Resultats de la cerca - Carlos Simmerling

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  1. 1
    Targeting structural flexibility in HIV-1 protease inhibitor binding

    Targeting structural flexibility in HIV-1 protease inhibitor binding per Viktor Horn̆ák, Carlos Simmerling

    Publicat 2006
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  2. 2
    Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit Solvent Simulations of Proteins on CPUs and GPUs

    Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit Solvent Simulations of Proteins on CPUs and GPUs per He Huang, Carlos Simmerling

    Publicat 2018
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  3. 3
    Solution Structure of HIV-1 Protease Flaps Probed by Comparison of Molecular Dynamics Simulation Ensembles and EPR Experiments

    Solution Structure of HIV-1 Protease Flaps Probed by Comparison of Molecular Dynamics Simulation Ensembles and EPR Experiments per Fangyu Ding, Melinda Layten, Carlos Simmerling

    Publicat 2008
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  4. 4
    Coupling of Replica Exchange Simulations to a Non-Boltzmann Structure Reservoir

    Coupling of Replica Exchange Simulations to a Non-Boltzmann Structure Reservoir per Adrián E. Roitberg, Asim Okur, Carlos Simmerling

    Publicat 2007
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  5. 5
    Protein storytelling through physics

    Protein storytelling through physics per Emiliano Brini, Carlos Simmerling, Ken A. Dill

    Publicat 2020
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  6. 6
    Modified Replica Exchange Simulation Methods for Local Structure Refinement

    Modified Replica Exchange Simulation Methods for Local Structure Refinement per Xiaolin Cheng, Guanglei Cui, Viktor Horn̆ák, Carlos Simmerling

    Publicat 2005
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  7. 7
    HIV-1 Protease Flaps Spontaneously Close to the Correct Structure in Simulations Following Manual Placement of an Inhibitor into the Open State

    HIV-1 Protease Flaps Spontaneously Close to the Correct Structure in Simulations Following Manual Placement of an Inhibitor into the Open State per Viktor Horn̆ák, Asim Okur, Robert C. Rizzo, Carlos Simmerling

    Publicat 2006
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  8. 8
    HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations

    HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations per Viktor Horn̆ák, Asim Okur, Robert C. Rizzo, Carlos Simmerling

    Publicat 2006
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  9. 9
    Improved Generalized Born Solvent Model Parameters for Protein Simulations

    Improved Generalized Born Solvent Model Parameters for Protein Simulations per Thi Hong Hai Nguyen, Daniel R. Roe, Carlos Simmerling

    Publicat 2013
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  10. 10
    A partial nudged elastic band implementation for use with large or explicitly solvated systems

    A partial nudged elastic band implementation for use with large or explicitly solvated systems per Christina Bergonzo, Arthur J. Campbell, Ross C. Walker, Carlos Simmerling

    Publicat 2009
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  11. 11
    Advances in free-energy-based simulations of protein folding and ligand binding

    Advances in free-energy-based simulations of protein folding and ligand binding per Alberto Pérez, Joseph A. Morrone, Carlos Simmerling, Ken A. Dill

    Publicat 2016
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  12. 12
    Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins

    Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins per Thi Hong Hai Nguyen, Alberto Pérez, Sherry Bermeo, Carlos Simmerling

    Publicat 2015
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  13. 13
    Folding Simulations for Proteins with Diverse Topologies Are Accessible in Days with a Physics-Based Force Field and Implicit Solvent

    Folding Simulations for Proteins with Diverse Topologies Are Accessible in Days with a Physics-Based Force Field and Implicit Solvent per Thi Hong Hai Nguyen, James Maier, He Huang, Victoria Perrone, Carlos Simmerling

    Publicat 2014
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  14. 14
    ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

    ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB per James Maier, Carmenza Martinez, Koushik Kasavajhala, Lauren Wickstrom, Kevin Hauser, Carlos Simmerling

    Publicat 2015
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  15. 15
    Comparison of multiple Amber force fields and development of improved protein backbone parameters

    Comparison of multiple Amber force fields and development of improved protein backbone parameters per Viktor Horn̆ák, Robert Abel, Asim Okur, Bentley Strockbine, Adrián E. Roitberg, Carlos Simmerling

    Publicat 2006
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  16. 16
    Grid-Based Backbone Correction to the ff12SB Protein Force Field for Implicit-Solvent Simulations

    Grid-Based Backbone Correction to the ff12SB Protein Force Field for Implicit-Solvent Simulations per Alberto Pérez, Justin L. MacCallum, Emiliano Brini, Carlos Simmerling, Ken A. Dill

    Publicat 2015
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  17. 17
    k-Means NANI: An Improved Clustering Algorithm for Molecular Dynamics Simulations

    k-Means NANI: An Improved Clustering Algorithm for Molecular Dynamics Simulations per Lexin Chen, Daniel R. Roe, Matthew Kochert, Carlos Simmerling, Ramón Alain Miranda‐Quintana

    Publicat 2024
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  18. 18
    Generalized Born Model with a Simple, Robust Molecular Volume Correction

    Generalized Born Model with a Simple, Robust Molecular Volume Correction per John Mongan, Carlos Simmerling, J. Andrew McCammon, David A. Case, Alexey V. Onufriev

    Publicat 2006
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  19. 19
    Drug Pressure Selected Mutations in HIV-1 Protease Alter Flap Conformations

    Drug Pressure Selected Mutations in HIV-1 Protease Alter Flap Conformations per Luis Galiano, Fangyu Ding, Angelo M. Veloro, Mandy E. Blackburn, Carlos Simmerling, Gail E. Fanucci

    Publicat 2008
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  20. 20
    Dynamic Behavior of DNA Base Pairs Containing 8-Oxoguanine

    Dynamic Behavior of DNA Base Pairs Containing 8-Oxoguanine per Xiaolin Cheng, Catherine Kelso, Viktor Horn̆ák, Carlos de los Santos, Arthur P. Grollman, Carlos Simmerling

    Publicat 2005
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