Bridging AI and biological discovery: novel applications of language models in enzyme prediction and protein classification = AI와 생물학적 발견의 연결: 효소 예측 및 단백질 분류에서 언어 기반 딥러닝 모델의 적용|RISS 상세보기

목차 (Table of Contents)

Content
Abstract 3
Chapter 1. Introduction 6
A. Bioinformatics with Biological Big Data and AI Advances 6
B. An Overview of Artificial Intelligence 7

Content
Abstract 3
Chapter 1. Introduction 6
A. Bioinformatics with Biological Big Data and AI Advances 6
B. An Overview of Artificial Intelligence 7
C. Machine Learning and Deep Learning in Biology 11
D. Application of Deep Learning in this Research 15
Chapter 2. Prediction Model for Specific Enzyme Reaction: SPRINT
(Substrate-Product-Reaction Inference with deep Neural neT) 17
A. Background 17
1) Overview of Enzyme Reaction Screening 17
2) Prior Research 19
3) Objective 20
B. Material and Methods 21
1) Data Collection from Three Reaction Databases 21
2) Data Curation and Preprocessing for SPRINT 22
3) Model Architecture and Training Procedures 24
4) Data for Case Study: Plastic DB 26
5) Methodologies for Validation and Evaluation 28
C. Results 29
1) Predictive Performance of SPRINT 29
2) Model Performance by Enzyme EC Classification 30
3) Evaluation Across Protein Sequence Identity 31
4) External data validation: Plastic DB (PETase) 32
Chapter 3. Prediction Model for Enzyme Turnover Number: KITCAT
(Kinetic Inference Tool for Catalysis Activity Turnover rate) 35
A. Background 35
1) Description of kcat Parameter in Enzyme Kinetics 35
2) Prior Research 36
3) Objective 37
B. Material and Methods 38
1) Collection of kcat Dataset 38
2) Data Preprocessing for KITCAT 41
3) Model Structure and Training Methods 41
4) Methodologies for Validation and Evaluation 44
C. Results 46
1) Predictive Performance of KITCAT 46
2) Model Performance by Enzyme EC Classification 47
3) Evaluation Across Protein Sequence Identity 49
4) Model Comparison with Another Research 49
Chapter 4. Concluding Remarks and Further Works 51
A. Discussion on the Application of Biological Data Using Deep
Learning 51
B. Conclusion 54
References 56
국문초록 64

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Bridging AI and biological discovery: novel applications of language models in enzyme prediction and protein classification = AI와 생물학적 발견의 연결: 효소 예측 및 단백질 분류에서 언어 기반 딥러닝 모델의 적용

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