HiSIF-DTA: A Hierarchical Semantic Information Fusion Framework for Drug-Target Affinity Prediction

Authors: Bi, X., Zhang, S., Ma, W., Jiang, H., Wei, Z.

Source: IEEE Journal of Biomedical and Health Informatics IEEE J. Biomed. Health Inform. Biomedical and Health Informatics, IEEE Journal of. 29(3):1579-1590 Mar, 2025

MTTSCL: protein subcellular localization prediction using multi-task learning

Authors: Yu, Liang, Wu, Xiang, Li, Yan, Huang, Zhaoyang, Liu, Ziqi

Source: 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Bioinformatics and Biomedicine (BIBM), 2024 IEEE International Conference on. :1308-1313 Dec, 2024

Relation: 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Protein Representation Learning with Sequence Information Embedding: Does it Always Lead to a Better Performance?

Authors: Tan, Yang, Zheng, Lirong, Zhong, Bozitao, Hong, Liang, Zhou, Bingxin

Source: 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Bioinformatics and Biomedicine (BIBM), 2024 IEEE International Conference on. :233-239 Dec, 2024

Relation: 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Clustering for Protein Representation Learning

Authors: Quan, Ruijie, Wang, Wenguan, Ma, Fan, Fan, Hehe, Yang, Yi

Source: 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) CVPR Computer Vision and Pattern Recognition (CVPR), 2024 IEEE/CVF Conference on. :319-329 Jun, 2024

Relation: 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)

Deep Manifold Transformation for Protein Representation Learning

Authors: Hu, Bozhen, Zang, Zelin, Tan, Cheng, Li, Stan Z.

Source: ICASSP 2024 - 2024 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) Acoustics, Speech and Signal Processing (ICASSP), ICASSP 2024 - 2024 IEEE International Conference on. :1801-1805 Apr, 2024

Relation: ICASSP 2024 - 2024 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)

CollaPPI: A Collaborative Learning Framework for Predicting Protein-Protein Interactions

Authors: Ma, W., Bi, X., Jiang, H., Zhang, S., Wei, Z.

Source: IEEE Journal of Biomedical and Health Informatics IEEE J. Biomed. Health Inform. Biomedical and Health Informatics, IEEE Journal of. 28(5):3167-3177 May, 2024

A Transferability-Based Method for Evaluating the Protein Representation Learning

Authors: Hu, F., Zhang, W., Huang, H., Li, W., Li, Y., Yin, P.

Source: IEEE Journal of Biomedical and Health Informatics IEEE J. Biomed. Health Inform. Biomedical and Health Informatics, IEEE Journal of. 28(5):3158-3166 May, 2024

TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks

Authors: Nourani, E., Asgari, E., McHardy, A.C., Mofrad, M.R.

Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics IEEE/ACM Trans. Comput. Biol. and Bioinf. Computational Biology and Bioinformatics, IEEE/ACM Transactions on. 19(6):3744-3753 Jan, 2022

IDRBP-PPCT: Identifying Nucleic Acid-Binding Proteins Based on Position-Specific Score Matrix and Position-Specific Frequency Matrix Cross Transformation

Authors: Wang, N., Zhang, J., Liu, B.

Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics IEEE/ACM Trans. Comput. Biol. and Bioinf. Computational Biology and Bioinformatics, IEEE/ACM Transactions on. 19(4):2284-2293 Aug, 2022

Learning protein language contrastive models with multi-knowledge representation

Authors: Xu, Wenjun ^{a, 1}, Xia, Yingchun ^{a, 1}, Sun, Bifan ^a, Zhao, Zihao ^a, Tang, Lianggui ^a, Zhou, Xiaobo ^{a, b}, Wang, Qingyong ^{a, b, ⁎}, Gu, Lichuan ^{a, b, c, ⁎}

Source: In Future Generation Computer Systems March 2025 164

Protein2Vec: Aligning Multiple PPI Networks with Representation Learning

Authors: Gao, J., Tian, L., Lv, T., Wang, J., Song, B., Hu, X.

Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics IEEE/ACM Trans. Comput. Biol. and Bioinf. Computational Biology and Bioinformatics, IEEE/ACM Transactions on. 18(1):240-249 Jan, 2021

AnnoPRO: a strategy for protein function annotation based on multi-scale protein representation and a hybrid deep learning of dual-path encoding

Authors: Lingyan Zheng, Shuiyang Shi, Mingkun Lu, Pan Fang, Ziqi Pan, Hongning Zhang, Zhimeng Zhou, Hanyu Zhang, Minjie Mou, Shijie Huang, Lin Tao, Weiqi Xia, Honglin Li, Zhenyu Zeng, Shun Zhang, Yuzong Chen, Zhaorong Li, Feng Zhu

Source: Genome Biology, Vol 25, Iss 1, Pp 1-22 (2024)

Subject Terms: Protein function annotation, Long-tail problem, Protein representation, Pre-training, LSTM, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/e654abfe23f9473fa0b7b7f2b439d1d8

Aligning Multiple PPI Networks with Representation Learning on Networks

Authors: Song, Bo, Gao, Jianliang, Du, Hongliang, Chen, Zheng, Hu, Xiaohua

Source: 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Bioinformatics and Biomedicine (BIBM), 2018 IEEE International Conference on. :136-141 Dec, 2018

Relation: 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

PSSM-PROREP: A Flexible Web Server for Generating Various Position Specific Score Matrix-derived Protein Representations

Authors: Yang, Runtao, Zhang, Chengjin, Zhang, Lina

Source: 2018 IEEE International Conference on Information and Automation (ICIA) Information and Automation (ICIA), 2018 IEEE International Conference on. :1524-1529 Aug, 2018

Relation: 2018 IEEE International Conference on Information and Automation (ICIA)

Drug-target binding affinity prediction using message passing neural network and self supervised learning

Authors: Leiming Xia, Lei Xu, Shourun Pan, Dongjiang Niu, Beiyi Zhang, Zhen Li

Source: BMC Genomics, Vol 24, Iss 1, Pp 1-11 (2023)

Subject Terms: Drug-target binding affinity, Self-supervised learning method, Molecular representation, Protein representation, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/26c1ebd462d94143a3947decb84b4afe

CysPresso: a classification model utilizing deep learning protein representations to predict recombinant expression of cysteine-dense peptides

Authors: Sébastien Ouellet, Larissa Ferguson, Angus Z. Lau, Tony K. Y. Lim

Source: BMC Bioinformatics, Vol 24, Iss 1, Pp 1-17 (2023)

Subject Terms: Protein representation, Recombinant expression, Cysteine-dense peptide, Knottin, Deep learning, AlphaFold, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/2ef221f1244a441880541c7820f01406

How to approach machine learning-based prediction of drug/compound–target interactions

Authors: Heval Atas Guvenilir, Tunca Doğan

Source: Journal of Cheminformatics, Vol 15, Iss 1, Pp 1-36 (2023)

Subject Terms: Drug discovery and repurposing, Drug–target interaction prediction, Protein descriptors, Learned protein embeddings, Protein representation learning, Benchmark analysis, Information technology, T58.5-58.64, Chemistry, QD1-999

File Description: electronic resource

Relation: https://doaj.org/toc/1758-2946

Access URL: https://doaj.org/article/c6682b1be6c2439097c1459f640060f5

A Multimodal Protein Representation Framework for Quantifying Transferability Across Biochemical Downstream Tasks

Authors: Fan Hu, Yishen Hu, Weihong Zhang, Huazhen Huang, Yi Pan, Peng Yin

Source: Advanced Science, Vol 10, Iss 22, Pp n/a-n/a (2023)

Subject Terms: protein representation, multi‐modal, transferability, downstream tasks, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2198-3844

Access URL: https://doaj.org/article/687d03d8b9834052aaa3fc3cac28ac6d

ROSS: A rapid protein structure alignment algorithm

Authors: Fadel, Ahmed S., Belal, Mohamed, Mostafa, Mostafa-Sami M.

Source: 2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology Computational Intelligence in Bioinformatics and Computational Biology, 2014 IEEE Conference on. :1-5 May, 2014

Relation: 2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)

Multimodal protein representation learning and target-aware variational auto-encoders for protein-binding ligand generation

Authors: Nhat Khang Ngo, Truong Son Hy

Source: Machine Learning: Science and Technology, Vol 5, Iss 2, p 025021 (2024)

Subject Terms: protein representation learning, protein-ligand binding, ligand generation, geometric deep learning, large language models, multimodal architecture, Computer engineering. Computer hardware, TK7885-7895, Electronic computers. Computer science, QA75.5-76.95

File Description: electronic resource

Relation: https://doaj.org/toc/2632-2153

Access URL: https://doaj.org/article/843fd2850fff4ec2bed14b7584fe2c2e