Daisuke Kihara

Purdue University West Lafayette — United States

Biochemistry, Genetics and Molecular Biology · Life Sciences

60h-index12.2kcitations465works3.12yr avg
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Research Topics

Protein Structure and Dynamics(196), Enzyme Structure and Function(133), Machine Learning in Bioinformatics(99), Bioinformatics and Genomic Networks(76), RNA and protein synthesis mechanisms(75)

Publications462 total

Computational approaches for RNA structure prediction and design
Cell Reports Physical Science·2026Open Access
Ferritin iron uptake and oxidation are dynamically modulated by nucleotide phosphate architecture via electrostatic gating
International Journal of Biological Macromolecules·2026
BPS2026 – NuFold and NuFold DB: Deep learning approach for RNA structure prediction and database of predicted structures
Biophysical Journal·2026
Blind Prediction of Complex Water and Ion Ensembles Around <scp>RNA</scp> in <scp>CASP16</scp>
Proteins Structure Function and Bioinformatics·2025· 1 citedOpen Access
MVGFormer: Multi-view perspective with graph-guided transformer for cryo-ET segmentation
Knowledge-Based Systems·2025Open Access
Blind prediction of complex water and ion ensembles around RNA in CASP16
2025Open Access
Structural Insights and Functional Dynamics of β-Lactoglobulin Fibrils
Nano Letters·2025· 1 cited
Proteomic analysis of metabolic adaptation in a unicellular cyanobacterium during light-dark cycles and nitrogen fixation
Scientific Reports·2025Open Access
Author response for "Blind Prediction of Complex Water and Ion Ensembles Around &lt;scp&gt;RNA&lt;/scp&gt; in &lt;scp&gt;CASP16&lt;/scp&gt;"
2025
Distance-AF improves predicted protein structure models by AlphaFold2 with user-specified distance constraints
Communications Biology·2025Open Access
Semi-MoE: Mixture-of-Experts meets Semi-Supervised Histopathology Segmentation
arXiv (Cornell University)·2025Open Access
CryoDataBot: a pipeline to curate cryoEM datasets for AI-driven structural biology
2025Open Access
When does structure modeling go wrong? A PDB-scale analysis of protein structure model validation using DAQ Score
Structural Dynamics·2025Open Access
EMSuite Server: Advanced Tools for Cryo-EM Structure Modeling, Validation, and Refinement
Structural Dynamics·2025Open Access
SHREC 2025: Protein surface shape retrieval including electrostatic potential
Computers & Graphics·2025· 2 citedOpen Access
<scp>AlphaFold</scp> model quality self‐assessment improvement via deep graph learning
Protein Science·2025· 2 citedOpen Access
Structure Modeling Protocols for Protein Multimer and <scp>RNA</scp> in <scp>CASP16</scp> With Enhanced <scp>MSAs</scp> , Model Ranking, and Deep Learning
Proteins Structure Function and Bioinformatics·2025· 4 citedOpen Access
Divergence of an extracellular contractile injection system infectivity elucidated by high resolution structural studies of its tail-baseplate complex
2025Open Access
Dynamics of Sheath Subunit of a Contractile Injection System Studied at Atomic Level During Host Infection
Microscopy and Microanalysis·2025Open Access
DMcloud: Macromolecular Structure Modeling with Local Structure Fitting for Medium to Low Resolution Cryo-EM Maps
Microscopy and Microanalysis·2025· 2 cited
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Frequent Co-authors

Jeffrey Skolnick(9), Genki Terashi(9), Jianlin Cheng(7), Juan Esquivel‐Rodríguez(7), Lee Sael(6), Paul A. Bates(6), Brian G. Pierce(6), Juan Fernández‐Recio(6), Dima Kozakov(6), Charles Christoffer(6), Chaok Seok(5), Alexandre M. J. J. Bonvin(5), Xiaoqin Zou(5), Sándor Vajda(5), Jeffrey J. Gray(5), Woong‐Hee Shin(4), Marc F. Lensink(4), Sameer Velankar(4), Sergei Grudinin(4), Zhiping Weng(4)