Author details

Full Name

Yuko Tsuchiya

Affiliation

ORCID

Career Start Year

2004

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36570321	Protein-protein interaction prediction methods: from docking-based to AI-based approaches.	Biophys Rev	2022
34615896	Autoencoder-based detection of the residues involved in G protein-coupled receptor signaling.	Scientific Reports	2021
33334100	Rebuilding Ring-Type Assembly of Peroxiredoxin by Chemical Modification.	Bioconjugate Chemistry	2021
32621216	Structural Modeling and Ligand-Binding Prediction for Analysis of Structure-Unknown and Function-Unknown Proteins Using FORTE Alignment and PoSSuM Pocket Search.	Methods Mol Biol	2020
32166610	Neural networks for protein structure and function prediction and dynamic analysis.	Biophys Rev	2020
31386362	Autoencoder-Based Detection of Dynamic Allostery Triggered by Ligand Binding Based on Molecular Dynamics.	Journal of Chemical Information and Modeling	2019
31488862	Actin Cytoskeletal Reorganization Function of JRAB/MICAL-L2 Is Fine-tuned by Intramolecular Interaction between First LIM Zinc Finger and C-terminal Coiled-coil Domains.	Scientific Reports	2019
28815765	New tools and functions in data-out activities at Protein Data Bank Japan (PDBj).	Protein Sci	2018
28992359	A study of CDR3 loop dynamics reveals distinct mechanisms of peptide recognition by T-cell receptors exhibiting different levels of cross-reactivity.	Immunology	2018
27789697	Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.	Nucleic Acids Res	2017
27582384	Conformational plasticity of JRAB/MICAL-L2 provides "law and order" in collective cell migration.	Molecular Biology of the Cell	2016
26749247	The diversity of H3 loops determines the antigen-binding tendencies of antibody CDR loops.	Protein Science	2016
27333035	Ligand-induced Ordering of the C-terminal Tail Primes STING for Phosphorylation by TBK1.	eBioMedicine	2016
27456364	Substrate recognition of N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii.	Journal of Structural Biology	2016
26491019	Retinoblastoma-binding Protein 4-regulated Classical Nuclear Transport Is Involved in Cellular Senescence.	Journal of Biological Chemistry	2015
26607293	Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target.	Sci Rep	2015
25064566	Kotai Antibody Builder: automated high-resolution structural modeling of antibodies.	Bioinformatics	2014
24155158	Blind prediction of interfacial water positions in CAPRI.	Proteins	2014
24756852	High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations.	Proteins	2014
24746687	Crystal structure of FtsA from Staphylococcus aureus.	FEBS Letters	2014
23843247	Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.	Proteins	2013
22887034	Dynamic features of homodimer interfaces calculated by normal-mode analysis.	Protein Science	2012
22001016	Community-wide assessment of protein-interface modeling suggests improvements to design methodology.	J Mol Biol	2011
21918618	Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction.	Adv Appl Bioinform Chem	2009
21918609	Discrimination between biological interfaces and crystal-packing contacts.	Adv Appl Bioinform Chem	2008
17803239	Docking of protein molecular surfaces with evolutionary trace analysis.	Proteins	2007
16837482	Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity.	Protein Eng Des Sel	2006
16817901	Silencing the constitutive active transcription factor CREB by the LKB1-SIK signaling cascade.	FEBS J	2006
16844993	PreBI: prediction of biological interfaces of proteins in crystals.	Nucleic Acids Res	2006
16125724	Structure of the central hub of bacteriophage Mu baseplate determined by X-ray crystallography of gp44.	Journal of Molecular Biology	2005
15613393	PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces.	Bioinformatics	2005
15146487	Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces.	Proteins	2004