Distributed all-atom simulations of intrinsically unstructured proteins

The Computational Biophysics Group at the Universitat Pompeu Fabra (GRIB-UPF) hosts two unique computational resources dedicated to the execution of large scale molecular dynamics (MD) simulations: (a) the ACMD molecular-dynamics software, used on standard personal computers with graphical processing units (GPUs); and (b) the GPUGRID. net computing network, supported by users distributed worldwide that volunteer GPUs for biomedical research. We leveraged these resources and developed studies, protocols and open-source software to elucidate energetics and pathways of a number of biomolecular systems, with a special focus on flexible proteins with many degrees of freedom. First, we characterized ion permeation through the bactericidal model protein Gramicidin A conducting one of the largest studies to date with the steered MD biasing methodology. Next, we addressed an open problem in structural biology, the determination of drug-protein association kinetics; we reconstructed the binding free energy, association, and dissaciociation rates of a drug like model system through a spatial decomposition and a Makov-chain analysis. The work was published in the Proceedings of the National Academy of Sciences and become one of the few landmark papers elucidating a ligand-binding pathway. Furthermore, we investigated the unstructured Kinase Inducible Domain (KID), a 28-peptide central to signalling and transcriptional response; the kinetics of this challenging system was modelled with a Markovian approach in collaboration with Frank Noe’s group at the Freie University of Berlin. The impact of the funding includes three peer-reviewed publication on high-impact journals; three more papers under review; four MD analysis components, released as open-source software; MD protocols; didactic material, and code for the hosting group.

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The Food Assistance Monthly Participation Report is a monthly summary of Food Assistance program participation, Statewide and for each Iowa county. Breakouts are reported for participants also in the FIP program, those only receiving Food Assistance, and those that are receiving economic assistance under other programs (primarily Medicaid). This report may also be known as the F-1 Report.

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F-1 Food Assistance Program State Summary, February, 2005

The Food Assistance Monthly Participation Report is a monthly summary of Food Assistance program participation, Statewide and for each Iowa county. Breakouts are reported for participants also in the FIP program, those only receiving Food Assistance, and those that are receiving economic assistance under other programs (primarily Medicaid). This report may also be known as the F-1 Report.