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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

681

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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

552

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3

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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

303

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Theoretical and Computational Chemistry

Working Paper

D3R Grand Challenge 4: Blind Prediction of Protein-Ligand Poses, Affinity Rankings, and Relative Binding Free Energies

conor parks, Zied Gaieb, Michael Chiu, Huanwang Yang, Chenghua Shao, W. Patrick Walters, Johanna M. Jansen, Georgia McGaughey, Richard A. Lewis, Scott D. Bembenek, Michael K. Ameriks, Tara Mirzadegan, Stephen K. Burley, Rommie Amaro, Michael Gilson

Version 1 posted 19 December 2019

1,076

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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

852

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1

Citations

Biological and Medicinal Chemistry

Working Paper

Evaluation of Binding Site Comparison Algorithms and Proteometric Machine Learning Models in the Detection of Protein Pockets Capable of Binding the Same Ligand

Zied Gaieb, conor parks, Rommie Amaro

Version 1 posted 31 July 2019

528

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1

Citations

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

381

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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

708

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Biological and Medicinal Chemistry

Working Paper

D3R Grand Challenge 3: Blind Prediction of Protein-Ligand Poses and Affinity Rankings

Zied Gaieb, Conor Parks, Michael Chiu, Huanwang Yang, Chenghua Shao, Patrick Walters, Millard Lambert, Neysa Nevins, Scott D. Bembenek, Stephen K. Burley, Rommie E. Amaro, Michael K. Gilson

Version 1 posted 06 July 2018

684

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1

Citations

Biological and Medicinal Chemistry

Working Paper

Determinants of Substrate Specificity in APOBEC3B

Jeffrey Wagner, Özlem Demir, Michael A. Carpenter, Hideki Aihara, Daniel A. Harki, Reuben S. Harris, Rommie E. Amaro

Version 1 posted 04 May 2018

954

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17 results in Rommie Amaro in Authors: Rommie Amaro

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

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

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

D3R Grand Challenge 4: Blind Prediction of Protein-Ligand Poses, Affinity Rankings, and Relative Binding Free Energies

Machine Learning for Acute Oral System Toxicity Regression and Classification

Evaluation of Binding Site Comparison Algorithms and Proteometric Machine Learning Models in the Detection of Protein Pockets Capable of Binding the Same Ligand

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

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

D3R Grand Challenge 3: Blind Prediction of Protein-Ligand Poses and Affinity Rankings

Determinants of Substrate Specificity in APOBEC3B

17 results in Authors: Rommie Amaro