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Positive Charge Introduction on the Surface of Thermostabilized PET Hydrolase Facilitates PET Binding and Degradation

ACS catalysis, 2021-07, Vol.11 (14), p.8550-8564

2021

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Role of backbone strain in de novo design of complex α/β protein structures

Nature communications, 2021-06, Vol.12 (1), p.3921-3921, Article 3921

2021

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The register shift rules for βαβ-motifs for de novo protein design

PloS one, 2021-08, Vol.16 (8), p.e0256895-e0256895

2021

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Control over overall shape and size in de novo designed proteins

Proceedings of the National Academy of Sciences - PNAS, 2015-10, Vol.112 (40), p.E5478-E5485

2015

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Forced protein unfolding leads to highly elastic and tough protein hydrogels

Nature communications, 2013-12, Vol.4 (1), p.2974-2974, Article 2974

2013

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Actin retrograde flow actively aligns and orients ligand-engaged integrins in focal adhesions

Proceedings of the National Academy of Sciences - PNAS, 2017-10, Vol.114 (40), p.10648-10653

2017

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RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite

PloS one, 2011-06, Vol.6 (6), p.e20161-e20161

2011

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Folding-Based Molecular Simulations Reveal Mechanisms of the Rotary Motor F₁-ATPase

Proceedings of the National Academy of Sciences - PNAS, 2006-04, Vol.103 (14), p.5367-5372

2006

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Direction of actin flow dictates integrin LFA-1 orientation during leukocyte migration

Nature communications, 2017-12, Vol.8 (1), p.2047-16, Article 2047

2017

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CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work

Journal of chemical theory and computation, 2011-06, Vol.7 (6), p.1979-1989

2011

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Consistency principle for protein design

Biophysics and Physicobiology, 2019, Vol.16, pp.304-309

2019

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Networks of electrostatic and hydrophobic interactions modulate the complex folding free energy surface of a designed βα protein

Proceedings of the National Academy of Sciences - PNAS, 2019-04, Vol.116 (14), p.6806-6811

2019

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State-Targeting Stabilization of Adenosine A2A Receptor by Fusing a Custom-Made De Novo Designed α-Helical Protein

International journal of molecular sciences, 2021-11, Vol.22 (23), p.12906

2021

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Multiple-Basin Energy Landscapes for Large-Amplitude Conformational Motions of Proteins: Structure-Based Molecular Dynamics Simulations

Proceedings of the National Academy of Sciences - PNAS, 2006-08, Vol.103 (32), p.11844-11849

2006

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How Protein Thermodynamics and Folding Mechanisms Are Altered by the Chaperonin Cage: Molecular Simulations

Proceedings of the National Academy of Sciences - PNAS, 2003-09, Vol.100 (20), p.11367-11372

2003

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Inventing Novel Protein Folds

Journal of molecular biology, 2024-09, p.168791, Article 168791

2024

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3SBA-01 Toward design of molecular motors(Rise of molecular machines,Symposium,The 52th Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri, 2014/08/20, Vol.54(supplement1-2), pp.S136

Nobuyasu, Koga

2014

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Restricted sidechain plasticity in the structures of native proteins and complexes

Protein science, 2011-04, Vol.20 (4), p.753-757

2011

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Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations

Proceedings of the National Academy of Sciences - PNAS, 2009-10, Vol.106 (43), p.18237-18242

2009

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Design of allosteric sites into rotary motor V1-ATPase by restoring lost function of pseudo-active sites

Nature chemistry, 2023-11, Vol.15 (11), p.1591-1598

2023

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Principles for designing ideal protein structures

Nature (London), 2012-11, Vol.491 (7423), p.222-227

2012

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Robust folding of a de novo designed ideal protein even with most of the core mutated to valine

Proceedings of the National Academy of Sciences - PNAS, 2020-12, Vol.117 (49), p.31149-31156

2020

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Exploration of novel αβ-protein folds through de novo design

Nature structural & molecular biology, 2023-08, Vol.30 (8), p.1132-1140

2023

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The register shift rules for [beta][alpha][beta]-motifs for de novo protein design

PloS one, 2021-08, Vol.16 (8), p.e0256895

2021

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Consistency Principle for Protein Design

Seibutsu butsuri = Biophysics, 2020, Vol.60 (6), p.325-330

2020

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Positive Charge Introduction on the Surface of Thermostabilized PET Hydrolase Facilitates PET Binding and Degradation

Role of backbone strain in de novo design of complex α/β protein structures

The register shift rules for βαβ-motifs for de novo protein design

Control over overall shape and size in de novo designed proteins

Forced protein unfolding leads to highly elastic and tough protein hydrogels

Actin retrograde flow actively aligns and orients ligand-engaged integrins in focal adhesions

RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite

Folding-Based Molecular Simulations Reveal Mechanisms of the Rotary Motor F₁-ATPase

Direction of actin flow dictates integrin LFA-1 orientation during leukocyte migration

CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work

Consistency principle for protein design

Networks of electrostatic and hydrophobic interactions modulate the complex folding free energy surface of a designed βα protein

State-Targeting Stabilization of Adenosine A2A Receptor by Fusing a Custom-Made De Novo Designed α-Helical Protein

Multiple-Basin Energy Landscapes for Large-Amplitude Conformational Motions of Proteins: Structure-Based Molecular Dynamics Simulations

How Protein Thermodynamics and Folding Mechanisms Are Altered by the Chaperonin Cage: Molecular Simulations

Inventing Novel Protein Folds

3SBA-01 Toward design of molecular motors(Rise of molecular machines,Symposium,The 52th Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Restricted sidechain plasticity in the structures of native proteins and complexes

Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations

Design of allosteric sites into rotary motor V1-ATPase by restoring lost function of pseudo-active sites

Principles for designing ideal protein structures

Robust folding of a de novo designed ideal protein even with most of the core mutated to valine

Exploration of novel αβ-protein folds through de novo design

The register shift rules for [beta][alpha][beta]-motifs for de novo protein design

Consistency Principle for Protein Design

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