Yanxing Wang

Yanxing Wang

AMOEBA Force Field
Deep Learning
Biomolecular Simulation
Drug Discovery

Projects

Research Projects

Incorporation of Neural Networks into AMOEBA Force Field
Jun. 2022 - Present Advisor: Pengyu Ren @ The University of Texas at Austin

  • Aim for higher accuracy by using a neural network term in place of the current AMOEBA intramolecular terms;
  • Promising results seen with a preliminary model covering limited chemical elements;
  • Extension of the model to a broader range of chemical elements is ongoing;
  • Software development of Tinker9 is ongoing to improve the accessibility of the model to a broader community.

Large Scale Ab Initio Conformational Energy Profiling for Small Molecules
Jun. 2022 - Nov. 2022 Advisor: Pengyu Ren @ The University of Texas at Austin

  • Data-driven deep learning methods for force field development require high-quality geometry and energy data;
  • Hybrid protocol of GFN2-xTB geometry optimization followed by single-point energy calculations with high-level DFT achieves reliable results while being hundreds of times faster;
  • The protocol can be applied to a large dataset of small molecules to generate conformational energy profiles.

TF3P: Three-dimensional Force Fields Fingerprint Learned by Deep Capsular Network.
Nov. 2018 - May 2020 Advisor: Liangren Zhang, Zhenming Liu @ Peking University

  • Developed a new 3D fingerprint, TF3P, using the deep capsular network;
  • TF3P outperforms other fingerprints on retrieving similar targets by similar ligands.

DeepScaffold: A Comprehensive Tool for Scaffold-Directed Drug Discovery Using Deep Learning
Aug. 2018 - June. 2019 Advisor: Liangren Zhang, Zhenming Liu @ Peking University

  • Developed graph-based deep generative models for scaffold-based molecular derivatization;
  • Demonstrated the excellent performance of the model using molecular docking.

Discovery of Novel Inhibitors of Glycogen Synthase Kinase-3$\alpha$ for Treatment of Acute Myeloid Leukemia
Aug. 2017 - Dec. 2018 Advisor: Liangren Zhang, Zhenming Liu @ Peking University

  • Identified a novel chemical series of GSK-3$\alpha$ inhibitors by structure-based virtual screening;
  • Summarized the structure-activity relationship (SAR) by similarity search;
  • Demonstrate their excellent anti-leukemia effects in vitro;
  • Elucidated the SAR by molecular docking and dynamics simulations.

QSAR of Acylphloroglucinol-Based Meroterpenoid Inhibitors of KSHV From Hypericum Japonicum
Jan. 2018 - Mar. 2018 Advisor: Liangren Zhang, Zhenming Liu @ Peking University

  • Field-based 3D QSAR of KSHV inhibitors extracted from Hypericum japonicum.

Discovery of New GSK-3$\beta$ Inhibitors Through Structure-Based Virtual Screening
Apr. 2017 - Aug. 2017 Advisor: Liangren Zhang, Zhenming Liu @ Peking University

  • Binding modes prediction by molecular docking and dynamics simulations.

Activating Thioesterification in Synthesis of Peptidyl Thioesters by Peroglutamyl Imide
Feb. 2017 - Mar. 2017 Advisor: Suwei Dong @ Peking University

  • Synthesis of peptide-glutamylhydrazine-resin complex.

Internal Activation of Peptidyl Selenoprolyl Thioester in Peptide Ligation in Pro-Cys Site
July 2016 - Jan. 2017 Advisor: Suwei Dong @ Peking University

  • Synthesis of $\gamma$-selenoproline;
  • Synthesis of selenocystine;
  • Synthesis of west-side peptidyl thioesters.

Synthesis of Proline Derivatives
July 2015 - Aug. 2016 Advisor: Suwei Dong @ Peking University

  • Lab skill training on organic synthesis.