Publications by authors named "David Cerutti"

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Recent Developments in Amber Biomolecular Simulations.
David A Case, David S Cerutti, Vinícius Wilian D Cruzeiro, Thomas A Darden, Robert E Duke

J Chem Inf Model· August 2025

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STORMM: Structure and topology replica molecular mechanics for chemical simulations.
David S Cerutti, Rafal Wiewiora, Simon Boothroyd, Woody Sherman

J Chem Phys· July 2024

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AmberTools.
David A Case, Hasan Metin Aktulga, Kellon Belfon, David S Cerutti, G Andrés Cisneros

J Chem Inf Model· October 2023

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Correction: Histidine protonation controls structural heterogeneity in the cyanobacteriochrome AnPixJg2.
Aditya G Rao, Christian Wiebeler, Saumik Sen, David S Cerutti, Igor Schapiro

Phys Chem Chem Phys· June 2021

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Histidine protonation controls structural heterogeneity in the cyanobacteriochrome AnPixJg2.
Aditya G Rao, Christian Wiebeler, Saumik Sen, David S Cerutti, Igor Schapiro

Phys Chem Chem Phys· March 2021

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A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics.
Anthony T Bogetti, Hannah E Piston, Jeremy M G Leung, Chino C Cabalteja, Darian T Yang, David S Cerutti

J Chem Phys· August 2020

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Fast Implementation of the Nudged Elastic Band Method in AMBER.
Delaram Ghoreishi, David S Cerutti, Zachary Fallon, Carlos Simmerling, Adrian E Roitberg

J Chem Theory Comput· August 2019

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Molecular Dynamics Simulations of Macromolecular Crystals.
David S Cerutti, David A Case

Wiley Interdiscip Rev Comput Mol Sci· November 2018

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GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features.
Tai-Sung Lee, David S Cerutti, Dan Mermelstein, Charles Lin, Scott LeGrand

J Chem Inf Model· October 2018

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Molecular Dynamics of Oxazole Yellow Dye in its Ground and First Excited Electronic States in Solution and when Intercalated in dsDNA.
Chi Jin, David Cerutti, Robert I Cukier

J Phys Chem B· November 2017

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Links between the charge model and bonded parameter force constants in biomolecular force fields.
David S Cerutti, Karl T Debiec, David A Case, Lillian T Chong

J Chem Phys· October 2017

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On the fly estimation of host-guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge.
Nupur Bansal, Zheng Zheng, David S Cerutti, Kenneth M Merz

J Comput Aided Mol Des· January 2017

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Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model.
Karl T Debiec, David S Cerutti, Lewis R Baker, Angela M Gronenborn, David A Case

J Chem Theory Comput· August 2016

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OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins.
Edward Harder, Wolfgang Damm, Jon Maple, Chuanjie Wu, Mark Reboul, David S Cerutti

J Chem Theory Comput· January 2016

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Multi-Level Ewald: A hybrid multigrid / Fast Fourier Transform approach to the electrostatic particle-mesh problem.
David S Cerutti, David A Case

J Chem Theory Comput· December 2015

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ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins.
David S Cerutti, William C Swope, Julia E Rice, David A Case

J Chem Theory Comput· October 2014

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Peptide crystal simulations reveal hidden dynamics.
Pawel A Janowski, David S Cerutti, James Holton, David A Case

J Am Chem Soc· May 2013

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Derivation of fixed partial charges for amino acids accommodating a specific water model and implicit polarization.
David S Cerutti, Julia E Rice, William C Swope, David A Case

J Phys Chem B· February 2013

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Alchemical prediction of hydration free energies for SAMPL.
David L Mobley, Shaui Liu, David S Cerutti, William C Swope, Julia E Rice

J Comput Aided Mol Des· May 2012

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Second-contact shell mutation diminishes streptavidin-biotin binding affinity through transmitted effects on equilibrium dynamics.
Loren Baugh, Isolde Le Trong, David S Cerutti, Nital Mehta, Susanne Gülich

Biochemistry· January 2012

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Simulations of a protein crystal with a high resolution X-ray structure: evaluation of force fields and water models.
David S Cerutti, Lydia Freddolino, Robert E Duke, David A Case

J Phys Chem B· October 2010

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A distal point mutation in the streptavidin-biotin complex preserves structure but diminishes binding affinity: experimental evidence of electronic polarization effects?
Loren Baugh, Isolde Le Trong, David S Cerutti, Susanne Gülich, Patrick S Stayton

Biochemistry· June 2010

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Staggered Mesh Ewald: An extension of the Smooth Particle-Mesh Ewald method adding great versatility.
David S Cerutti, Robert E Duke, Thomas A Darden, Terry P Lybrand

J Chem Theory Comput· September 2009

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Dynamics of the streptavidin-biotin complex in solution and in its crystal lattice: distinct behavior revealed by molecular simulations.
David S Cerutti, Isolde Le Trong, Ronald E Stenkamp, Terry P Lybrand

J Phys Chem B· May 2009

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Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics.
David S Cerutti, Robert Duke, Lydia Freddolino, Hao Fan, Terry P Lybrand

J Chem Theory Comput· October 2008

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