, Germany (website), and Prof. Nguyen Manh Duc from Materials Science and Scientific Computing Department, United Kingdom Atomic Energy Authority for various bioinformatics and computational biology expertise. We also collaborate with various research groups in Biology, Chemistry, Pharmaceutical Science inside and outside of Vietnam.
As a start, we focus on the TSPO 18kDa translocator protein. This protein is an important membrane protein that is expressed at high levels in the outer mitochondrial membrane of steroidogenic cells of the nervous system. It is known to show elevated expression in response to a variety of brain inflammations such as cancers, Alzheimer's and Parkinson's diseases, disorders such as depression and anxiety. Therefore, it has been exploited as bio-tracer for brain inflammation using highly specific synthetic ligands such as PK11195.
The increased expression levels of TSPO can be monitored by positron emission tomography (PET) scan. Hence, radiolabeled ligands such as PK11195 may sensitively recognize lesions and active disease processes of the brain. Moreover, they can be used to develop synthetic ligands that act as both diagnostic and therapeutic tools. Based on bioinformatics methods, all-atom molecular dynamics, and the NDD server aims to provide in-silico high-throughput structure-based ligand screening to detect potential lead candidates. Initially, our team focus on highlighting the PK11195-induced stability of the mouse TSPO tertiary structure and its oligomeric states.
Our current results include homology models of human TSPO protein based on its sequence alignment with bacterial and mouse TSPO. Both types of oligomer, monomer and dimer, have been constructed. The binding poses with of the ligand PK11195 in the cavity of the TSPO protein are also constructed. Unfortunately, at the moment, we cannot publicly provide the models for these structures pending discussions with our partners. However, they are available upon request. Please contact Prof. Toan T. Nguyen (toannt AT vnu DOT edu DOT vn) for more information.
Meanwhile, you are free to use various computational and bioinformatic tools that we posted. Most of the tools use automated procedure to perform user input request. As such, your exprience and success varies depending on specific situation.
These automated tools are provided on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are solely responsible for determining the appropriateness of the results of provided by these tools.
We provide academic related support, manually modelling, ligand and protein docking, and multiscale biomolecule simulation service. Please contact us for more details.
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