Dong Si - Publications, H-index & Citations

Dong Si

washington bothell university

20H指数

113论文数

2.0K被引数

收录论文 19

发表时间

ContrastQA: A label-guided graph contrastive learning-based approach for protein complex structure quality assessment ContrastQA：基于标签引导图对比学习的蛋白质复合物结构质量评估方法

Protein Science

IF5.2

2026-08-13

PREAI

Lei Zhang; Rui Ding; Xiao Chen; Jie Hou; Dong Si; Yang Wang; Keying Lin; Renzhi Cao

Beyond current boundaries: Integrating deep learning and AlphaFold for enhanced protein structure prediction from low-resolution cryo-EM maps 超越当前边界：整合深度学习与AlphaFold，以从低分辨率冷冻电镜图谱中增强蛋白质结构预测

computational chemistry

IF3.1

2025-05-27

PREAI

Xin Ma; Dong Si

Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge

NATURE METHODS

IF32.1

2024-06-25

OAAI

Lawson, Catherine L.; Kryshtafovych, Andriy; Pintilie, Grigore D.; Burley, Stephen K.; Cerny, Jiri; Chen, Vincent B.; Emsley, Paul; Gobbi, Alberto; Joachimiak, Andrzej; Noreng, Sigrid; Prisant, Michael G.; Read, Randy J.; Richardson, Jane S.; Rohou, Alexis L.; Schneider, Bohdan; Sellers, Benjamin D.; Shao, Chenghua; Sourial, Elizabeth; Williams, Chris I.; Williams, Christopher J.; Yang, Ying; Abbaraju, Venkat; Afonine, Pavel V.; Baker, Matthew L.; Bond, Paul S.; Blundell, Tom L.; Burnley, Tom; Campbell, Arthur; Cao, Renzhi; Cheng, Jianlin; Chojnowski, Grzegorz; Cowtan, K. D.; DiMaio, Frank; Esmaeeli, Reza; Giri, Nabin; Grubmueller, Helmut; Hoh, Soon Wen; Hou, Jie; Hryc, Corey F.; Hunte, Carola; Igaev, Maxim; Joseph, Agnel P.; Kao, Wei-Chun; Kihara, Daisuke; Kumar, Dilip; Lang, Lijun; Lin, Sean; Subramaniya, Sai R. Maddhuri Venkata; Mittal, Sumit; Mondal, Arup; Moriarty, Nigel W.; Muenks, Andrew; Murshudov, Garib N.; Nicholls, Robert A.; Olek, Mateusz; Palmer, Colin M.; Perez, Alberto; Pohjolainen, Emmi; Pothula, Karunakar R.; Rowley, Christopher N.; Sarkar, Daipayan; Schaefer, Luisa U.; Schlicksup, Christopher J.; Schroeder, Gunnar F.; Shekhar, Mrinal; Si, Dong; Singharoy, Abhishek; Sobolev, Oleg V.; Terashi, Genki; Vaiana, Andrea C.; Vedithi, Sundeep C.; Verburgt, Jacob; Wang, Xiao; Warshamanage, Rangana; Winn, Martyn D.; Weyand, Simone; Yamashita, Keitaro; Zhao, Minglei; Schmid, Michael F.; Berman, Helen M.; Chiu, Wah

Enhancing cryo-EM structure prediction with DeepTracer and AlphaFold2 integration 使用DeepTracer和AlphaFold2集成增强cryo-em结构预测

BRIEFINGS IN BIOINFORMATICS

IF7.7

2024-04-12

OAAI

Chen, Jason; Zia, Ayisha; Luo, Albert; Meng, Hanze; Wang, Fengbin; Hou, Jie; Cao, Renzhi; Si, Dong

ComplexQA: a deep graph learning approach for protein complex structure assessment

BRIEFINGS IN BIOINFORMATICS

IF7.7

2023-10-31

PREAI

Zhang, Lei; Wang, Sheng; Hou, Jie; Si, Dong; Zhu, Junyong; Cao, Renzhi

Fast and automated protein-DNA/RNA macromolecular complex modeling from cryo-EM maps

BRIEFINGS IN BIOINFORMATICS

IF7.7

2023-01-22

OAAI

Nakamura, Andrew; Meng, Hanze; Zhao, Minglei; Wang, Fengbin; Hou, Jie; Cao, Renzhi; Si, Dong

Superiorization-inspired unrolled SART algorithm with U-Net generated perturbations for sparse-view and limited-angle CT reconstruction 具有u-net生成扰动的超受启发的展开SART算法，用于稀疏视图和有限角度CT重建

PHYSICS IN MEDICINE AND BIOLOGY

IF3.4

2022-12-07

PREAI

Jia, Yiran; McMichael, Noah; Mokarzel, Pedro; Thompson, Brandon; Si, Dong; Humphries, Thomas

Structure of Geobacter OmcZ filaments suggests extracellular cytochrome polymers evolved independently multiple times

ELIFE

IF0

2022-09-05

OAAI

Wang, Fengbin; Chan, Chi Ho; Suciu, Victor; Mustafa, Khawla; Ammend, Madeline; Si, Dong; Hochbaum, Allon, I; Egelman, Edward H.; Bond, Daniel R.

DeepTracer-ID: De novo protein identification from cryo-EM maps

BIOPHYSICAL JOURNAL

IF3.1

2022-08-01

OAAI

Chang, Luca; Wang, Fengbin; Connolly, Kiernan; Meng, Hanze; Su, Zhangli; Cvirkaite-Krupovic, Virginija; Krupovic, Mart; Egelman, Edward H.; Si, Dong

Recent Progress of Machine Learning in Gene Therapy 机器学习在基因治疗中的研究进展

CURRENT GENE THERAPY

IF3.3

2022-04-01

PREAI

Hunt, Cassandra; Montgomery, Sandra; Berkenpas, Joshua William; Sigafoos, Noel; Oakley, John Christian; Espinosa, Jacob; Justice, Nicola; Kishaba, Kiyomi; Hippe, Kyle; Si, Dong; Hou, Jie; Ding, Hui; Cao, Renzhi

ZoomQA: residue-level protein model accuracy estimation with machine learning on sequential and 3D structural features

BRIEFINGS IN BIOINFORMATICS

IF7.7

2021-09-22

OAAI

Hippe, Kyle; Lilley, Cade; Berkenpas, Joshua William; Pocha, Ciri Chandana; Kishaba, Kiyomi; Ding, Hui; Hou, Jie; Si, Dong; Cao, Renzhi

Artificial intelligence advances for de novo molecular structure modeling in cryo-electron microscopy 低温电子显微镜中从头分子结构建模的人工智能进展

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE

IF27

2021-05-15

OAAI

Si, Dong; Nakamura, Andrew; Tang, Runbang; Guan, Haowen; Hou, Jie; Firozi, Ammaar; Cao, Renzhi; Hippe, Kyle; Zhao, Minglei

A Raspberry Pi-Based Traumatic Brain Injury Detection System for Single-Channel Electroencephalogram

SENSORS

IF3.5

2021-04-15

OAAI

Dhillon, Navjodh Singh; Sutandi, Agustinus; Vishwanath, Manoj; Lim, Miranda M.; Cao, Hung; Si, Dong

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

NATURE METHODS

IF32.1

2021-02-04

OAAI

Lawson, Catherine L.; Kryshtafovych, Andriy; Adams, Paul D.; Afonine, Pavel, V; Baker, Matthew L.; Barad, Benjamin A.; Bond, Paul; Burnley, Tom; Cao, Renzhi; Cheng, Jianlin; Chojnowski, Grzegorz; Cowtan, Kevin; Dill, Ken A.; DiMaio, Frank; Farrell, Daniel P.; Fraser, James S.; Herzik, Mark A., Jr.; Hoh, Soon Wen; Hou, Jie; Hung, Li-Wei; Igaev, Maxim; Joseph, Agnel P.; Kihara, Daisuke; Kumar, Dilip; Mittal, Sumit; Monastyrskyy, Bohdan; Olek, Mateusz; Palmer, Colin M.; Patwardhan, Ardan; Perez, Alberto; Pfab, Jonas; Pintilie, Grigore D.; Richardson, Jane S.; Rosenthal, Peter B.; Sarkar, Daipayan; Schafer, Luisa U.; Schmid, Michael F.; Schroder, Gunnar F.; Shekhar, Mrinal; Si, Dong; Singharoy, Abishek; Terashi, Genki; Terwilliger, Thomas C.; Vaiana, Andrea; Wang, Liguo; Wang, Zhe; Wankowicz, Stephanie A.; Williams, Christopher J.; Winn, Martyn; Wu, Tianqi; Yu, Xiaodi; Zhang, Kaiming; Berman, Helen M.; Chiu, Wah

DeepTracer for fast de novo cryo-EM protein structure modeling and special studies on CoV-related complexes DeepTracer用于快速从头冷冻EM蛋白质结构建模和CoV相关复合物的特殊研究

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IF9.1

2020-12-23

109

OAAI

Pfab, Jonas; Phan, Nhut Minh; Si, Dong

Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density Maps 从高分辨率cryo-em密度图预测蛋白质骨架结构的深度学习

SCIENTIFIC REPORTS

IF3.9

2020-03-09

OAAI