Daisuke Kihara

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 1%percentile

11.9Author DataRank

Indexed papers

15in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 15 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment

Proteins Structure Function and Bioinformatics(2021)10.1002/prot.26222

Top 9%

2.3DataRank

Top 9%127 citations

Guillaume Brysbaert, Théo Mauri, Nurul Nadzirin, Sameer Velankar, Raphaël A. G. Chaleil +95 more

Papers

Driven by 106 papers — median percentile 64. Top paper: “Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment”.

Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment

Proteins Structure Function and Bioinformatics(2021)10.1002/prot.26222

Top 9%

2.3DataRank

Top 9%127 citations

Guillaume Brysbaert, Théo Mauri, Nurul Nadzirin, Sameer Velankar, Raphaël A. G. Chaleil +95 more

Real-time structure search and structure classification for AlphaFold protein models

Communications Biology(2022)10.1038/s42003-022-03261-8

Top 11%

2.0DataRank

Top 11%63 citations

Vijay Bharadwaj, Charles Christoffer, Genki Terashi, Zicong Zhang, Rashidedin Jahandideh +3 more

Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment

Proteins Structure Function and Bioinformatics(2023)10.1002/prot.26609

Top 11%

1.9DataRank

Top 11%81 citations

Guillaume Brysbaert, Nessim Raouraoua, Paul A. Bates, Marco Giulini, Rodrigo V. Honorato +95 more

Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge

Nature Methods(2024)10.1038/s41592-024-02321-7

Top 23%

0.871DataRank

Top 23%18 citations

Andriy Kryshtafovych, Grigore Pintilie, S.K. Burley, Jiri Cerny, Vincent B. Chen +76 more

VESPER: global and local cryo-EM map alignment using local density vectors

Nature Communications(2021)10.1038/s41467-021-22401-y

Top 24%

0.850DataRank

Top 24%31 citations

Genki Terashi, Charles Christoffer, Siyang Chen, Daisuke Kihara, Xusi Han

Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study

PROTEOMICS(2023)10.1002/pmic.202200323

Top 25%

0.815DataRank

Top 25%26 citations

Qifang Xu, Gerardo Tauriello, Lorenzo Pantolini, Torsten Schwede, Frédéric Cazals +41 more

A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography

Molecular Biology and Evolution(2024)10.1093/molbev/msae036

Top 31%

0.644DataRank

Top 31%22 citations

Phillip A. Morin, Susanne Meyer, Li‐Fang Chu, Jeff K. Jacobsen, Jessica Antosiewicz‐Bourget +31 more

NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation

Nature Communications(2025)10.1038/s41467-025-56261-7

N/A

0.598DataRank · unranked

53 citations

Zicong Zhang, Nabil Ibtehaz, Xiao Wang, Tsukasa Nakamura, Pranav Punuru +2 more

DAQ-Score Database: assessment of map–model compatibility for protein structure models from cryo-EM maps

Nature Methods(2023)10.1038/s41592-023-01876-1

Top 36%

0.544DataRank

Top 36%18 citations

Xiao Wang, Genki Terashi, Daisuke Kihara, Tsukasa Nakamura

Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment

Utrecht University Repository (Utrecht University)(2023)10.22541/au.168888815.53957253/v1

Top 36%

0.540DataRank

Top 36%17 citations

Guillaume Brysbaert, Nessim Raouraoua, Paul A. Bates, Marco Giulini, Rodrigo V. Honorato +95 more

A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

BMC Biology(2022)10.1186/s12915-022-01427-8

N/A

0.489DataRank · unranked

25 citations

Chentao Yang, Giulio Formenti, Kalpana Raja, Lili Yan, Alan Tracey +24 more

Protein Data Bank Japan: Computational Resources for Analysis of Protein Structures

Journal of Molecular Biology(2025)10.1016/j.jmb.2025.169013

Top 44%

0.424DataRank

Top 44%13 citations

Chioko Nagao, Matsuyuki Shirota, Tsukasa Nakamura, Toshiaki Katayama, Daisuke Kihara +3 more

Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.12.147033

Top 48%

0.375DataRank

Top 48%7 citations

Andriy Kryshtafovych, Paul D. Adams, Pavel V. Afonine, Matthew L. Baker, Benjamin A. Barad +49 more

Protein Data Bank Japan: Improved tools for sequence‐oriented analysis of protein structures

Protein Science(2025)10.1002/pro.70052

Top 49%

0.363DataRank

Top 49%9 citations

Chioko Nagao, Matsuyuki Shirota, Tsukasa Nakamura, Toshiaki Katayama, Daisuke Kihara +3 more

Real-Time Structure Search and Structure Classification for AlphaFold Protein Models

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.21.465371

N/A

0.360DataRank · unranked

10 citations

Vijay Bharadwaj, Charles Christoffer, Genki Terashi, Zicong Zhang, Rashidedin Jahandideh +3 more

Chromosome level genome assembly of the Etruscan shrew Suncus etruscus

Scientific Data(2024)10.1038/s41597-024-03011-x

Top 70%

0.165DataRank

Top 70%2 citations

Susanne Meyer, Li‐Fang Chu, Linelle Abueg, Jessica Antosiewicz‐Bourget, Jennifer Balacco +21 more

CryoDataBot: a pipeline to curate cryoEM datasets for AI-driven structural biology

GigaScience(2025)10.1093/gigascience/giaf127

Top 78%

0.104DataRank

Top 78%1 citations

Leon Wu, Michael Rebelo, Shi Feng, Xinye Yu, Farhanaz Farheen +3 more

A remarkable genetic shift in a transmitted/founder virus broadens antibody responses against HIV-1

eLife(2024)10.7554/elife.92379

N/A

0.104DataRank · unranked

1 citations

Gherman Uritskiy, Marthandan Mahalingam, Himanshu Batra, Subhash Chand, Hung V. Trinh +13 more

A Remarkable Genetic Shift in a Transmitted/Founder Virus Broadens Antibody Responses Against HIV-1

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.16.448593

N/A

0.104DataRank · unranked

1 citations

Gherman Uritskiy, Marthandan Mahalingam, Himanshu Batra, Subhash Chand, Hung V. Trinh +13 more

Super-Resolution Cryo-EM Maps With 3D Deep Generative Networks

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.12.426430

N/A

0DataRank · unranked

5 citations

Genki Terashi, Daisuke Kihara, Sai Raghavendra Maddhuri Venkata Subramaniya

Evolutionary dynamics of indels in SARS-CoV-2 spike glycoprotein

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.30.454557

N/A

0DataRank · unranked

2 citations

Nagib Ahsan, Chunhui Xu, Lingtao Su, Jacob Verburgt, Luca Fornelli +3 more

SHREC 2021: Surface-based Protein Domains Retrieval

Zenodo (CERN European Organization for Nuclear Research)(2021)10.2312/3dor.20211308

N/A

0DataRank · unranked

1 citations

Tunde Aderinwale, Charles Christoffer, Woong‐Hee Shin, Genki Terashi, Xiao Wang +19 more

Application of Sequence Embedding in Protein Sequence-Based Predictions

arXiv (Cornell University)(2021)10.48550/arxiv.2110.07609

N/A

0DataRank · unranked

1 citations

Daisuke Kihara, Nabil Ibtehaz

Residue-wise local quality estimation for protein models from cryo-EM maps

Nature Methods(2022)10.1038/s41592-022-01574-4

N/A

0DataRank · unranked

60 citations

Xiao Wang, Sai Raghavendra Maddhuri Venkata Subramaniya, J.J.G. Tesmer, Daisuke Kihara, Genki Terashi

Protein model refinement for cryo-EM maps using AlphaFold2 and the DAQ score

Acta Crystallographica Section D Structural Biology(2022)10.1107/s2059798322011676

N/A

0DataRank · unranked

18 citations

Xiao Wang, Daisuke Kihara, Genki Terashi

Modeling protein–nucleic acid complexes with extremely large conformational changes using Flex‐LZerD

PROTEOMICS(2022)10.1002/pmic.202200322

N/A

0DataRank · unranked

13 citations

Daisuke Kihara, Charles Christoffer

Protein Structural Modeling for Electron Microscopy Maps Using VESPER and MAINMAST

Current Protocols(2022)10.1002/cpz1.494

N/A

0DataRank · unranked

11 citations

Genki Terashi, Daisuke Kihara, Eman Alnabati

RL-MLZerD: Multimeric protein docking using reinforcement learning

Frontiers in Molecular Biosciences(2022)10.3389/fmolb.2022.969394

N/A

0DataRank · unranked

15 citations

Charles Christoffer, Daisuke Kihara, Tunde Aderinwale

Domain-Based Protein Docking with Extremely Large Conformational Changes

Journal of Molecular Biology(2022)10.1016/j.jmb.2022.167820

N/A

0DataRank · unranked

15 citations

Daisuke Kihara, Charles Christoffer

ContactPFP: Protein Function Prediction Using Predicted Contact Information

Frontiers in Bioinformatics(2022)10.3389/fbinf.2022.896295

N/A

0DataRank · unranked

14 citations

Sean T. Flannery, Aashish Jain, Daisuke Kihara, Yuki Kagaya

MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field

Frontiers in Molecular Biosciences(2022)10.3389/fmolb.2022.935411

N/A

0DataRank · unranked

8 citations

Juan Esquivel‐Rodríguez, Genki Terashi, Daisuke Kihara, Eman Alnabati

OC_Finder: Osteoclast Segmentation, Counting, and Classification Using Watershed and Deep Learning

Frontiers in Bioinformatics(2022)10.3389/fbinf.2022.819570

N/A

0DataRank · unranked

10 citations

Mizuho Kittaka, Yilin He, Yiwei Zhang, Yasuyoshi Ueki, Daisuke Kihara +1 more

A high-quality blue whale genome, segmental duplications, and historical demography

Research Square(2022)10.21203/rs.3.rs-1910240/v1

N/A

0DataRank · unranked

7 citations

Phillip A. Morin, Susanne Meyer, Li‐Fang Chu, Jeff K. Jacobsen, Jessica Antosiewicz‐Bourget +31 more

Protein Model Refinement for Cryo-EM Maps Using DAQ score

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.23.505034

N/A

0DataRank · unranked

1 citations

Xiao Wang, Daisuke Kihara, Genki Terashi

CryoREAD: de novo structure modeling for nucleic acids in cryo-EM maps using deep learning

Nature Methods(2023)10.1038/s41592-023-02032-5

N/A

0DataRank · unranked

49 citations

Genki Terashi, Daisuke Kihara, Xiao Wang

Computational prediction of disordered binding regions

Computational and Structural Biotechnology Journal(2023)10.1016/j.csbj.2023.02.018

N/A

0DataRank · unranked

44 citations

Daisuke Kihara, Lukasz Kurgan, Sushmita Basu

Domain-PFP allows protein function prediction using function-aware domain embedding representations

Communications Biology(2023)10.1038/s42003-023-05476-9

N/A

0DataRank · unranked

35 citations

Yuki Kagaya, Daisuke Kihara, Nabil Ibtehaz

PDA-Pred: Predicting the binding affinity of protein-DNA complexes using machine learning techniques and structural features

Methods(2023)10.1016/j.ymeth.2023.03.002

N/A

0DataRank · unranked

30 citations

Daisuke Kihara, M. Michael Gromiha, K. Harini

Enhancing cryo-EM maps with 3D deep generative networks for assisting protein structure modeling

Bioinformatics(2023)10.1093/bioinformatics/btad494

N/A

0DataRank · unranked

18 citations

Genki Terashi, Daisuke Kihara, Sai Raghavendra Maddhuri Venkata Subramaniya

Heterogeneity in Lowe Syndrome: Mutations Affecting the Phosphatase Domain of OCRL1 Differ in Impact on Enzymatic Activity and Severity of Cellular Phenotypes

Biomolecules(2023)10.3390/biom13040615

N/A

0DataRank · unranked

8 citations

Swetha Ramadesikan, Adrianna F. Black, Charles Christoffer, Andrés Felipe Pacheco Pacheco, Sneha Subramanian +6 more

Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches

Frontiers in Molecular Biosciences(2023)10.3389/fmolb.2023.1110567

N/A

0DataRank · unranked

5 citations

Keiko Kumazawa, Kenichiro Imai, Takatsugu Hirokawa, Daisuke Kihara, Woong‐Hee Shin

Pairwise and Multi-chain Protein Docking Enhanced Using LZerD Web Server

Methods in molecular biology(2023)10.1007/978-1-0716-3327-4_28

N/A

0DataRank · unranked

4 citations

Charles Christoffer, M. Michael Gromiha, Daisuke Kihara, K. Harini

Recent Deep Learning Applications to Structure-Based Drug Design

Methods in molecular biology(2023)10.1007/978-1-0716-3441-7_13

N/A

0DataRank · unranked

4 citations

Anika Jain, Daisuke Kihara, Jacob Verburgt

Distance-AF: Modifying Predicted Protein Structure Models by Alphafold2 with User-Specified Distance Constraints

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.01.569498

N/A

0DataRank · unranked

13 citations

Zicong Zhang, Yuki Kagaya, Genki Terashi, Bowen Zhao, Yi Xiong +2 more

NuFold: A Novel Tertiary RNA Structure Prediction Method Using Deep Learning with Flexible Nucleobase Center Representation

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.20.558715

N/A

0DataRank · unranked

12 citations

Zicong Zhang, Nabil Ibtehaz, Xiao Wang, Tsukasa Nakamura, David Huang +2 more

Integrated Protocol of Protein Structure Modeling for Cryo-EM with Deep Learning and Structure Prediction

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.19.563151

N/A

0DataRank · unranked

4 citations

Xiao Wang, Devashish Prasad, Tsukasa Nakamura, Zhu Han, Daisuke Kihara +1 more

Improved Peptide Docking with Privileged Knowledge Distillation using Deep Learning

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.01.569671

N/A

0DataRank · unranked

4 citations

Jacob Verburgt, Yuki Kagaya, Charles Christoffer, Daisuke Kihara, Zicong Zhang

ACC-UNet: A Completely Convolutional UNet model for the 2020s

arXiv (Cornell University)(2023)10.48550/arxiv.2308.13680

N/A

0DataRank · unranked

2 citations

Daisuke Kihara, Nabil Ibtehaz

Assembly of Protein Complexes In and On the Membrane with Predicted Spatial Arrangement Constraints

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.20.563303

N/A

0DataRank · unranked

1 citations

K. Harini, Gupta Archit, Daisuke Kihara, Charles Christoffer

GO2Sum: Generating Human Readable Functional Summary of Proteins from GO Terms

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.10.566665

N/A

0DataRank · unranked

1 citations

Nabil Ibtehaz, Daisuke Kihara, Swagarika Jaharlal Giri

Domain-PFP: Protein Function Prediction Using Function-Aware Domain Embedding Representations

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.23.554486

N/A

0DataRank · unranked

0 citations

Yuki Kagaya, Daisuke Kihara, Nabil Ibtehaz

Unveiling the stochastic nature of human heteropolymer ferritin self‐assembly mechanism

Protein Science(2024)10.1002/pro.5104

N/A

0DataRank · unranked

20 citations

Jeremie Fish, Genki Terashi, Yuanyuan Zhang, Daisuke Kihara, Paolo Arosio +1 more

Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences

Briefings in Bioinformatics(2024)10.1093/bib/bbaf016

N/A

0DataRank · unranked

11 citations

Jing Yu, Daisuke Kihara, Lukasz Kurgan, Sushmita Basu

Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints

Journal of Molecular Biology(2024)10.1016/j.jmb.2024.168486

N/A

0DataRank · unranked

4 citations

K. Harini, Gupta Archit, Daisuke Kihara, Charles Christoffer

GO2Sum: generating human-readable functional summary of proteins from GO terms

npj Systems Biology and Applications(2024)10.1038/s41540-024-00358-0

N/A

0DataRank · unranked

4 citations

Nabil Ibtehaz, Daisuke Kihara, Swagarika Jaharlal Giri

DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.20.576370

N/A

0DataRank · unranked

9 citations

Zhu Han, Genki Terashi, Manav Taluja, Daisuke Kihara, Xiao Wang

AFM-RL: Large Protein Complex Docking Using AlphaFold-Multimer and Reinforcement Learning

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.20.576386

N/A

0DataRank · unranked

2 citations

Rashidedin Jahandideh, Zicong Zhang, Bowen Zhao, Yi Xiong, Daisuke Kihara +1 more

Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge

Research Square(2024)10.21203/rs.3.rs-3864137/v1

N/A

0DataRank · unranked

2 citations

Andriy Kryshtafovych, Grigore Pintilie, S.K. Burley, Jiri Cerny, Vincent Chen +76 more

AlphaFold Model Quality Self-Assessment Improvement Via Deep Graph Learning

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.18.604136

N/A

0DataRank · unranked

2 citations

Zicong Zhang, Daisuke Kihara, Jacob Verburgt

Editorial: Expert opinions in protein bioinformatics: 2022

Frontiers in Bioinformatics(2024)10.3389/fbinf.2023.1338560

N/A

0DataRank · unranked

1 citations

Daisuke Kihara

Predicting transcriptional activation domain function using Graph Neural Networks

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.05.08.593266

N/A

0DataRank · unranked

1 citations

Bradley K. Broyles, Yuanyuan Zhang, Nabil Ibtehaz, Alexandre M. Erkine, Daisuke Kihara +1 more

Proteomic analysis of unicellular cyanobacterium Crocosphaera subtropica ATCC 51142 under extended light or dark growth

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.29.605499

N/A

0DataRank · unranked

1 citations

Swagarika Jaharlal Giri, Louis A. Sherman, Daisuke Kihara, Uma K. Aryal, Punyatoya Panda

Reviewer #2 (Public Review): A Remarkable Genetic Shift in a Transmitted/Founder Virus Broadens Antibody Responses Against HIV-1

(2024)10.7554/elife.92379.1.sa0

N/A

0DataRank · unranked

0 citations

Gherman Uritskiy, Marthandan Mahalingam, Himanshu Batra, Subhash Chand, Hung V. Trinh +13 more

A Remarkable Genetic Shift in a Transmitted/Founder Virus Broadens Antibody Responses Against HIV-1

eLife(2024)10.7554/elife.92379.1

N/A

0DataRank · unranked

0 citations

Gherman Uritskiy, Marthandan Mahalingam, Himanshu Batra, Subhash Chand, Hung V. Trinh +13 more

Reviewer #1 (Public Review): A Remarkable Genetic Shift in a Transmitted/Founder Virus Broadens Antibody Responses Against HIV-1

(2024)10.7554/elife.92379.2.sa1

N/A

0DataRank · unranked

0 citations

Gherman Uritskiy, Marthandan Mahalingam, Himanshu Batra, Subhash Chand, Hung V. Trinh +13 more

A remarkable genetic shift in a transmitted/founder virus broadens antibody responses against HIV-1

eLife(2024)10.7554/elife.92379.3

N/A

0DataRank · unranked

0 citations

Gherman Uritskiy, Marthandan Mahalingam, Himanshu Batra, Subhash Chand, Hung V. Trinh +13 more

Vox-UDA: Voxel-wise Unsupervised Domain Adaptation for Cryo-Electron Subtomogram Segmentation with Denoised Pseudo Labeling

arXiv (Cornell University)(2024)10.48550/arxiv.2406.18610

N/A

0DataRank · unranked

0 citations

Xingjian Li, Jinglong Shi, Huaming Chen, Bo Du, Daisuke Kihara +4 more

Genetic adaptation despite high gene flow in a range-expanding population

(2024)10.22541/au.172115088.83825068/v1

N/A

0DataRank · unranked

0 citations

Benjamin Daniels, William Hemstrom, Cataixa López, Yuki Kagaya, Daisuke Kihara +5 more

SHREC2024: Non-rigid Complementary Shapes Retrieval in Protein-protein Interactions

HAL (Le Centre pour la Communication Scientifique Directe)(2024)10.2312/3dor.20241173

Top 100%

0DataRank

Top 100%0 citations

Н А Зарубина, Camille Depenveiller, Nguyen, Hoang-Phuc, Vong, Vinh-Toan, M-T Tran +6 more

Effect of phosphorylation barcodes on arrestin binding to a chemokine receptor

Nature(2025)10.1038/s41586-025-09024-9

N/A

0DataRank · unranked

28 citations

Christopher T. Schafer, Somnath Mukherjee, Kai Wang, Martin Gustavsson, James R. Fuller +11 more

AI-based methods for biomolecular structure modeling for Cryo-EM

Current Opinion in Structural Biology(2025)10.1016/j.sbi.2025.102989

N/A

0DataRank · unranked

17 citations

Genki Terashi, Han Zhu, Daisuke Kihara, Farhanaz Farheen

Advancing structure modeling from cryo-EM maps with deep learning

Biochemical Society Transactions(2025)10.1042/bst20240784

N/A

0DataRank · unranked

10 citations

Genki Terashi, Zicong Zhang, Daisuke Kihara, Shu Li

AI-based quality assessment methods for protein structure models from cryo-EM

Current Research in Structural Biology(2025)10.1016/j.crstbi.2025.100164

N/A

0DataRank · unranked

6 citations

Genki Terashi, Farhanaz Farheen, Tsukasa Nakamura, Daisuke Kihara, Zhu Han

Structure Modeling Protocols for Protein Multimer and RNA in CASP16 With Enhanced MSAs , Model Ranking, and Deep Learning

Proteins Structure Function and Bioinformatics(2025)10.1002/prot.70033

N/A

0DataRank · unranked

6 citations

Tsukasa Nakamura, Jacob Verburgt, Anika Jain, Genki Terashi, Pranav Punuru +6 more

Distance-AF improves predicted protein structure models by AlphaFold2 with user-specified distance constraints

Communications Biology(2025)10.1038/s42003-025-08783-5

N/A

0DataRank · unranked

5 citations

Zicong Zhang, Yuki Kagaya, Genki Terashi, Bowen Zhao, Yi Xiong +2 more

AlphaFold model quality self‐assessment improvement via deep graph learning

Protein Science(2025)10.1002/pro.70274

N/A

0DataRank · unranked

3 citations

Zicong Zhang, Daisuke Kihara, Jacob Verburgt

MVGFormer: Multi-view perspective with graph-guided transformer for cryo-ET segmentation

Knowledge-Based Systems(2025)10.1016/j.knosys.2025.114810

N/A

0DataRank · unranked

2 citations

Xingjian Li, Huan Wang, Jiahua Shi, Huaming Chen, Yizhou Zhao +6 more

Proteomic analysis of metabolic adaptation in a unicellular cyanobacterium during light-dark cycles and nitrogen fixation

Scientific Reports(2025)10.1038/s41598-025-21588-0

N/A

0DataRank · unranked

2 citations

Swagarika Jaharlal Giri, Venkatesh P. Thirumalaikumar, Louis A. Sherman, Daisuke Kihara, Uma K. Aryal +1 more

Integrative Protein Assembly With LZerD and Deep Learning in CAPRI 47–55

Proteins Structure Function and Bioinformatics(2025)10.1002/prot.26818

N/A

0DataRank · unranked

3 citations

Yuki Kagaya, Jacob Verburgt, Genki Terashi, Woong‐Hee Shin, Anika Jain +8 more

SHREC 2025: Protein surface shape retrieval including electrostatic potential

Computers & Graphics(2025)10.1016/j.cag.2025.104394

N/A

0DataRank · unranked

2 citations

Camille Depenveiller, Atsushi Tatsuma, Tin Barisin, Eugen Rusakov, Udo Göbel +23 more

Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16

Proteins Structure Function and Bioinformatics(2025)10.1002/prot.70079

N/A

0DataRank · unranked

1 citations

Elisa Posani, Eugene F. Baulin, Janusz M. Bujnicki, Giovanni Bussi, Thomas E. Cheatham +46 more

Learning with Privileged Knowledge Distillation for Improved Peptide–Protein Docking

ACS Omega(2025)10.1021/acsomega.5c00967

N/A

0DataRank · unranked

2 citations

Jacob Verburgt, Yuki Kagaya, Charles Christoffer, Daisuke Kihara, Zicong Zhang

Vox-UDA: Voxel-wise Unsupervised Domain Adaptation for Cryo-Electron Subtomogram Segmentation with Denoised Pseudo-Labeling

Proceedings of the AAAI Conference on Artificial Intelligence(2025)10.1609/aaai.v39i1.32019

N/A

0DataRank · unranked

2 citations

Xingjian Li, Jinglong Shi, Huaming Chen, Bo Du, Daisuke Kihara +4 more

Structure Modeling Protocols for Protein Multimer and RNA in CASP16 with Enhanced MSAs, Model Ranking, and Deep Learning

(2025)10.22541/au.174478900.09405488/v1

N/A

0DataRank · unranked

0 citations

Tsukasa Nakamura, Jacob Verburgt, Anika Jain J, Genki Terashi, Pranav Punuru +6 more

Blind prediction of complex water and ion ensembles around RNA in CASP16

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.03.685595

N/A

0DataRank · unranked

0 citations

Elisa Posani, Eugene F. Baulin, Janusz M. Bujnicki, Giovanni Bussi, Thomas E. Cheatham +46 more

Structure of bacteriophage P1 head provides insight into capsid polymorphism

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.26.689930

N/A

0DataRank · unranked

0 citations

Tsukasa Nakamura, Genki Terashi, Veer S. Bhatt, Kyung-Ho Kim, Shankararaman Chellam +3 more

Current Challenges and Opportunities in Designing Protein–Protein Interaction Targeted Drugs

Advances and Applications in Bioinformatics and Chemistry(2020)10.2147/aabc.s235542

N/A

0DataRank · unranked

64 citations

Keiko Kumazawa, Kenichiro Imai, Takatsugu Hirokawa, Daisuke Kihara, Woong‐Hee Shin

Queryome: Orchestrating Retrieval, Reasoning, and Synthesis across Biomedical Literature

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.64898/2025.12.22.696019

N/A

0DataRank · unranked

0 citations

Nabil Ibtehaz, Swagarika Jaharlal Giri, Harsha Srirangam, Emilia A Tugolukova, Daisuke Kihara +1 more

Computational structure modeling for diverse categories of macromolecular interactions

Current Opinion in Structural Biology(2020)10.1016/j.sbi.2020.05.017

N/A

0DataRank · unranked

33 citations

Charles Christoffer, Daipayan Sarkar, Eman Alnabati, Daisuke Kihara, Tunde Aderinwale

2DKD: a toolkit for content-based local image search

Source Code for Biology and Medicine(2020)10.1186/s13029-020-0077-1

N/A

0DataRank · unranked

2 citations

Daisuke Kihara, Atilla Sit, Julian S. DeVille

Protein Docking Model Evaluation by Graph Neural Networks

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.30.424859

N/A

0DataRank · unranked

23 citations

Sean T. Flannery, Daisuke Kihara, Xiao Wang

Protein Contact Map Denoising Using Generative Adversarial Networks

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.26.174300

N/A

0DataRank · unranked

9 citations

Genki Terashi, Aashish Jain, Yuki Kagaya, Daisuke Kihara, Sai Raghavendra Maddhuri Venkata Subramaniya

AttentiveDist: Protein Inter-Residue Distance Prediction Using Deep Learning with Attention on Quadruple Multiple Sequence Alignments

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.24.396770

N/A

0DataRank · unranked

4 citations

Genki Terashi, Yuki Kagaya, Sai Raghavendra Maddhuri Venkata Subramaniya, Charles Christoffer, Daisuke Kihara +1 more

Emap2sec+: Detecting Protein and DNA/RNA Structures in Cryo-EM Maps of Intermediate Resolution Using Deep Learning

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.08.22.262675

N/A

0DataRank · unranked

2 citations

Eman Alnabati, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi, Daisuke Kihara +1 more

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

Nature Methods(2021)10.1038/s41592-020-01051-w

N/A

0DataRank · unranked

119 citations

Andriy Kryshtafovych, Paul D. Adams, Pavel V. Afonine, Matthew L. Baker, Benjamin A. Barad +49 more

LZerD webserver for pairwise and multiple protein–protein docking

Nucleic Acids Research(2021)10.1093/nar/gkab336

N/A

0DataRank · unranked

104 citations

Siyang Chen, Vijay Bharadwaj, Tunde Aderinwale, Vidhur Kumar, Matin Hormati +2 more

Protein Docking Model Evaluation by Graph Neural Networks

Frontiers in Molecular Biosciences(2021)10.3389/fmolb.2021.647915

N/A

0DataRank · unranked

100 citations

Sean T. Flannery, Daisuke Kihara, Xiao Wang

LZerD Protein-Protein Docking Webserver Enhanced With de novo Structure Prediction

Frontiers in Molecular Biosciences(2021)10.3389/fmolb.2021.724947

N/A

0DataRank · unranked

51 citations

Vijay Bharadwaj, Ryan Luu, Daisuke Kihara, Charles Christoffer

CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps

Matter(2021)10.1016/j.matt.2021.09.004

N/A

0DataRank · unranked

51 citations

Genki Terashi, Chitrak Gupta, Daipayan Sarkar, Gaspard Debussche, Nicholas J. Sisco +11 more

Detecting protein and DNA/RNA structures in cryo-EM maps of intermediate resolution using deep learning

Nature Communications(2021)10.1038/s41467-021-22577-3

N/A

0DataRank · unranked

47 citations

Eman Alnabati, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi, Daisuke Kihara +1 more

Mass spectrometry‐based proteomic platforms for better understanding of SARS‐CoV‐2 induced pathogenesis and potential diagnostic approaches

PROTEOMICS(2021)10.1002/pmic.202000279

N/A

0DataRank · unranked

36 citations

R. Shyama Prasad Rao, Rashaun S. Wilson, Ujwal Punyamurtula, Fernanda Salvato, Max Petersen +9 more

Analyzing effect of quadruple multiple sequence alignments on deep learning based protein inter-residue distance prediction

Scientific Reports(2021)10.1038/s41598-021-87204-z

N/A

0DataRank · unranked

27 citations

Genki Terashi, Yuki Kagaya, Sai Raghavendra Maddhuri Venkata Subramaniya, Charles Christoffer, Daisuke Kihara +1 more

Genotype & phenotype in Lowe Syndrome: specific OCRL1 patient mutations differentially impact cellular phenotypes

Human Molecular Genetics(2021)10.1093/hmg/ddab025

N/A

0DataRank · unranked

18 citations

Lisette Skiba, Jennifer Lee, Kayalvizhi Madhivanan, Daipayan Sarkar, Agustina De La Fuente +6 more

Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps

Journal of Chemical Information and Modeling(2021)10.1021/acs.jcim.1c00230

N/A

0DataRank · unranked

17 citations

Genki Terashi, Daisuke Matsuoka, Daisuke Kihara, Yuji Sugita, Takaharu Mori

Protein contact map refinement for improving structure prediction using generative adversarial networks

Bioinformatics(2021)10.1093/bioinformatics/btab220

N/A

0DataRank · unranked

13 citations

Genki Terashi, Aashish Jain, Yuki Kagaya, Daisuke Kihara, Sai Raghavendra Maddhuri Venkata Subramaniya

Surface-based protein domains retrieval methods from a SHREC2021 challenge

Journal of Molecular Graphics and Modelling(2021)10.1016/j.jmgm.2021.108103

N/A

0DataRank · unranked

3 citations

Tunde Aderinwale, Charles Christoffer, Woong‐Hee Shin, Genki Terashi, Xiao Wang +19 more

Daisuke Kihara

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