Pre-Training of Equivariant Graph Matching Networks with Conformation Flexibility for Drug Binding

Fang Wu, Shuting Jin, Yinghui Jiang, Xurui Jin, Bowen Tang, Zhangming Niu, Xiangrong Liu, Qiang Zhang, Xiangxiang Zeng, Stan Z. Li

Research output: Contribution to journalArticlepeer-review

20 Scopus citations

Abstract

The latest biological findings observe that the motionless “lock-and-key” theory is not generally applicable and that changes in atomic sites and binding pose can provide important information for understanding drug binding. However, the computational expenditure limits the growth of protein trajectory-related studies, thus hindering the possibility of supervised learning. A spatial-temporal pre-training method based on the modified equivariant graph matching networks, dubbed ProtMD which has two specially designed self-supervised learning tasks: atom-level prompt-based denoising generative task and conformation-level snapshot ordering task to seize the flexibility information inside molecular dynamics (MD) trajectories with very fine temporal resolutions is presented. The ProtMD can grant the encoder network the capacity to capture the time-dependent geometric mobility of conformations along MD trajectories. Two downstream tasks are chosen to verify the effectiveness of ProtMD through linear detection and task-specific fine-tuning. A huge improvement from current state-of-the-art methods, with a decrease of 4.3% in root mean square error for the binding affinity problem and an average increase of 13.8% in the area under receiver operating characteristic curve and the area under the precision-recall curve for the ligand efficacy problem is observed. The results demonstrate a strong correlation between the magnitude of conformation's motion in the 3D space and the strength with which the ligand binds with its receptor.

Original languageEnglish
Article number2203796
JournalAdvanced Science
Volume9
Issue number33
DOIs
StatePublished - 24 Nov 2022
Externally publishedYes

Keywords

  • deep learning
  • drug binding
  • molecular dynamics
  • pre-training method

ASJC Scopus subject areas

  • Medicine (miscellaneous)
  • General Chemical Engineering
  • General Materials Science
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • General Engineering
  • General Physics and Astronomy

Fingerprint

Dive into the research topics of 'Pre-Training of Equivariant Graph Matching Networks with Conformation Flexibility for Drug Binding'. Together they form a unique fingerprint.

Cite this