INFORMATICS MEBI 590
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This 1 page Class Notes was uploaded by Marguerite Quigley on Wednesday September 9, 2015. The Class Notes belongs to MEBI 590 at University of Washington taught by Staff in Fall. Since its upload, it has received 17 views. For similar materials see /class/192266/mebi-590-university-of-washington in Medical Education And Biomedical Informatics at University of Washington.
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Date Created: 09/09/15
Mi Biomedical and Health Informatics Lecture Series Tuesday December 2 2008 Room RR134 12001250 pm Valerie Daggett PhD Professor Bioengineering College of Engineering and School ofMedicine Adjunct Professor Biochemistry Department Adjunct and Core Professor Biomedical and Health Informatics Director of Biomolecular Structure and Design Program University of Washington quotDynameomicsquot The goal of Dynarneomics is to perform atomistic molecular dynamics MD simulations of representative proteins from all known folds in explicit water in their native state and along their thermal unfolding pathways Here we present 188 fold representatives and their native state mmulations and analyses These 188 targets represent 67 ofall the structures in the Protein Data Bank Agregate statistics are presented that show the mmulation results are unbiased by fold topology or experimental origin ofthe structure The behavior of several speci c targets is highlighted to illustrate some of the general properties in the full data set and to demonstrate the role ofMD in understanding protein function and stability As an exam le of what can be learned from mining the Dynarneomics database we identi ed a protein fold with heightened localized dynamics In one member of this fold family the motion affects the exposure ofits phosphorylation ate and acts as an entropy sink to offset another portion of the protein that is relatively immobile in order to present a conmstent interface for protein docking In another member of this family a polymorphism in the highly mobile region leads to a host of disease phenotypes To encourage understanding ofthe relationships between protein dynamics function and disease we have constructed a web ate complementary to the PDB which allows access to a novel hybrid relational multidimensional database to view and interrogate mmulations of the top 30 targets ht wwwd arneomicsor dynarneomics database should also be useful for determining the rules governing protein folding and kinetic stability which should aid in deciphering genomic information and for protein engineering and design This database contains both the largest collection of protein mmulations and protein structures in the world Dr Dagett has 23 years of experience performing simulations ofproteins She developed the approach of simulating protein unfolding to characterize the folding process She also was the rst to use simulation methods to map conformational changes associated with arnyloidoms At UW she was a founding member and is now the Director ofthe Biomolecular Structure and Design Program She is Pl olell Human Frontiers of Science Microsoft DOE and other grants Until very recently she was a charter member of the NIH Mairoimolecular Structure and Function B Study Section She has also evaluated grants for many other sponsors including DOE NASNRC BBSRC MRC The Wellcome Trust the Hereditary Disease dation and various Nll l proiects Dr Dagett is the Senior Editor of Protein Engineering Design and Selection PEDS and she is on several editorial boards Biochemistry Structure and Biomedical Computation Review BCR She is coieditor of the Current Opinion in Structural Biology issues on Folding and Binding 2007 and 2009 She was elected to the Biophysical Society Council 200772010 and she has organized several international meetings Dr Dagett has published 160 scienti c papers which have garnered over 6000 utations
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