Digital Library[ Search Result ]
Pretrained Large Language Model-based Drug-Target Binding Affinity Prediction for Mutated Proteins
Taeung Song, Jin Hyuk Kim, Hyeon Jun Park, Jonghwan Choi
http://doi.org/10.5626/JOK.2025.52.6.539
Drug development is a costly and time-consuming process. Accurately predicting the impact of protein mutations on drug-target binding affinity remains a major challenge. Previous studies have utilized long short-term memory (LSTM) and transformer models for amino acid sequence processing. However, LSTMs suffer from long-sequence dependency issues, while transformers face high computational costs. In contrast, pretrained large language models (pLLMs) excel in handling long sequences, yet prompt-based approaches alone are insufficient for accurate binding affinity prediction. This study proposed a method that could leverage pLLMs to analyze protein structural data, transform it into embedding vectors, and use a separate machine learning model for numerical binding affinity prediction. Experimental results demonstrated that the proposed approach outperformed conventional LSTM and prompt-based methods, achieving lower root mean square error (RMSE) and higher Pearson correlation coefficient (PCC), particularly in mutation-specific predictions. Additionally, performance analysis of pLLM quantization confirmed that the method maintained sufficient accuracy with reduced computational cost.
AttDRP: Attention Mechanism-based Model for Anti-Cancer Drug Response Prediction
Jonghwan Choi, Sangmin Seo, Sanghyun Park
http://doi.org/10.5626/JOK.2021.48.6.713
Resistance to anti-cancer drugs makes chemotherapy ineffective for cancer patients. Drug resistance is caused by genetic alterations in cancer cells. Many studies have investigated drug responses of diverse cancer cell lines to various anti-cancer drugs to understand drug response mechanisms. Existing studies have proposed machine learning models for drug response prediction to find effective anti-cancer drugs. However, currently there are no models to learn the relationship between anticancer drugs and genes to improve the prediction accuracy. In this paper, we proposed a predictive model AttDRP that could identify important genes associated with anti-cancer drugs and predict drug responses based on identified genes. AttDRP exhibited better predictive accuracy than existing models and we found that the attention scores of AttDRP could be effective tools to analyze molecular structures of anticancer drugs. We hope that our proposed method would contribute to the development of precision medicine for effective chemotherapy. Resistance to anti-cancer drugs makes chemotherapy ineffective for cancer patients. Drug resistance is caused by genetic alterations in cancer cells. Many studies have investigated drug responses of diverse cancer cell lines to various anti-cancer drugs to understand drug response mechanisms. Existing studies have proposed machine learning models for drug response prediction to find effective anti-cancer drugs. However, currently there are no models to learn the relationship between anticancer drugs and genes to improve the prediction accuracy. In this paper, we proposed a predictive model AttDRP that could identify important genes associated with anti-cancer drugs and predict drug responses based on identified genes. AttDRP exhibited better predictive accuracy than existing models and we found that the attention scores of AttDRP could be effective tools to analyze molecular structures of anticancer drugs.
Identification of Heterogeneous Prognostic Genes and Prediction of Cancer Outcome using PageRank
http://doi.org/10.5626/JOK.2018.45.1.61
The identification of genes that contribute to the prediction of prognosis in patients with cancer is one of the challenges in providing appropriate therapies. To find the prognostic genes, several classification models using gene expression data have been proposed. However, the prediction accuracy of cancer prognosis is limited due to the heterogeneity of cancer. In this paper, we integrate microarray data with biological network data using a modified PageRank algorithm to identify prognostic genes. We also predict the prognosis of patients with 6 cancer types (including breast carcinoma) using the K-Nearest Neighbor algorithm. Before we apply the modified PageRank, we separate samples by K-Means clustering to address the heterogeneity of cancer. The proposed algorithm showed better performance than traditional algorithms for prognosis. We were also able to identify cluster-specific biological processes using GO enrichment analysis.
Search
Journal of KIISE
- ISSN : 2383-630X(Print)
- ISSN : 2383-6296(Electronic)
- KCI Accredited Journal
Editorial Office
- Tel. +82-2-588-9240
- Fax. +82-2-521-1352
- E-mail. chwoo@kiise.or.kr