New Protocol for Predicting the Ligand-Binding Site and Mode Based on the 3D-RISM/KH Theory-Reference-Cited by-同舟云学术

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New Protocol for Predicting the Ligand-Binding Site and Mode Based on the 3D-RISM/KH Theory

Published:2020-03-16 Issue:4 Volume:16 Page:2864-2876
ISSN:1549-9618
Container-title:Journal of Chemical Theory and Computation
language:en
Short-container-title:J. Chem. Theory Comput.

Author:

Sugita Masatake¹²^ORCID,Hamano Masataka¹,Kasahara Kota¹^ORCID,Kikuchi Takeshi¹,Hirata Fumio³

Affiliation:

1. Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1, Noji-higashi, Kusatsu, Shiga 525-8577, Japan

2. Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-76, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550, Japan

3. Toyota Physical and Chemical Research Institute, 41-1, Yokomichi, Nagakute, Aichi 480-1192, Japan

Funder

Ministry of Education, Culture, Sports, Science and Technology

Publisher

American Chemical Society (ACS)

Subject

Physical and Theoretical Chemistry,Computer Science Applications

Link

https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.9b01069

Reference48 articles.

1. Three-Dimensional Pharmacophore Methods in Drug Discovery

2. Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

3. Advancing Drug Discovery through Enhanced Free Energy Calculations

4. Unraveling hot spots in binding interfaces: progress and challenges

5. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

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1. Identification of potential agonist-like molecules for α2-adrenergic receptor by multi-layer virtual screening to combat sinusitis;Computers in Biology and Medicine;2023-12

2. 3D-RISM-AI: A Machine Learning Approach to Predict Protein–Ligand Binding Affinity Using 3D-RISM;The Journal of Physical Chemistry B;2022-08-15

3. Discovering novel inhibitors of P2Y12 receptor using structure-based virtual screening, molecular dynamics simulation and MMPBSA approaches;Computers in Biology and Medicine;2022-08

4. Integral equation models for solvent in macromolecular crystals;The Journal of Chemical Physics;2022-01-07

5. A molecular solvation theory simulation of liquid alkyl esters of acetic acid with the 3D Reference Interaction Site Model;Journal of Molecular Liquids;2021-12

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