Synergy and Complementarity between Focused Machine Learning and Physics-Based Simulation in Affinity Prediction-Reference-Cited by-同舟云学术

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Synergy and Complementarity between Focused Machine Learning and Physics-Based Simulation in Affinity Prediction

Published:2021-12-10 Issue:12 Volume:61 Page:5948-5966
ISSN:1549-9596
Container-title:Journal of Chemical Information and Modeling
language:en
Short-container-title:J. Chem. Inf. Model.

Author:

Cleves Ann E.¹^ORCID,Johnson Stephen R.²,Jain Ajay N.³^ORCID

Affiliation:

1. Applied Science, BioPharmics LLC, Santa Rosa, California 95404, United States

2. Computer-Assisted Drug-Design, Bristol-Myers Squibb Company, Princeton, New Jersey 08648, United States

3. Research and Development, BioPharmics LLC, Santa Rosa, California 95404, United States

Publisher

American Chemical Society (ACS)

Subject

Library and Information Sciences,Computer Science Applications,General Chemical Engineering,General Chemistry

Link

https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.1c01382

Reference39 articles.

1. High-Throughput Calculation of Protein−Ligand Binding Affinities: Modification and Adaptation of the MM-PBSA Protocol to Enterprise Grid Computing

2. Rapid Estimation of Relative Protein−Ligand Binding Affinities Using a High-Throughput Version of MM-PBSA

3. Large-Scale Application of High-Throughput Molecular Mechanics with Poisson−Boltzmann Surface Area for Routine Physics-Based Scoring of Protein−Ligand Complexes

4. End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design

5. Alchemical free energy methods for drug discovery: progress and challenges

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1. Machine Learning Meets Physics-based Modeling: A Mass-spring System to Predict Protein-ligand Binding Affinity;Current Medicinal Chemistry;2024-08-01

2. From UK-2A to florylpicoxamid: Active learning to identify a mimic of a macrocyclic natural product;Journal of Computer-Aided Molecular Design;2024-04-17

3. Ligand binding free energy evaluation by Monte Carlo Recursion;Computational Biology and Chemistry;2023-04

4. Designing Collagen-Binding Peptide with Enhanced Properties Using Hydropathic Free Energy Predictions;Applied Sciences;2023-03-06

5. Pathfinder-Driven Chemical Space Exploration and Multiparameter Optimization in Tandem with Glide/IFD and QSAR-Based Active Learning Approach to Prioritize Design Ideas for FEP+ Calculations of SARS-CoV-2 PLpro Inhibitors;Molecules;2022-12-05

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