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List of works by Daisuke Kuroda

A Peptoid with Extended Shape in Water

scientific article published on 23 August 2019

An epitope-directed antibody affinity maturation system utilizing mammalian cell survival as readout

scientific article published on 29 March 2019

Antibody Affinity Maturation by Computational Design

scientific article published on 01 January 2018

Assessing the Heterogeneity of the Fc-Glycan of a Therapeutic Antibody Using an engineered FcγReceptor IIIa-Immobilized Column

scientific article published on 2 March 2018

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

scientific article

Computer-aided antibody design

scientific article

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

scientific article published on 12 August 2015

Design and Synthesis of Potent and Highly Selective Orexin 1 Receptor Antagonists with a Morphinan Skeleton and Their Pharmacologies

scientific article published on 4 January 2017

Effects of a remote mutation from the contact paratope on the structure of CDR-H3 in the anti-HIV neutralizing antibody PG16

scientific article published on 27 December 2019

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

scientific article published on 18 January 2020

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

scientific article published on 14 March 2019

Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27

scientific article

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

scientific article published on 08 December 2019

Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody

scientific article published on 01 July 2018

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

scientific article published on 25 April 2016

Macromolecular modeling and design in Rosetta: recent methods and frameworks

scientific article published on 01 June 2020

Mechanism of dimerization and structural features of human LI-cadherin

scientific article published on 06 August 2021

Modeling and docking of antibody structures with Rosetta.

scientific article published on 26 January 2017

Modulation of a conformational ensemble by a small molecule that inhibits key protein-protein interactions involved in cell adhesion

Per-Residue Program of Multiple Backbone Dihedral Angles of β-Peptoids via Backbone Substitutions

scientific article published on 21 January 2020

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

scientific article published on 14 January 2019

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

scientific article

Pushing the Backbone in Protein-Protein Docking.

scientific article

Regulation of cadherin dimerization by chemical fragments as a trigger to inhibit cell adhesion

Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification.

scientific article

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

scientific article (publication date: 2013)

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

scientific article published on 19 April 2016

Structural Basis for Antigen Recognition by Methylated Lysine Specific Antibodies

scientific article published on 10 December 2020

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

scientific article published in November 2008

Structural insights into the reaction mechanism of S-adenosyl-L-homocysteine hydrolase.

scientific article

Structures of the prefusion form of measles virus fusion protein in complex with inhibitors.

scientific article published on 20 February 2018

Systematic classification of CDR-L3 in antibodies: implications of the light chain subtypes and the VL-VH interface

scientific article published on 01 April 2009

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

scientific article published in PLoS ONE

Use of amino acid composition to predict epitope residues of individual antibodies.

scientific article

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