Combining self-organizing maps and hierarchical clustering for protein–ligand interaction analysis in post-fragment molecular orbital calculation

Yusuke Kawashima; Natsumi Mori; Norihito Kawashita; Yu-Shi Tian; Tatsuya Takagi

doi:10.1273/cbij.21.1

Combining self-organizing maps and hierarchical clustering for protein–ligand interaction analysis in post-fragment molecular orbital calculation

Chem-Bio Informatics Journal ◽

10.1273/cbij.21.1 ◽

2021 ◽

Vol 21 (0) ◽

pp. 1-10

Author(s):

Yusuke Kawashima ◽

Natsumi Mori ◽

Norihito Kawashita ◽

Yu-Shi Tian ◽

Tatsuya Takagi

Keyword(s):

Molecular Orbital ◽

Hierarchical Clustering ◽

Interaction Analysis ◽

Molecular Orbital Calculation ◽

Self Organizing Maps ◽

Ligand Interaction ◽

Fragment Molecular Orbital ◽

Protein Ligand Interaction ◽

Self Organizing

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Protein ligand interaction analysis against new CaMKK2 inhibitors by use of X-ray crystallography and the fragment molecular orbital (FMO) method

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2020.107599 ◽

2020 ◽

Vol 99 ◽

pp. 107599 ◽

Cited By ~ 1

Author(s):

Daisuke Takaya ◽

Hideaki Niwa ◽

Junko Mikuni ◽

Kana Nakamura ◽

Noriko Handa ◽

...

Keyword(s):

Molecular Orbital ◽

Interaction Analysis ◽

Ligand Interaction ◽

X Ray ◽

Fragment Molecular Orbital ◽

X Ray Crystallography ◽

Protein Ligand Interaction

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Binding interaction analysis of RNA aptamer-Fc region of human immunoglobulin G using fragment molecular orbital calculation

Chemical Physics Letters ◽

10.1016/j.cplett.2019.136854 ◽

2020 ◽

Vol 738 ◽

pp. 136854 ◽

Cited By ~ 2

Author(s):

Hisae Yoshida ◽

Koki Sato ◽

Takeshi Ishikawa ◽

Taiichi Sakamoto ◽

Kenji Yamagishi

Keyword(s):

Molecular Orbital ◽

Immunoglobulin G ◽

Interaction Analysis ◽

Molecular Orbital Calculation ◽

Human Immunoglobulin ◽

Rna Aptamer ◽

Binding Interaction ◽

Human Immunoglobulin G ◽

Fragment Molecular Orbital

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VISCANA: Visualized Cluster Analysis of Protein−Ligand Interaction Based on the ab Initio Fragment Molecular Orbital Method for Virtual Ligand Screening

Journal of Chemical Information and Modeling ◽

10.1021/ci050262q ◽

2006 ◽

Vol 46 (1) ◽

pp. 221-230 ◽

Cited By ~ 84

Author(s):

Shinji Amari ◽

Masahiro Aizawa ◽

Junwei Zhang ◽

Kaori Fukuzawa ◽

Yuji Mochizuki ◽

...

Keyword(s):

Cluster Analysis ◽

Ab Initio ◽

Molecular Orbital ◽

Orbital Method ◽

Molecular Orbital Method ◽

Ligand Interaction ◽

Fragment Molecular Orbital ◽

Ligand Screening ◽

Virtual Ligand Screening ◽

Protein Ligand Interaction

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Combining Hierarchical Clustering and Self-Organizing Maps for Exploratory Analysis of Gene Expression Patterns

Journal of Proteome Research ◽

10.1021/pr025521v ◽

2002 ◽

Vol 1 (5) ◽

pp. 467-470 ◽

Cited By ~ 34

Author(s):

Javier Herrero ◽

Joaquín Dopazo

Keyword(s):

Gene Expression ◽

Hierarchical Clustering ◽

Expression Patterns ◽

Exploratory Analysis ◽

Gene Expression Patterns ◽

Self Organizing Maps ◽

Self Organizing

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Intermolecular interaction among Remdesivir, RNA and RNA-dependent RNA polymerase of SARS-CoV-2 analyzed by fragment molecular orbital calculation

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2020.107695 ◽

2020 ◽

Vol 100 ◽

pp. 107695

Author(s):

Koichiro Kato ◽

Teruki Honma ◽

Kaori Fukuzawa

Keyword(s):

Rna Polymerase ◽

Intermolecular Interaction ◽

Molecular Orbital ◽

Molecular Orbital Calculation ◽

Rna Dependent Rna Polymerase ◽

Fragment Molecular Orbital

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Visualizing Attribute Interdependencies Using Mutual Information, Hierarchical Clustering, Multidimensional Scaling, and Self-organizing Maps

10.1109/hicss.2007.608 ◽

2007 ◽

Cited By ~ 5

Author(s):

Derek Nazareth ◽

Ehsan Soofi ◽

Huimin Zhao

Keyword(s):

Mutual Information ◽

Multidimensional Scaling ◽

Hierarchical Clustering ◽

Self Organizing Maps ◽

Self Organizing

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High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.0c00273 ◽

2020 ◽

Vol 60 (7) ◽

pp. 3361-3368

Author(s):

Koichiro Kato ◽

Tomohide Masuda ◽

Chiduru Watanabe ◽

Naoki Miyagawa ◽

Hideo Mizouchi ◽

...

Keyword(s):

Machine Learning ◽

Molecular Orbital ◽

High Precision ◽

Atomic Charge ◽

Molecular Orbital Calculation ◽

Fragment Molecular Orbital

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An unsupervised method of classifying remotely sensed images using Kohonen self‐organizing maps and agglomerative hierarchical clustering methods

International Journal of Remote Sensing ◽

10.1080/01431160701442146 ◽

2008 ◽

Vol 29 (11) ◽

pp. 3171-3207 ◽

Cited By ~ 51

Author(s):

M. L. Gonçalves ◽

M. L. A. Netto ◽

J. A. F. Costa ◽

J. Zullo Júnior

Keyword(s):

Hierarchical Clustering ◽

Remotely Sensed ◽

Agglomerative Hierarchical Clustering ◽

Clustering Methods ◽

Self Organizing Maps ◽

Unsupervised Method ◽

Hierarchical Clustering Methods ◽

Remotely Sensed Images ◽

Self Organizing

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Interaction Analysis of FABP4 Inhibitors by X-ray Crystallography and Fragment Molecular Orbital Analysis

ACS Medicinal Chemistry Letters ◽

10.1021/acsmedchemlett.6b00040 ◽

2016 ◽

Vol 7 (4) ◽

pp. 435-439 ◽

Cited By ~ 11

Author(s):

Uno Tagami ◽

Kazutoshi Takahashi ◽

Shunsuke Igarashi ◽

Chieko Ejima ◽

Tomomi Yoshida ◽

...

Keyword(s):

Molecular Orbital ◽

Interaction Analysis ◽

X Ray ◽

Fragment Molecular Orbital ◽

X Ray Crystallography ◽

Molecular Orbital Analysis ◽

Orbital Analysis

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Defensive islanding using self-organizing maps neural networks and hierarchical clustering

2015 IEEE Eindhoven PowerTech ◽

10.1109/ptc.2015.7232427 ◽

2015 ◽

Cited By ~ 5

Author(s):

Mohammed Mahdi ◽

Istemihan Genc

Keyword(s):

Neural Networks ◽

Hierarchical Clustering ◽

Self Organizing Maps ◽

Self Organizing

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