Search Results - Carlos Simmerling

Carlos Simmerling

Carlos Simmerling is a full professor of chemistry at the State University of New York at Stony Brook. He is associate director of the Louis and Beatrice Laufer Center for Physical and Quantitative Biology. Simmerling received his Bachelor of Arts in 1991 from the University of Illinois at Chicago and then his doctorate in 1994 from the same institution. His postdoctoral work was performed at the University of California, San Francisco under the direction of Peter Kollman. His primary field of interest is computational structural biology with a focus on methods of conformational sampling and protein structure prediction. He is a member of the AMBER development team. Provided by Wikipedia
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  1. 1
    Targeting structural flexibility in HIV-1 protease inhibitor binding

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

    Published 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 by He Huang, Carlos Simmerling

    Published 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 by Fangyu Ding, Melinda Layten, Carlos Simmerling

    Published 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 by Adrián E. Roitberg, Asim Okur, Carlos Simmerling

    Published 2007
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  5. 5
    Protein storytelling through physics

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

    Published 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 by Xiaolin Cheng, Guanglei Cui, Viktor Horn̆ák, Carlos Simmerling

    Published 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 by Viktor Horn̆ák, Asim Okur, Robert C. Rizzo, Carlos Simmerling

    Published 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 by Viktor Horn̆ák, Asim Okur, Robert C. Rizzo, Carlos Simmerling

    Published 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 by Thi Hong Hai Nguyen, Daniel R. Roe, Carlos Simmerling

    Published 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 by Christina Bergonzo, Arthur J. Campbell, Ross C. Walker, Carlos Simmerling

    Published 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 by Alberto Pérez, Joseph A. Morrone, Carlos Simmerling, Ken A. Dill

    Published 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 by Thi Hong Hai Nguyen, Alberto Pérez, Sherry Bermeo, Carlos Simmerling

    Published 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 by Thi Hong Hai Nguyen, James Maier, He Huang, Victoria Perrone, Carlos Simmerling

    Published 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 by James Maier, Carmenza Martinez, Koushik Kasavajhala, Lauren Wickstrom, Kevin Hauser, Carlos Simmerling

    Published 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 by Viktor Horn̆ák, Robert Abel, Asim Okur, Bentley Strockbine, Adrián E. Roitberg, Carlos Simmerling

    Published 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 by Alberto Pérez, Justin L. MacCallum, Emiliano Brini, Carlos Simmerling, Ken A. Dill

    Published 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 by Lexin Chen, Daniel R. Roe, Matthew Kochert, Carlos Simmerling, Ramón Alain Miranda‐Quintana

    Published 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 by John Mongan, Carlos Simmerling, J. Andrew McCammon, David A. Case, Alexey V. Onufriev

    Published 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 by Luis Galiano, Fangyu Ding, Angelo M. Veloro, Mandy E. Blackburn, Carlos Simmerling, Gail E. Fanucci

    Published 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 by Xiaolin Cheng, Catherine Kelso, Viktor Horn̆ák, Carlos de los Santos, Arthur P. Grollman, Carlos Simmerling

    Published 2005
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