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Research in our laboratory seeks to fuse computational and experimental efforts to investigate proteins, the fundamental molecules of biology, and their interactions with small molecule substrates, therapeutics, or probes. We develop computational methods with three major ambitions in mind: 1) to enable protein structure elucidation of membrane proteins the primary target of most therapeutics and large macromolecular complexes such as viruses; 2) design proteins with novel structure and/or function to explore novel approaches to protein therapeutics and deepen our understanding of protein folding pathways, and 3) understand the relation between chemical structure and biological activity quantitatively in order to design more efficient and more specific drugs. Crucial for our success is the experimental validation of our computational approaches which we pursue in our laboratory or in collaboration with other scientists.
Current research applications focus on new approaches to a) drug and probe development for neurodegenerative disorders and diseases including Schizophrenia, Alzheimer's, and Parkinson?s, b) understanding the structural determinants of antidepressant binding to neurotransmitter transporters, c) cardiac arrhythmia as caused by the complex interplay of potassium channel regulation and drug interactions, d) multidrug resistance in cancer and bacterial cells related to multidrug transporter proteins, and e) structural basis of viral infections and antibody activity.
The BioChemical Library (BCL) is our primary venue of testing new algorithms and ideas. We plan to solicit your help through BOINC for many of the aforementioned projects by letting the BCL run on your computers. Right now we are only in the initial phase and focus on a single application: protein folding.
We implemented an exciting new algorithm for protein folding into the BCL. We expect that it will be superior for folding large and membrane proteins, many of which are important targets for therapeutics. To verify this expectation we need to complete a benchmark - folding 54 proteins at least 100,000 times possible up to 1,000,000 times. We plan to post these jobs to BOINC shortly. Thanks again for helping us and I will keep you updated once we get results...
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