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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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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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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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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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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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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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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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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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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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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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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.6493-6493, Article 6493

2023

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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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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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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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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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Asteroid Catalog Using AKARI: AKARI/IRC Mid-Infrared Asteroid Survey

Publications of the Astronomical Society of Japan, 2011-10, Vol.63 (5), p.1117-1138

2011

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Current advances in biopharmaceutical informatics: guidelines, impact and challenges in the computational developability assessment of antibody therapeutics

mAbs, 2022-12, Vol.14 (1), p.2020082-2020082

2022

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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

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

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

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

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

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

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

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

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

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

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

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

Discovery of Two TNO-like Bodies in the Asteroid Belt

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

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

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

Asteroid Catalog Using AKARI: AKARI/IRC Mid-Infrared Asteroid Survey

Current advances in biopharmaceutical informatics: guidelines, impact and challenges in the computational developability assessment of antibody therapeutics

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