the importance of assessing the <strongstyle="color: #8a61ad;">generalization capability</strong> when researching model algorithms in the protein design realm. She noted that some current models, such as DLKcat, suffer from
weak generalization abilities. In response to Professor Cui's suggestions, we systematically worked on improvements, addressing each point.
<strongstyle="color: #8a61ad;">The role:</strong> Professor Xie has extensive experience in both academia and industry, providing us with guidance on the
direction of our research topics and technical approach.
</p>
<p>
<strongstyle="color: #8a61ad;">Profile:</strong> Professor Xie Zhen is a professor at the Center for Synthetic and Systems Biology at Tsinghua University,
as well as the founder and chief scientist of Syngentech.
<strongstyle="color: #8a61ad;">The role:</strong> Professor Xie has extensive experience in both academia and industry, providing us with guidance on the
direction of our research topics and technical approach.
</p>
<p>
<strongstyle="color: #8a61ad;">Profile:</strong> Professor Xie Zhen is a professor at the Center for Synthetic and Systems Biology at Tsinghua University,
as well as the founder and chief scientist of Syngentech.
</p>
<p>
After communicating with several protein design and optimization companies, we have transitioned our focus from protein optimization design to antibody optimization design. However,
we haven't yet identified a specific task. Before establishing a concrete plan, we learned about recent breakthroughs in using artificial intelligence for de novo antibody design and
...
...
@@ -320,43 +313,29 @@
We aim to delve deeper into using machine learning and deep learning tools to address challenges in this domain, incorporating considerations for antibody structures. When we propose a preliminary
technical route. We once again communicated with Professor Xie, who acknowledged our idea and expressed anticipation for us to construct a comprehensive automated tool and introduce innovative aspects.
<strongstyle="color: #8a61ad;">The role:</strong> Ziting Zhang provided us with an in-depth introduction to immunological knowledge related to antibodies. As a researcher in the field of immunology,
she expressed that our project holds significant meaning.
</p>
<p>
<strongstyle="color: #8a61ad;">Profile:</strong> Ziting Zhang is a Ph.D. student in Bioinformatics at Tsinghua University, and she possesses unique insights in immunology.
Moreover, Zhang Ziting was a member of the Tsinghua-A team in 2020.
<strongstyle="color: #8a61ad;">The role:</strong> Ziting Zhang provided us with an in-depth introduction to immunological knowledge related to antibodies. As a researcher in the field of immunology,
she expressed that our project holds significant meaning.
</p>
<p>
<strongstyle="color: #8a61ad;">Profile:</strong> Ziting Zhang is a Ph.D. student in Bioinformatics at Tsinghua University, and she possesses unique insights in immunology.
Moreover, Zhang Ziting was a member of the Tsinghua-A team in 2020.
</p>
<p>
Ziting Zhang also pursued her undergraduate studies in the Department of Automation at Tsinghua University. Currently, her research interests converge at the intersection of bioinformatics.
Through exchanges with her, we gained a deeper understanding of immunological knowledge related to antibodies and how to leverage the advantages of our team's background in information.
She believes that our team's project this year holds considerable meaningand looks forward to the richness and experience of the Tsinghua-A team participating in the iGEM competition again after three years.
<strongstyle="color: #8a61ad;">The role:</strong> Xiangzhe Kong provided us with a lot of advice on CDR algorithm design, which helped us to understand the current situation
in the field of antibody CDR design in the international arena.
</p>
<p>
<strongstyle="color: #8a61ad;">Profile:</strong> Xiangzhe Kong is a Ph.D. student at the Department of Computer Science, Tsinghua University, and the author of "Conditional Antibody Design as 3D Equivariant Graph Translation"
(ICLR 2023 Outstanding Paper Honorable Mention). He possesses extensive experience in computational de novo antibody design, especially CDR design.
<strongstyle="color: #8a61ad;">The role:</strong> Xiangzhe Kong provided us with a lot of advice on CDR algorithm design, which helped us to understand the current situation
in the field of antibody CDR design in the international arena.
</p>
<p>
<strongstyle="color: #8a61ad;">Profile:</strong> Xiangzhe Kong is a Ph.D. student at the Department of Computer Science, Tsinghua University, and the author of "Conditional Antibody Design as 3D Equivariant Graph Translation"
(ICLR 2023 Outstanding Paper Honorable Mention). He possesses extensive experience in computational de novo antibody design, especially CDR design.
</p>
<p>
Antibodies are divided into constant and variable regions, within the variable region are the high-frequency mutated CDR regions (where the antigen comes into contact with the antibody), and the relatively conserved and
species-specific FR regions. As the antigen-antibody binding region, CDR has garnered significant attention in the academic field, and there are a lot of difficulties in the design of CDR region, especially CDR-H3 loop.
...
...
@@ -364,21 +343,14 @@
essential aspects of designing CDR regions from sequence to structure, and learned about some details of Equivariant Graph Neural Networks (EGNs). Through this exchange, we gained insights into the unique characteristics of
CDR regions and came to a full realization of the high variability of the CDR H3 loop. Based on this understanding, we made improvements to the structural scoring aspect of our project.
<strongstyle="color: #8a61ad;">The role:</strong> Wenbo Guo gave us valuable suggestions on our algorithms.
</p>
<p>
<strongstyle="color: #8a61ad;">Profile:</strong> Wenbo Guo is a postdoctoral fellow in the bioinformatics direction at Tsinghua University, and has worked on classifying and annotating rare cell types using
OCLR (One Class Logistic Regression) promoted by One Class classifier.
<strongstyle="color: #8a61ad;">The role:</strong> Wenbo Guo gave us valuable suggestions on our algorithms.
</p>
<p>
<strongstyle="color: #8a61ad;">Profile:</strong> Wenbo Guo is a postdoctoral fellow in the bioinformatics direction at Tsinghua University, and has worked on classifying and annotating rare cell types using
OCLR (One Class Logistic Regression) promoted by One Class classifier.
</p>
<p>
Since we apply One Class approach to scoring antibody sequences from rare species, we introduced our project and consulted with Dr. Guo about the key advantages of the one-class approach. Dr. Guo noted that the approach exhibits excellent scalability,
making it highly suitable for our application scenario. Additionally, we also sought advice from Zeyu Chen, who is a Ph.D. student from the same research group. Dr. Chen recommended that we first experiment with methods such as SVM one class and IsolationForest,
