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Chemistry

D-Index
54
Citations
42208
World Ranking
12431
National Ranking
3312

Research.com Recognitions

  • 2016 - Fellow of the American Chemical Society

Overview

Carlos Simmerling is affiliated with Stony Brook University in the United States. Their research primarily spans the fields of Biochemistry, Genetics and Molecular Biology, and Medicine. Within these broad areas, they focus on several subfields including Molecular Biology, Infectious Diseases, Materials Chemistry, Ecology, and Atomic and Molecular Physics, and Optics.

The main topics of Carlos Simmerling's work encompass Protein Structure and Dynamics, SARS-CoV-2 and COVID-19 Research, RNA and protein synthesis mechanisms, Enzyme Structure and Function, Bacteriophages and microbial interactions, COVID-19 Clinical Research Studies, and Photosynthetic Processes and Mechanisms.

Frequent co-authors include Darya Stepanenko, Lorenzo Casalino, Rommie E. Amaro, Evangelos A. Coutsias, and Lauren Raguette. These collaborations suggest ongoing partnerships with scholars active in molecular biology and computational simulations.

Carlos Simmerling has contributed a number of recent papers to scientific literature. Some notable publications are:

  • AmberTools, 2023, Journal of Chemical Information and Modeling
  • AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics, 2021, The International Journal of High Performance Computing Applications
  • The flexibility of ACE2 in the context of SARS-CoV-2 infection, 2020, Biophysical Journal
  • SARS-CoV-2 spike conformation determines plasma neutralizing activity elicited by a wide panel of human vaccines, 2022, Science Immunology
  • Protein storytelling through physics, 2020, Science

Their publications appear regularly in journals such as bioRxiv (Cold Spring Harbor Laboratory), Journal of Chemical Theory and Computation, Biophysical Journal, Journal of Chemical Information and Modeling, and The Journal of Physical Chemistry B. Notably, the most frequent publication venues are bioRxiv with 9 publications and the Journal of Chemical Theory and Computation with 8 publications.

Carlos Simmerling was awarded the title of Fellow of the American Chemical Society in 2016.

Best Publications

  • The Amber biomolecular simulation programs

    David A. Case;Thomas E. Cheatham;Tom Darden;Holger Gohlke

  • ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

    James A. Maier;Carmenza Martinez;Koushik Kasavajhala;Lauren Wickstrom

  • Comparison of multiple Amber force fields and development of improved protein backbone parameters.

    Viktor Hornak;Robert Abel;Asim Okur;Bentley Strockbine

  • ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution.

    Chuan Tian;Koushik Kasavajhala;Kellon A. A. Belfon;Lauren Raguette

  • AmberTools

    Unknown

  • All-Atom Structure Prediction and Folding Simulations of a Stable Protein

    Carlos Simmerling;Bentley Strockbine;Adrian E. Roitberg

  • Improved Generalized Born Solvent Model Parameters for Protein Simulations

    Hai Nguyen;Daniel R. Roe;Carlos Simmerling

  • Generalized Born Model with a Simple, Robust Molecular Volume Correction

    John Mongan;Carlos Simmerling;J. Andrew McCammon;David A. Case

  • HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations

    Viktor Hornak;Asim Okur;Robert C. Rizzo;Carlos Simmerling

  • Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber

    Tyler Luchko;Sergey Gusarov;Daniel R. Roe;Carlos Simmerling

  • Evaluating the performance of the ff99SB force field based on NMR scalar coupling data.

    Lauren Wickstrom;Asim Okur;Carlos Simmerling

  • Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solvent.

    Hai Nguyen;James Maier;He Huang;Victoria Perrone

  • MOIL: A program for simulations of macromolecules

    Ron Elber;Ron Elber;Adrian Roitberg;Adrian Roitberg;Carlos Simmerling;Carlos Simmerling;Robert Goldstein

  • Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model

    Asim Okur;Lauren Wickstrom;Melinda Layten;Raphäel Geney

  • Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation.

    Daniel R. Roe;Asim Okur;Lauren Wickstrom;Viktor Hornak

  • Inhibition of the Bacterial Enoyl Reductase FabI by Triclosan: A Structure−Reactivity Analysis of FabI Inhibition by Triclosan Analogues†

    Sharada Sivaraman;Todd J. Sullivan;Francis Johnson;Polina Novichenok

  • Structure of Acyl Carrier Protein Bound to FabI, the FASII Enoyl Reductase from Escherichia coli

    Salma Rafi;Polina Novichenok;Subramaniapillai Kolappan;Xujie Zhang

  • Advances in free-energy-based simulations of protein folding and ligand binding.

    Alberto Perez;Joseph A Morrone;Carlos Simmerling;Ken A Dill

  • Investigation of Salt Bridge Stability in a Generalized Born Solvent Model.

    Raphaël Geney;Melinda Layten;Roberto Gomperts;and Viktor Hornak

  • Modified replica exchange simulation methods for local structure refinement.

    Xiaolin Cheng;Guanglei Cui;Viktor Hornak;Carlos Simmerling

  • AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics

    Lorenzo Casalino;Abigail C. Dommer;Zied Gaieb;Emilia P. Barros

  • Targeting structural flexibility in HIV-1 protease inhibitor binding

    Viktor Hornak;Carlos Simmerling

Frequent Co-Authors

Peter J. Tonge
Peter J. Tonge Stony Brook University
Adrian E. Roitberg
Adrian E. Roitberg University of Florida
Ron Elber
Ron Elber The University of Texas at Austin
Daniel P. Raleigh
Daniel P. Raleigh Stony Brook University
Arthur P. Grollman
Arthur P. Grollman Stony Brook University
Steven O. Smith
Steven O. Smith Stony Brook University
David A. Case
David A. Case Rutgers, The State University of New Jersey
Iwao Ojima
Iwao Ojima Stony Brook University
Kevin H. Gardner
Kevin H. Gardner City University of New York
Alberto Perez
Alberto Perez University of Florida

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