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Theoretical and Computational Chemistry

Working Paper

Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach

Benjamin R. Jagger, Christoper T. Lee, Rommie Amaro

Version 1 posted 02 July 2018

649

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Theoretical and Computational Chemistry

Working Paper

SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine

Lane Votapka, Andrew Stokely, Anupam Ojha, Rommie Amaro

Version 2 posted 26 April 2022

699

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Earth, Space, and Environmental Chemistry

Working Paper

Revealing the Impacts of Chemical Complexity on Submicron Sea Spray Aerosol Morphology

Abigail Dommer, Nicholas Wauer, Kyle Angle, Aakash Davasam, Patiemma Rubio, Man Luo, Clare Morris, Kimberly Prather, Vicki Grassian, Rommie Amaro

Version 1 posted 13 February 2023

328

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Theoretical and Computational Chemistry

Working Paper

CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding

Suzanne Ackloo, Rima Al-awar, Rommie E. Amaro, Cheryl H. Arrowsmith, Hatylas Azevedo, Robert A. Batey, Yoshua Bengio, Ulrich A.K. Betz, Cristian G. Bologa, John D. Chodera, Wendy D. Cornell, Ian Dunham, Gerhard F. Ecker, Kristina Edfeldt, Aled M. Edwards, Michael K. Gilson, Claudia R. Gordijo, Gerhard Hessler, Alexander Hillisch, Anders Hogner, John J. Irwin, Johanna M. Jansen, Daniel Kuhn, Andrew R. Leach, Alpha A. Lee, Uta Lessel, John Moult, Ingo Muegge, Tudor I. Oprea, Benjamin G. Perry, Patrick Riley, Kumar Singh Saikatendu, Vijayaratnam Santhakumar, Matthieu Schapira, Cora Scholten, Matthew H. Todd, Masoud Vedadi, Andrea Volkamer, Timothy M. Willson

Version 1 posted 22 October 2021

2,248

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Theoretical and Computational Chemistry

Working Paper

DeepWEST: Deep learning of kinetic models with the Weighted Ensemble Simulation Toolkit for enhanced sampling

Anupam Ojha, Saumya Thakur, Surl-Hee Ahn, Rommie Amaro

Version 3 posted 02 December 2022

728

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Theoretical and Computational Chemistry

Working Paper

An introductory tutorial to the SEEKR2 (Simulation enabled estimation of kinetic rates v. 2) multiscale milestoning software [Article v1.0]

Anupam Ojha, Lane Votapka, Gary Huber, Shang Gao, Rommie Amaro

Version 1 posted 04 September 2023

368

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1

Citations

Theoretical and Computational Chemistry

Working Paper

An Analysis of Proteochemometric and Conformal Prediction Machine Learning Protein-Ligand Binding Affinity Models

conor parks, Zied Gaieb, Rommie Amaro

Version 1 posted 29 January 2020

685

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Physical Chemistry

Working Paper

Calcium Bridging Drives Polysaccharide Co-Adsorption to a Proxy Sea Surface Microlayer

Kimberly Carter-Fenk, Abigail Dommer, Michelle E Fiamingo, Jeongin Kim, Rommie Amaro, Heather Allen

Version 1 posted 01 April 2021

392

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Analytical Chemistry

Working Paper

Positively bound: Remapping of Increased Positive Charge Drives SARS-CoV-2 Spike Evolution to Optimize its Binding to Cell Surface Receptors

Sang Hoon Kim, Fiona L. Kearns, Mia A. Rosenfeld, Lane Votapka, Lorenzo Casalino, Micah Papanikolas, Rommie E. Amaro, Ronit Freeman

Version 1 posted 19 October 2022

565

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3

Citations

Theoretical and Computational Chemistry

Working Paper

Machine Learning for Acute Oral System Toxicity Regression and Classification

conor parks, Zied Gaieb, Rommie Amaro

Version 1 posted 28 August 2019

884

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1

Citations

Refine Search

18 results in Rommie Amaro in Authors: Rommie Amaro

Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach

SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine

Revealing the Impacts of Chemical Complexity on Submicron Sea Spray Aerosol Morphology

CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding

DeepWEST: Deep learning of kinetic models with the Weighted Ensemble Simulation Toolkit for enhanced sampling

An introductory tutorial to the SEEKR2 (Simulation enabled estimation of kinetic rates v. 2) multiscale milestoning software [Article v1.0]

An Analysis of Proteochemometric and Conformal Prediction Machine Learning Protein-Ligand Binding Affinity Models

Calcium Bridging Drives Polysaccharide Co-Adsorption to a Proxy Sea Surface Microlayer

Positively bound: Remapping of Increased Positive Charge Drives SARS-CoV-2 Spike Evolution to Optimize its Binding to Cell Surface Receptors

Machine Learning for Acute Oral System Toxicity Regression and Classification

18 results in Authors: Rommie Amaro