YW

Yingze Wang

0000-0002-1706-3791

Behavior, Animalphysics.bio-phphysics.chem-phZebrafishAnxietycs.LGDisease Models, AnimalDrug DesignDrug DiscoveryDrug screening

On Valency

published · living versions

MoLRSI: A Recursive Self-Improving AI agent for Molecular Discovery

with Yikun Zhang, Xiwei Cheng, Mingze Yuan, Yu Zhang +13

1 version

W_ka3rjr2vv1 · current

Preprints & journals

21 papers in the corpus · 2021–2026

Terrestrial jumping assay for adult zebrafish as a potential tool to assess motor, affective and drug-evoked phenotypes.

Bai, Ruyue, Li, Zichen, Wang, Yimeng et al.

0 citations

425864882026Behavioural brain research. 2026;515:116414

Towards zebrafish models of personality disorders.

Cai, Huiling, Suo, Qinglu, Li, Qiuyin et al.

0 citations

425566462026Behavioural brain research. 2026;515:116406

TorchFF: A high-performance GPU-accelerated differentiable force field library.

Wang, Yingze, Abdullah, Aalim S, Mohanakrishnan, Rohith Srinivaas et al.

0 citations

425230442026The Journal of chemical physics. 2026;165(4)

Energetics of Noncovalent Interactions of Protein-Ligand Complexes for Drug Discovery.

Wang, Yingze, Shin, Dong Jun, Head-Gordon, Martin et al.

1 citation

423168342026Journal of chemical information and modeling. 2026;66(13):7722-7735

Overt physiological responses and atypical behavior evoked in adult zebrafish in the novel tank test by two acute 'survival' stressors.

Song, Yunzhe, Cui, Jiahao, Cai, Huiling et al.

3 citations

420197862026Behavioural processes. 2026;238:105381

LinkLlama: Enabling Large Language Model for Chemically Reasonable Linker Design.

Sun, Kunyang, Wang, Yingze, Purnomo, Justin et al.

0 citations

420396402026bioRxiv : the preprint server for biology. 2026

SynLlama: Generating Synthesizable Molecules and Their Analogs with Large Language Models.

Sun, Kunyang, Bagni, Dorian, Cavanagh, Joseph M et al.

18 citations

403219522025ArXiv. 2025

Improved Treatment of 1-4 Interactions in Force Fields for Molecular Dynamics Simulations.

Abdullah, Aalim S, Wang, Yingze, Menger, Maximilian F S J et al.

5 citations

411970202025Journal of chemical theory and computation. 2025;21(22):11669-11678

Polaris Challenge: Data-Driven Priors to Improve Docking for Pose Prediction.

Sun, Kunyang, Wang, Yingze, Purnomo, Justin et al.

1 citation

411460152026Journal of chemical information and modeling. 2025;65(21):12058-12067

dpdata: A Scalable Python Toolkit for Atomistic Machine Learning Data Sets.

Zeng, Jinzhe, Peng, Xingliang, Zhuang, Yong-Bin et al.

13 citations

411146682025Journal of chemical information and modeling. 2025;65(21):11497-11504

More Accurate Binding Free Energy Prediction Using Protein Homology and Ligand-Based Transfer Learning

Justin Purnomo, Caitlin Kim, Kunyang Sun et al.

0 citations

10.26434/chemrxiv-2025-2v8j52025ChemRxiv

Downregulation of Tra2α and Tra2β suppresses lipopolysaccharide-induced inflammation in macrophages by regulating MyD88 mRNA alternative splicing.

Fu, Yu, Zhang, Luyao, Wang, Yanjing et al.

0 citations

409862162026Molecular and cellular biochemistry. 2026;481(1):263-275

Assessing adult zebrafish despair-like behaviors in the small vertical cylinder immobility test (VCIT).

Wang, Jiyi, Bley, Vea, Jiang, Jiayou et al.

3 citations

409254162025Journal of neuroscience methods. 2025;424:110569

A Workflow to Create a High-Quality Protein-Ligand Binding Dataset for Training, Validation, and Prediction Tasks.

Wang, Yingze, Sun, Kunyang, Li, Jie et al.

25 citations

400933692026ArXiv. 2025

SRSF3 Knockdown Inhibits Lipopolysaccharide-Induced Inflammatory Response in Macrophages.

Fu, Yu, Wang, Yanjing, Zhang, Luyao et al.

9 citations

389210432024Current issues in molecular biology. 2024;46(6):6237-6247

Mining for Potent Inhibitors through Artificial Intelligence and Physics: A Unified Methodology for Ligand Based and Structure Based Drug Design.

Li, Jie, Zhang, Oufan, Sun, Kunyang et al.

6 citations

388430702024Journal of chemical information and modeling. 2024;64(24):9082-9097

Serine/Arginine-Rich Splicing Factor 7 Knockdown Inhibits Aerobic Glycolysis and Growth in HepG2 Cells by Regulating PKM2 Expression.

Shi, Weiye, Yao, Xu, Cao, Xueyu et al.

5 citations

387855692024Current issues in molecular biology. 2024;46(5):5023-5036

Leak Proof PDBBind: A Reorganized Dataset of Protein-Ligand Complexes for More Generalizable Binding Affinity Prediction.

Li, Jie, Guan, Xingyi, Zhang, Oufan et al.

22 citations

376450372026ArXiv. 2024

DMFF: An Open-Source Automatic Differentiable Platform for Molecular Force Field Development and Molecular Dynamics Simulation.

Wang, Xinyan, Li, Jichen, Yang, Lan et al.

49 citations

375893042023Journal of chemical theory and computation. 2023;19(17):5897-5909

DeePMD-kit v2: A software package for deep potential models.

Zeng, Jinzhe, Zhang, Duo, Lu, Denghui et al.

619 citations

375261632024The Journal of chemical physics. 2023;159(5)

Improving Molecular Pretraining with Complementary Featurizations

Yanqiao Zhu, Dingshuo Chen, Yuanqi Du et al.

1 citation

2209.15101v12022arXiv

Career total: 32 works. 21 are in this corpus.

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