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Theoretical and Computational Chemistry

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Machine Learning for Acute Oral System Toxicity Regression and Classification

conor parks, Zied Gaieb, Rommie Amaro

Version 1 posted 28 August 2019

924

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1

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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

979

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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

671

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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

1,114

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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

725

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1

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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

589

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1

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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

700

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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

424

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1

Citations

Biological and Medicinal Chemistry

Working Paper

NetSci: A Library for High Performance Biomolecular Simulation Network Analysis Computation

Andrew Stokely, Lane Votapka, Marcus Hock, Abigail Teitgen, J Andrew McCammon, Andrew McCullough, Rommie Amaro

Version 1 posted 28 May 2024

320

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Theoretical and Computational Chemistry

Working Paper

QMrebind: Incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations

Anupam Anand Ojha, Lane Votapka, Rommie Amaro

Version 2 posted 16 October 2023

498

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18 results in Rommie Amaro in Authors: Rommie Amaro

Machine Learning for Acute Oral System Toxicity Regression and Classification

Determinants of Substrate Specificity in APOBEC3B

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

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

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

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

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

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

NetSci: A Library for High Performance Biomolecular Simulation Network Analysis Computation

QMrebind: Incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations

18 results in Authors: Rommie Amaro