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Engineering Stability, Viscosity, and Immunogenicity of Antibodies by Computational Design

Journal of pharmaceutical sciences, 2020-05, Vol.109 (5), p.1631-1651

2020

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Controlling Nutritional Status (CONUT) score is a prognostic marker for gastric cancer patients after curative resection

Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association, 2018-03, Vol.21 (2), p.204-212

2018

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Shape complementarity and hydrogen bond preferences in protein-protein interfaces: implications for antibody modeling and protein-protein docking

Bioinformatics (Oxford, England), 2016-08, Vol.32 (16), p.2451-2456

2016

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Modeling and docking of antibody structures with Rosetta

Nature protocols, 2017-02, Vol.12 (2), p.401-416

2017

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Pushing the Backbone in Protein-Protein Docking

Structure (London), 2016-10, Vol.24 (10), p.1821-1829

2016

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How the protonation state of a phosphorylated amino acid governs molecular recognition: insights from classical molecular dynamics simulations

FEBS letters, 2020-03, Vol.594 (5), p.903-912

2020

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Delicate balance among thermal stability, binding affinity, and conformational space explored by single-domain VHH antibodies

Scientific reports, 2021-10, Vol.11 (1), p.20624-20624, Article 20624

2021

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Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease

Biophysics and Physicobiology, 2021, Vol.18, pp.215-222

2021

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Thermodynamic and computational analyses reveal the functional roles of the galloyl group of tea catechins in molecular recognition

PloS one, 2018-10, Vol.13 (10), p.e0204856-e0204856

2018

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Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires

Proceedings of the National Academy of Sciences - PNAS, 2016-05, Vol.113 (19), p.E2636-E2645

2016

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The nature of bright C-complex asteroids

Publications of the Astronomical Society of Japan, 2021-02, Vol.73 (1), p.240-255

2021

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Tumor associated macrophage expressing CD204 is associated with tumor aggressiveness of esophageal squamous cell carcinoma

Cancer science, 2013-08, Vol.104 (8), p.1112-1119

2013

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Phospholipid Membrane Fluidity Alters Ligand Binding Activity of a G Protein-Coupled Receptor by Shifting the Conformational Equilibrium

Biochemistry (Easton), 2019-02, Vol.58 (6), p.504-508

2019

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Exploring designability of electrostatic complementarity at an antigen-antibody interface directed by mutagenesis, biophysical analysis, and molecular dynamics simulations

Scientific reports, 2019-03, Vol.9 (1), p.4482, Article 4482

2019

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The Seimei telescope project and technical developments

Publications of the Astronomical Society of Japan, 2020-06, Vol.72 (3)

2020

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Peptoid-based reprogrammable template for cell-permeable inhibitors of protein-protein interactions

Chemical science (Cambridge), 2021-10, Vol.12 (4), p.13292-133

2021

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Discovery of Two TNO-like Bodies in the Asteroid Belt

Astrophysical journal. Letters, 2021-07, Vol.916 (1), p.L6

2021

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Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE)

PloS one, 2013-05, Vol.8 (5), p.e63906-e63906

2013

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(85989) 1999 JD6 : a first Barbarian asteroid detected by polarimetry in the NEA population

Astronomy and astrophysics (Berlin), 2021-02, Vol.646

2021

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Anion solvation enhanced by positive supercharging mutations preserves thermal stability of an antibody in a wide pH range

Biochemical and biophysical research communications, 2021-07, Vol.563, p.54-59

2021

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Molecular mechanism underlying the increased risk of colorectal cancer metastasis caused by single nucleotide polymorphisms in LI-cadherin gene

Scientific reports, 2023-04, Vol.13 (1), p.6493-11, Article 6493

2023

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Molecular basis for thermal stability and affinity in a VHH: Contribution of the framework region and its influence in the conformation of the CDR3

Protein science, 2022-11, Vol.31 (11), p.e4450-n/a

2022

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Blind prediction performance of RosettaAntibody 3.0: Grafting, relaxation, kinematic loop modeling, and full CDR optimization

Proteins, structure, function, and bioinformatics, 2014-08, Vol.82 (8), p.1611-1623

2014

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Design and Synthesis of Non-Peptide, Selective Orexin Receptor 2 Agonists

Journal of medicinal chemistry, 2015-10, Vol.58 (20), p.7931-7937

2015

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Structural classification of CDR-H3 revisited: A lesson in antibody modeling

Proteins, structure, function, and bioinformatics, 2008-11, Vol.73 (3), p.608-620

2008

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Engineering Stability, Viscosity, and Immunogenicity of Antibodies by Computational Design

Controlling Nutritional Status (CONUT) score is a prognostic marker for gastric cancer patients after curative resection

Shape complementarity and hydrogen bond preferences in protein-protein interfaces: implications for antibody modeling and protein-protein docking

Modeling and docking of antibody structures with Rosetta

Pushing the Backbone in Protein-Protein Docking

How the protonation state of a phosphorylated amino acid governs molecular recognition: insights from classical molecular dynamics simulations

Delicate balance among thermal stability, binding affinity, and conformational space explored by single-domain VHH antibodies

Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease

Thermodynamic and computational analyses reveal the functional roles of the galloyl group of tea catechins in molecular recognition

Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires

The nature of bright C-complex asteroids

Tumor associated macrophage expressing CD204 is associated with tumor aggressiveness of esophageal squamous cell carcinoma

Phospholipid Membrane Fluidity Alters Ligand Binding Activity of a G Protein-Coupled Receptor by Shifting the Conformational Equilibrium

Exploring designability of electrostatic complementarity at an antigen-antibody interface directed by mutagenesis, biophysical analysis, and molecular dynamics simulations

The Seimei telescope project and technical developments

Peptoid-based reprogrammable template for cell-permeable inhibitors of protein-protein interactions

Discovery of Two TNO-like Bodies in the Asteroid Belt

Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE)

(85989) 1999 JD6 : a first Barbarian asteroid detected by polarimetry in the NEA population

Anion solvation enhanced by positive supercharging mutations preserves thermal stability of an antibody in a wide pH range

Molecular mechanism underlying the increased risk of colorectal cancer metastasis caused by single nucleotide polymorphisms in LI-cadherin gene

Molecular basis for thermal stability and affinity in a VHH: Contribution of the framework region and its influence in the conformation of the CDR3

Blind prediction performance of RosettaAntibody 3.0: Grafting, relaxation, kinematic loop modeling, and full CDR optimization

Design and Synthesis of Non-Peptide, Selective Orexin Receptor 2 Agonists

Structural classification of CDR-H3 revisited: A lesson in antibody modeling

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