carlos simmerling

Professor

Stony Brook University

United States

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Dr. Carlos Simmerling is a Professor at Stony Brook University in the United States. His research focuses on molecular simulation techniques, particularly in relation to viral pandemics and protein structure stability. Recent articles highlight his work on the SARS-CoV-2 spike glycoprotein and advancements in molecular dynamics simulations. Dr. Simmerling is actively involved in developing tools and databases that enhance the understanding of protein interactions and conformational changes.

Articles (15)

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2025

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2024

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2024

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2024

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2024

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2024

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2023

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2023

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2022

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2022

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2022

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2021

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2020

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2020

Collaborators (5)

Miha Lukšič

SLOVENIA

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Evangelos Coutsias

Professor

Stony Brook University

UNITED STATES

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Maria Nagan

Stony Brook University

UNITED STATES

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Barbara Hribar-Lee

SLOVENIA

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Katarzyna Świderek

Profesor Titular de Universidad / Associate professor

Universitat Jaume I

SPAIN

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carlos simmerling

Research Interests

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About

Articles (15)

A Reflection on the Use of Molecular Simulation to Respond to SARS-CoV-2 Pandemic Threats

Exact Analytical Algorithm for the Solvent-Accessible Surface Area and Derivatives in Implicit Solvent Molecular Simulations on GPUs

Adjusting the Energy Profile for CH–O Interactions Leads to Improved Stability of RNA Stem-Loop Structures in MD Simulations

phosaa14SB and phosaa19SB: Updated Amber Force Field Parameters for Phosphorylated Amino Acids

k-Means NANI: An Improved Clustering Algorithm for Molecular Dynamics Simulations

Assessing pH-Dependent Conformational Changes in the Fusion Peptide Proximal Region of the SARS-CoV-2 Spike Glycoprotein

Exploring the Transferability of Replica Exchange Structure Reservoirs to Accelerate Generation of Ensembles for Alternate Hamiltonians or Protein Mutations

SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein

Rapid Rescoring and Refinement of Ligand–Receptor Complexes Using Replica Exchange Molecular Dynamics with a Monte Carlo Pose Reservoir

BioMThermDB 1.0: Thermophysical Database of Proteins in Solutions

Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir

GlycoGrip: Cell Surface-Inspired Universal Sensor for Betacoronaviruses

Quantitative Analysis of Protein Unfolded State Energetics: Experimental and Computational Studies Demonstrate That Non-Native Side-Chain Interactions Stabilize Local Native Backbone Structure

Exploring Protocols to Build Reservoirs to Accelerate Temperature Replica Exchange MD Simulations

Protein storytelling through physics

Collaborators (5)

Miha Lukšič

Evangelos Coutsias

Maria Nagan

Barbara Hribar-Lee

Katarzyna Świderek

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