GNN-based Antibody Structure Prediction using Quaternion and Euler Angle Combined Representation

Young Han Son; Dong Hee Shin; Ji Wung Han; Seong Hyeon Won; Tae Eui Kam

doi:10.1109/ICCE-Asia57006.2022.9954877

GNN-based Antibody Structure Prediction using Quaternion and Euler Angle Combined Representation

Young Han Son, Dong Hee Shin, Ji Wung Han, Seong Hyeon Won, Tae Eui Kam

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

2 Citations (Scopus)

Abstract

In recent years, antibodies have gained much attention because they are immune system proteins playing essential roles in vaccine development. Since the 3D structures of the proteins are related to various biological interactions, the importance of 3D protein structures has been highlighted from various researches and proper representation of orientations has become a significant issue in antibody structure prediction tasks. In this paper, we use the combination of Quaternion and Euler angle methods to obtain a rich representation of the rotation between orientations. The main advantage of the method is that both Quaternion and Euler angle methods can compensate for each other to achieve higher interpretability and expressivity than the single use each method. In the experiment, we compare the results of the proposed method to the competing method, and the experimental results show further improvement in Root Mean Square Deviation (RMSD) up to 4.92%, demonstrating the effectiveness and robustness of our proposed method.

Original language	English
Title of host publication	2022 IEEE International Conference on Consumer Electronics-Asia, ICCE-Asia 2022
Publisher	Institute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)	9781665464345
DOIs	https://doi.org/10.1109/ICCE-Asia57006.2022.9954877
Publication status	Published - 2022
Event	2022 IEEE International Conference on Consumer Electronics-Asia, ICCE-Asia 2022 - Yeosu, Korea, Republic of Duration: 2022 Oct 26 → 2022 Oct 28

Publication series

Name	2022 IEEE International Conference on Consumer Electronics-Asia, ICCE-Asia 2022

Conference

Conference	2022 IEEE International Conference on Consumer Electronics-Asia, ICCE-Asia 2022
Country/Territory	Korea, Republic of
City	Yeosu
Period	22/10/26 → 22/10/28

Bibliographical note

Funding Information:
This work was supported by Institute of Information and communications Technology Planning and Evaluation (IITP) grant funded by the Korea government(MSIT) (No. 2019-0-00079, Artificial Intelligence Graduate School Program(Korea University), National Research Foundation of Korea (NRF) grant funded by the Korea government(MSIT) (No. 2020R1C1C1013830, No. 2020R1A4A1018309). This research was also supported by National Research Foundation (NRF), Korea, under project BK21 FOUR operated by the Center for Teaching and Learning of Korea University

Funding Information:
This work was supported by Institute of Information & communications Technology Planning & Evaluation (IITP) grant funded by the Korea government(MSIT) (No. 2019-0-00079, Artificial Intelligence Graduate School Program(Korea University), National Research Foundation of Korea (NRF) grant funded by the Korea government(MSIT) (No. 2020R1C1C1013830, No. 2020R1A4A1018309). This research was also supported by National Research Foundation (NRF), Korea, under project BK21 FOUR operated by the Center for Teaching and Learning of Korea University.

Publisher Copyright:
© 2022 IEEE.

Keywords

3D structure prediction
Antibody
Euler angle
GNN
Quaternion
Rotation representation

ASJC Scopus subject areas

Computer Science Applications
Electrical and Electronic Engineering
Media Technology
Instrumentation

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1109/ICCE-Asia57006.2022.9954877

Cite this

Son, Y. H., Shin, D. H., Han, J. W., Won, S. H., & Kam, T. E. (2022). GNN-based Antibody Structure Prediction using Quaternion and Euler Angle Combined Representation. In 2022 IEEE International Conference on Consumer Electronics-Asia, ICCE-Asia 2022 (2022 IEEE International Conference on Consumer Electronics-Asia, ICCE-Asia 2022). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ICCE-Asia57006.2022.9954877

GNN-based Antibody Structure Prediction using Quaternion and Euler Angle Combined Representation. / Son, Young Han; Shin, Dong Hee; Han, Ji Wung et al.
2022 IEEE International Conference on Consumer Electronics-Asia, ICCE-Asia 2022. Institute of Electrical and Electronics Engineers Inc., 2022. (2022 IEEE International Conference on Consumer Electronics-Asia, ICCE-Asia 2022).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Son, YH, Shin, DH, Han, JW, Won, SH & Kam, TE 2022, GNN-based Antibody Structure Prediction using Quaternion and Euler Angle Combined Representation. in 2022 IEEE International Conference on Consumer Electronics-Asia, ICCE-Asia 2022. 2022 IEEE International Conference on Consumer Electronics-Asia, ICCE-Asia 2022, Institute of Electrical and Electronics Engineers Inc., 2022 IEEE International Conference on Consumer Electronics-Asia, ICCE-Asia 2022, Yeosu, Korea, Republic of, 22/10/26. https://doi.org/10.1109/ICCE-Asia57006.2022.9954877

Son YH, Shin DH, Han JW, Won SH, Kam TE. GNN-based Antibody Structure Prediction using Quaternion and Euler Angle Combined Representation. In 2022 IEEE International Conference on Consumer Electronics-Asia, ICCE-Asia 2022. Institute of Electrical and Electronics Engineers Inc. 2022. (2022 IEEE International Conference on Consumer Electronics-Asia, ICCE-Asia 2022). doi: 10.1109/ICCE-Asia57006.2022.9954877

Son, Young Han ; Shin, Dong Hee ; Han, Ji Wung et al. / GNN-based Antibody Structure Prediction using Quaternion and Euler Angle Combined Representation. 2022 IEEE International Conference on Consumer Electronics-Asia, ICCE-Asia 2022. Institute of Electrical and Electronics Engineers Inc., 2022. (2022 IEEE International Conference on Consumer Electronics-Asia, ICCE-Asia 2022).

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title = "GNN-based Antibody Structure Prediction using Quaternion and Euler Angle Combined Representation",

abstract = "In recent years, antibodies have gained much attention because they are immune system proteins playing essential roles in vaccine development. Since the 3D structures of the proteins are related to various biological interactions, the importance of 3D protein structures has been highlighted from various researches and proper representation of orientations has become a significant issue in antibody structure prediction tasks. In this paper, we use the combination of Quaternion and Euler angle methods to obtain a rich representation of the rotation between orientations. The main advantage of the method is that both Quaternion and Euler angle methods can compensate for each other to achieve higher interpretability and expressivity than the single use each method. In the experiment, we compare the results of the proposed method to the competing method, and the experimental results show further improvement in Root Mean Square Deviation (RMSD) up to 4.92%, demonstrating the effectiveness and robustness of our proposed method.",

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note = "Funding Information: This work was supported by Institute of Information and communications Technology Planning and Evaluation (IITP) grant funded by the Korea government(MSIT) (No. 2019-0-00079, Artificial Intelligence Graduate School Program(Korea University), National Research Foundation of Korea (NRF) grant funded by the Korea government(MSIT) (No. 2020R1C1C1013830, No. 2020R1A4A1018309). This research was also supported by National Research Foundation (NRF), Korea, under project BK21 FOUR operated by the Center for Teaching and Learning of Korea University Funding Information: This work was supported by Institute of Information & communications Technology Planning & Evaluation (IITP) grant funded by the Korea government(MSIT) (No. 2019-0-00079, Artificial Intelligence Graduate School Program(Korea University), National Research Foundation of Korea (NRF) grant funded by the Korea government(MSIT) (No. 2020R1C1C1013830, No. 2020R1A4A1018309). This research was also supported by National Research Foundation (NRF), Korea, under project BK21 FOUR operated by the Center for Teaching and Learning of Korea University. Publisher Copyright: {\textcopyright} 2022 IEEE.; 2022 IEEE International Conference on Consumer Electronics-Asia, ICCE-Asia 2022 ; Conference date: 26-10-2022 Through 28-10-2022",

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AU - Son, Young Han

AU - Shin, Dong Hee

AU - Han, Ji Wung

AU - Won, Seong Hyeon

AU - Kam, Tae Eui

N1 - Funding Information: This work was supported by Institute of Information and communications Technology Planning and Evaluation (IITP) grant funded by the Korea government(MSIT) (No. 2019-0-00079, Artificial Intelligence Graduate School Program(Korea University), National Research Foundation of Korea (NRF) grant funded by the Korea government(MSIT) (No. 2020R1C1C1013830, No. 2020R1A4A1018309). This research was also supported by National Research Foundation (NRF), Korea, under project BK21 FOUR operated by the Center for Teaching and Learning of Korea University Funding Information: This work was supported by Institute of Information & communications Technology Planning & Evaluation (IITP) grant funded by the Korea government(MSIT) (No. 2019-0-00079, Artificial Intelligence Graduate School Program(Korea University), National Research Foundation of Korea (NRF) grant funded by the Korea government(MSIT) (No. 2020R1C1C1013830, No. 2020R1A4A1018309). This research was also supported by National Research Foundation (NRF), Korea, under project BK21 FOUR operated by the Center for Teaching and Learning of Korea University. Publisher Copyright: © 2022 IEEE.

PY - 2022

Y1 - 2022

N2 - In recent years, antibodies have gained much attention because they are immune system proteins playing essential roles in vaccine development. Since the 3D structures of the proteins are related to various biological interactions, the importance of 3D protein structures has been highlighted from various researches and proper representation of orientations has become a significant issue in antibody structure prediction tasks. In this paper, we use the combination of Quaternion and Euler angle methods to obtain a rich representation of the rotation between orientations. The main advantage of the method is that both Quaternion and Euler angle methods can compensate for each other to achieve higher interpretability and expressivity than the single use each method. In the experiment, we compare the results of the proposed method to the competing method, and the experimental results show further improvement in Root Mean Square Deviation (RMSD) up to 4.92%, demonstrating the effectiveness and robustness of our proposed method.

AB - In recent years, antibodies have gained much attention because they are immune system proteins playing essential roles in vaccine development. Since the 3D structures of the proteins are related to various biological interactions, the importance of 3D protein structures has been highlighted from various researches and proper representation of orientations has become a significant issue in antibody structure prediction tasks. In this paper, we use the combination of Quaternion and Euler angle methods to obtain a rich representation of the rotation between orientations. The main advantage of the method is that both Quaternion and Euler angle methods can compensate for each other to achieve higher interpretability and expressivity than the single use each method. In the experiment, we compare the results of the proposed method to the competing method, and the experimental results show further improvement in Root Mean Square Deviation (RMSD) up to 4.92%, demonstrating the effectiveness and robustness of our proposed method.

KW - 3D structure prediction

KW - Antibody

KW - Euler angle

KW - GNN

KW - Quaternion

KW - Rotation representation

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BT - 2022 IEEE International Conference on Consumer Electronics-Asia, ICCE-Asia 2022

PB - Institute of Electrical and Electronics Engineers Inc.

T2 - 2022 IEEE International Conference on Consumer Electronics-Asia, ICCE-Asia 2022

Y2 - 26 October 2022 through 28 October 2022

ER -

GNN-based Antibody Structure Prediction using Quaternion and Euler Angle Combined Representation

Abstract

Publication series

Conference

Bibliographical note

Keywords

ASJC Scopus subject areas

UN SDGs

Access to Document

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