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Development of a Protocol for Membrane Permeability Prediction for Cyclic Peptides Based on Molecular Dynamics Simulation

Seibutsu Butsuri, 2023, Vol.63(3), pp.167-168

SUGITA, Masatake

2023

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Perspective: Structural fluctuation of protein and Anfinsen’s thermodynamic hypothesis

The Journal of chemical physics, 2018-01, Vol.148 (2), p.020901-020901

2018

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Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations

Journal of chemical information and modeling, 2021-07, Vol.61 (7), p.3681-3695

2021

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Molecular Recognition and Self-Organization in Life Phenomena Studied by a Statistical Mechanics of Molecular Liquids, the RISM/3D-RISM Theory

Molecules (Basel, Switzerland), 2021-01, Vol.26 (2), p.271

2021

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

Journal of chemical theory and computation, 2020-04, Vol.16 (4), p.2864-2876

2020

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Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations

Journal of chemical information and modeling, 2022-09, Vol.62 (18), p.4549-4560

2022

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A Systematic Analysis of the Binding Affinity between the Pim‑1 Kinase and Its Inhibitors Based on the MM/3D-RISM/KH Method

Journal of chemical information and modeling, 2017-11, Vol.57 (11), p.2789-2798

2017

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Computational Screening of a Functional Cyclodextrin Derivative for Suppressing a Side Effect of Doxorubicin

The journal of physical chemistry. B, 2021-03, Vol.125 (9), p.2308-2316

2021

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CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides

Journal of chemical information and modeling, 2023-04, Vol.63 (7), p.2240-2250

2023

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Amide-to-ester substitution as a stable alternative to N-methylation for increasing membrane permeability in cyclic peptides

Nature communications, 2023-03, Vol.14 (1), p.1416-1416, Article 1416

2023

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Realization of the structural fluctuation of biomolecules in solution: Generalized Langevin mode analysis

Journal of computational chemistry, 2023-04, Vol.44 (10), p.1031-1039

2023

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Predicting the binding free energy of the inclusion process of 2-hydroxypropyl-β-cyclodextrin and small molecules by means of the MM/3D-RISM method

Journal of physics. Condensed matter, 2016-09, Vol.28 (38), p.384002-384002

2016

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Analyses of the folding properties of ferredoxin-like fold proteins by means of a coarse-grained Gō model: Relationship between the free energy profiles and folding cores

Proteins, structure, function, and bioinformatics, 2014-06, Vol.82 (6), p.954-965

2014

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Incorporating into a Cα Go model the effects of geometrical restriction on Cα atoms caused by side chain orientations

Proteins, structure, function, and bioinformatics, 2013-08, Vol.81 (8), p.1434-1445

2013

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Analyses of the folding properties of ferredoxin-like fold proteins by means of a coarse-grained G model: Relationship between the free energy profiles and folding cores

Proteins, structure, function, and bioinformatics, 2014-06, Vol.82 (6), p.954-965

2014

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Investigating Characteristics of Folding Cores from Analyses of Folding Mechaniams on Multi-Transition Proteins by Means of a Coarse-Grained Go Model

Biophysical journal, 2014-01, Vol.106 (2), p.673a-673a

2014

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Incorporating into a C[alpha] Go model the effects of geometrical restriction on C[alpha] atoms caused by side chain orientations

Proteins, structure, function, and bioinformatics, 2013-08, Vol.81 (8), p.1434-1445

2013

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Predicting the Binding Mode of 2‑Hydroxypropyl-β-cyclodextrin to Cholesterol by Means of the MD Simulation and the 3D-RISM-KH Theory

The journal of physical chemistry. B, 2018-05, Vol.122 (21), p.5716-5725

2018

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Topological and sequence information predict that foldons organize a partially overlapped and hierarchical structure

Proteins, structure, function, and bioinformatics, 2015-10, Vol.83 (10), p.1900-1913

2015

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Topological and sequence information predict that foldons organize a partially overlapped and hierarchical structure: Partially Overlapped and Hierarchical Foldons

Proteins, structure, function, and bioinformatics, 2015-10, Vol.83 (10), p.1900-1913

2015

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Differential mode of cholesterol inclusion with 2‐hydroxypropyl‐cyclodextrins increases safety margin in treatment of Niemann‐Pick disease type C

British journal of pharmacology, 2021-07, Vol.178 (13), p.2727-2746

2021

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分子動力学シミュレーションに基づいた環状ペプチドの膜透過性予測技術の開発

生物物理, 2023, Vol.63(3), pp.167-168

杉田, 昌岳

2023

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Implication of the cause of differences in 3D structures of proteins with high sequence identity based on analyses of amino acid sequences and 3D structures

BMC research notes, 2014-09, Vol.7 (1), p.654-654, Article 654

2014

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2P059 An analysis of the relationship between the number of transitions and folding cores in multi-transition proteins by means of Go model(01C. Protein: Property)

Seibutsu Butsuri, 2013/09/13, Vol.53(supplement1-2), pp.S168

2013

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2P059 粗視化Goモデルを用いた多状態タンパクにおける遷移の回数とフォールディングコアとの関係の解析(01C.蛋白質:物性,ポスター,日本生物物理学会年会第51回(2013年度))

生物物理, 2013/09/13, Vol.53(supplement1-2), pp.S168

2013

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Development of a Protocol for Membrane Permeability Prediction for Cyclic Peptides Based on Molecular Dynamics Simulation

Perspective: Structural fluctuation of protein and Anfinsen’s thermodynamic hypothesis

Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations

Molecular Recognition and Self-Organization in Life Phenomena Studied by a Statistical Mechanics of Molecular Liquids, the RISM/3D-RISM Theory

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

Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations

A Systematic Analysis of the Binding Affinity between the Pim‑1 Kinase and Its Inhibitors Based on the MM/3D-RISM/KH Method

Computational Screening of a Functional Cyclodextrin Derivative for Suppressing a Side Effect of Doxorubicin

CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides

Amide-to-ester substitution as a stable alternative to N-methylation for increasing membrane permeability in cyclic peptides

Realization of the structural fluctuation of biomolecules in solution: Generalized Langevin mode analysis

Predicting the binding free energy of the inclusion process of 2-hydroxypropyl-β-cyclodextrin and small molecules by means of the MM/3D-RISM method

Analyses of the folding properties of ferredoxin-like fold proteins by means of a coarse-grained Gō model: Relationship between the free energy profiles and folding cores

Incorporating into a Cα Go model the effects of geometrical restriction on Cα atoms caused by side chain orientations

Analyses of the folding properties of ferredoxin-like fold proteins by means of a coarse-grained G model: Relationship between the free energy profiles and folding cores

Investigating Characteristics of Folding Cores from Analyses of Folding Mechaniams on Multi-Transition Proteins by Means of a Coarse-Grained Go Model

Incorporating into a C[alpha] Go model the effects of geometrical restriction on C[alpha] atoms caused by side chain orientations

Predicting the Binding Mode of 2‑Hydroxypropyl-β-cyclodextrin to Cholesterol by Means of the MD Simulation and the 3D-RISM-KH Theory

Topological and sequence information predict that foldons organize a partially overlapped and hierarchical structure

Topological and sequence information predict that foldons organize a partially overlapped and hierarchical structure: Partially Overlapped and Hierarchical Foldons

Differential mode of cholesterol inclusion with 2‐hydroxypropyl‐cyclodextrins increases safety margin in treatment of Niemann‐Pick disease type C

分子動力学シミュレーションに基づいた環状ペプチドの膜透過性予測技術の開発

Implication of the cause of differences in 3D structures of proteins with high sequence identity based on analyses of amino acid sequences and 3D structures

2P059 An analysis of the relationship between the number of transitions and folding cores in multi-transition proteins by means of Go model(01C. Protein: Property)

2P059 粗視化Goモデルを用いた多状態タンパクにおける遷移の回数とフォールディングコアとの関係の解析(01C.蛋白質:物性,ポスター,日本生物物理学会年会第51回(2013年度))

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