Dong Liu

ORCID: 0000-0002-6967-3348
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About
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Research Areas
  • Protein Structure and Dynamics
  • Enzyme Structure and Function
  • Cardiac electrophysiology and arrhythmias
  • Microbial metabolism and enzyme function
  • Ion channel regulation and function
  • Insect Resistance and Genetics
  • Protein Hydrolysis and Bioactive Peptides
  • Machine Learning in Materials Science
  • RNA and protein synthesis mechanisms
  • Pharmacological Effects of Natural Compounds
  • Machine Learning in Bioinformatics
  • Electromagnetic wave absorption materials
  • Biochemical Acid Research Studies
  • Magnetic Properties and Synthesis of Ferrites
  • Nicotinic Acetylcholine Receptors Study
  • Computational Drug Discovery Methods
  • Studies on Chitinases and Chitosanases
  • Ginger and Zingiberaceae research
  • Cell Image Analysis Techniques
  • Ginseng Biological Effects and Applications
  • Metalloenzymes and iron-sulfur proteins
  • Planarian Biology and Electrostimulation
  • Genetics, Bioinformatics, and Biomedical Research
  • Bioactive Natural Diterpenoids Research
  • Advancements in Battery Materials

Jiangxi Academy of Sciences
2024

Zhejiang University of Technology
2014-2024

Shandong Jiaotong University
2023

Sun Yat-sen University
2022

Peking Union Medical College Hospital
2017

Amgen (United States)
2012-2016

Shenzhen Polytechnic
2009-2016

Peking University
2011

Intel (United States)
2009

Nankai University
2009

Abstract Corneal injury can lead to severe vision impairment or even blindness. Although numerous methods are developed accelerate corneal wound healing, most of them passive treatments that rarely participate in controlling endogenous cell behaviors incompatible with nontransparent bandage. In this work, a wireless‐powered electrical bandage contact lens (EBCL) is generate localized external electric field healing and recovery. The wireless stimulation circuit employed flower‐shaped layout...

10.1002/advs.202202506 article EN cc-by Advanced Science 2022-09-08

Abstract This article reports and analyzes the results of protein complex model accuracy estimation by our methods (DeepUMQA3 GraphGPSM) in 15th Critical Assessment techniques for Structure Prediction (CASP15). The new deep learning‐based multimeric are proposed based on ensemble three‐level features coupling with residual/graph neural networks. For input model, we describe it from three levels: overall features, intra‐monomer inter‐monomer features. We designed an ultrafast shape...

10.1002/prot.26564 article EN Proteins Structure Function and Bioinformatics 2023-08-08

<ns4:p>Identification of small and large molecule pain therapeutics that target the genetically validated voltage-gated sodium channel Na<ns4:sub>V</ns4:sub>1.7 is a challenging endeavor under vigorous pursuit. The monoclonal antibody SVmab1 was recently published to bind DII voltage sensor domain block human currents in heterologous cells. We produced purified protein based on publically available sequence information, evaluated its activity battery binding functional assays. Herein, we...

10.12688/f1000research.9918.1 preprint EN cc-by F1000Research 2016-11-25

BRD9 and TAF1(2) have been regarded as significant targets of drug design for clinically treating acute myeloid leukemia, malignancies, inflammatory diseases. In this study, multiple short molecular dynamics simulations combined with the mechanics generalized Born surface area method were employed to investigate binding selectivity three ligands, 67B, 67C, 69G, BRD9/TAF1(2) IC50 values 230/59 nM, 1400/46 160/410 respectively. The computed free energies from MM-GBSA displayed good...

10.3390/molecules28062583 article EN cc-by Molecules 2023-03-12

Model quality assessment is a crucial part of protein structure prediction and gateway to proper usage models in biomedical applications. Many methods have been proposed for assessing the structural monomers, but few evaluating complex models. As becomes new challenge, there an urgent need model that can accurately assess accuracy interface residues structures.Here, we present DeepUMQA3, web server structures using deep neural networks. For input structure, features are extracted from three...

10.1093/bioinformatics/btad591 article EN cc-by Bioinformatics 2023-09-21

An antihypertensive peptide, Lys-Val-Leu-Pro-Val-Pro (KVLPVP), can reduce blood pressure in hypertensive rats after being orally administered. In this study, the transepithelial transport of intact KVLPVP was examined by Caco-2 monolayers. The results were as follows: (i) flux not saturable for apical (AP) to basolateral (BL) or BL-AP when concentration 1–8 mm. (ii) Sodium deoxycholate loosened tight junction cells and significantly improved process. (iii) Phenylarsine oxide, a transcytotic...

10.1271/bbb.80473 article EN Bioscience Biotechnology and Biochemistry 2009-02-23

The roots of Panax ginseng (ginseng) have been extensively used in traditional Chinese medicine. However, herb-drug interactions between and other co-administered drugs are not fully understood concerning the effect on drug metabolism clearance. current study aimed to elucidate total ginsenosides, a typical extract, regulation Cyp1a2, key enzyme regulate under normal inflammatory conditions mice. Female C57BL/6J mice treated with vehicle lipopolysaccharide (LPS) were intragastrically...

10.1021/acs.jafc.5b06170 article EN Journal of Agricultural and Food Chemistry 2016-02-28

HMMer is a widely-used bioinformatics software package that uses profile Hidden Markov Models (HMMs) to model the primary structure consensus of family protein or nucleic acid sequences. However, with rapid growth both sequence and databases, it more time-consuming run on traditional computer architecture. With development modern field programmable gate array (FPGA) technology, applications can be accelerated using CPU-FPGA cooperative system by mapping computational-intensive work onto...

10.1145/1508128.1508193 article EN 2009-02-22

In this work, the influence of Ca addition on power loss MnZn ferrites was investigated. Mn–Zn were prepared by conventional oxide ceramic process from calcined powders different particle sizes in equilibrium sintering atmosphere. It has been found that optimal amount varies for synthesized using size.

10.4028/www.scientific.net/msf.787.362 article EN Materials science forum 2014-04-01

This article reports and analyzes the results of protein complex model accuracy estimation by our methods (DeepUMQA3 GraphGPSM) in 15 Critical Assessment techniques for Structure Prediction (CASP15). The new deep learning-based multimeric are proposed based on ensemble three level features coupling with residual/graph neural networks. For input model, we describe it from levels: overall features, intra-monomer inter-monomer features. We designed an ultrafast shape recognition (USR) to...

10.22541/au.168170994.40559232/v1 preprint EN Authorea (Authorea) 2023-04-17

Gout is the second largest metabolic disease worldwide after diabetes, with acute gouty arthritis as most common symptom. Xanthine oxidase (XOD) and NOD like receptor-3 (NLRP3) inflammasome are key targets for gout treatment. Chlorogenic acid has been reported a good anti-inflammatory activity, Apigenin showed an excellent potential in XOD inhibition. Therefore, series of chlorogenic acid-apigenin (CA) conjugates varying linkers were designed synthesized dual XOD/NLRP3 inhibitors, their...

10.1248/cpb.c24-00263 article EN Chemical and Pharmaceutical Bulletin 2024-08-14

Abstract With the breakthrough of AlphaFold2 on monomers, research focus structure prediction has shifted to protein complexes, driving continued development new methods for multimer prediction. Therefore, it is crucial accurately estimate quality scores model independent used methods. In this work, we propose a physical-aware deep learning method, DeepUMQA-PA, evaluate residue-wise complex models. For input model, residue-based contact area and orientation features were first constructed...

10.1101/2024.10.31.621211 preprint EN bioRxiv (Cold Spring Harbor Laboratory) 2024-11-03

Abstract The scoring models used for protein structure modeling and ranking are mainly divided into unified field protein-specific functions. Although prediction has made tremendous progress since CASP14, the accuracy still cannot meet requirements to a certain extent. Especially, accurate of multi-domain orphan proteins remains challenge. Therefore, an efficient model should be developed urgently guide folding or through deep learning. In this work, we propose global based on equivariant...

10.1101/2023.01.17.524382 preprint EN cc-by-nc-nd bioRxiv (Cold Spring Harbor Laboratory) 2023-01-19

Abstract Model quality assessment is a crucial part of protein structure prediction and gateway to proper usage models in biomedical applications. Many methods have been proposed for assessing the structural monomers, but few evaluating complex models. As becomes new challenge, model that can provide accurate evaluation structures are urgently required. Here, we present DeepUMQA3, web server using deep neural network. For an input structure, features extracted from three levels overall...

10.1101/2023.04.24.538194 preprint EN cc-by-nd bioRxiv (Cold Spring Harbor Laboratory) 2023-04-28

─ 83 【Objective】Perioperative oral nutritional supple mentation (ONS) is one of the main measures for Enhanced Recovery After Surgery (ERAS) .This study intends to discuss specific function ONS.【Methodology】20 patients in ONS group: 15 cases gastric cancer, 5 transverse colon can cer.40 non-ONS Gastric carci noma 29 cases, cancer 11 cases.Patients group only took enteral nu trients until 6 hours and water 2 be fore operation.No bowel preparation.Enteral trition tube was established...

10.11638/jssmn.51.3_83 article EN The Japanese Journal of SURGICAL METABOLISM and NUTRITION 2017-01-01

Objective To explore the relation of gamma knife radiation doses and changes trigeminal nerves after irradiation by studying somatosensory evoked potentials (TSEP) characteristics nerve roots irradiated in normal animals. Methods Fifteen New Zealand rabbits were divided into 60 Gy group, 80 100 120 group control accordance with random number table (n=3). The first 4 groups used Gamma Plan 5.34 planning system to design targets doses. target was placed at root entry zone, bilateral...

10.3760/cma.j.issn.1671-8925.2018.02.007 article EN Chinese Journal of Neuromedicine 2018-02-15
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