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Paper of the Month
The relationship between water bridges and the polyproline II conformation: a large-scale analysis of molecular dynamics simulations and crystal structures
Law P.B. and Daggett V.
PEDS 23:27-33, 2010
It has been suggested that denatured proteins are predisposed toward the left-handed polyproline II (PII) conformation. One possible source of PII stability in the denatured state is water bridges. More...
*** Visit our New dynameomics.org Website ***
Watch movies and
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the world's largest public collection of molecular dynamics data
Goals: Realistic simulation of protein dynamics, unfolding/folding, and conformational transitions linked to disease.
Latest News
- The National Energy Research Scientific Computing Center (NERSC) has awarded the Daggett Group 2 million hours for 2010 for their molecular dynamics simulations. This time will used for the Dynameomics Project, ALS-associated SOD SNPs, and the Prion Project, among others.
- Congratulations go out to undergraduate Sara Calhoun who was awarded a Washington Research Foundation Fellowship!
- We have recently developed an XML schema for standardizing, cataloging and sharing parameters and molecular definitions for molecular mechanics force fields.
- The Microsoft External Research booklet on Socially Relevant Computing featured an article on the Dynameomics Project and how it pertains to understanding and developing treatments for diseases such as Alzheimers, Parkinson's, and cancer.
- The Daggett Group and other labs are working with Microsoft External Research to create a GrayWulf cluster optimized to analyze their Dynameomics data. Read more about the project in this report from Microsoft and on the msdn eScience blog.
- The Daggett Group was awarded 1.5 million hours on the National Energy Research Scientific Computing Center (NERSC) for 2009! This computer time supports the Dynameomics Project.
- The Dynameomics Project, which began running on the supercomputers at NERSC in 2005 with the goal of simulating the unfolding pathways of all known protein folds, was listed as a major accomplishment in Advanced Scientific Computing Research at Lawrence Berkeley National Lab.
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