Works matching DE "MOLECULAR dynamics"

Results: 5000

Exploring the role of hepsin in prostate cancer: bioinformatics, molecular Docking and molecular dynamics simulations.

Published in:

Discover Oncology, 2025, v. 16, n. 1, p. 1, doi. 10.1007/s12672-025-03045-6

By:

Peng, Hongying;
Du, Dan;
Hu, Zhonggui;
Xia, Zhiliang

Publication type:

Article

Correction: Development of a subunit vaccine against the cholangiocarcinoma causing Opisthorchis viverrini : a computational approach.

Published in:

2025

By:

Shah, Mohibullah;
Sitara, Farva;
Sarfraz, Asifa;
Shehroz, Muhammad;
Wara, Tehreem Ul;
Perveen, Asia;
Ullah, Najeeb;
Zaman, Aqal;
Nishan, Umar;
Ahmed, Sarfraz;
Ullah, Riaz;
Ali, Essam A.;
Ojha, Suvash Chandra

Publication type:

Correction Notice

ColdstartCPI: Induced-fit theory-guided DTI predictive model with improved generalization performance.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-61745-7

By:

Zhao, Qichang;
Zhao, Haochen;
Guo, Linyuan;
Zheng, Kai;
Li, Yajie;
Ling, Qiao;
Tang, Jing;
Li, Yaohang;
Wang, Jianxin

Publication type:

Article

Effects of alloying and Ni segregation at grain boundaries on the mechanical response of Cu–Ni alloys.

Published in:

Journal of Materials Science, 2025, v. 60, n. 27, p. 11664, doi. 10.1007/s10853-025-11104-0

By:

Chang, Yajun;
Yang, Xu;
Guo, Xin;
Ren, Junqiang;
Xue, Hongtao;
Li, Junchen;
Lu, Xuefeng

Publication type:

Article

A Quantum Strategy for the Simulation of Large Proteins: From Fragmentation in Small Proteins to Scalability in Complex Systems.

Published in:

Electronics (2079-9292), 2025, v. 14, n. 13, p. 2601, doi. 10.3390/electronics14132601

By:

Atchade-Adelomou, Parfait;
Coronas Sala, Laia

Publication type:

Article

Eutectic Mixtures Based on Oleic Acid and Pulsed Electric Fields: A Strategy for the Extraction of Astaxanthin from Dry Biomass of Xanthophyllomyces dendrorhous.

Published in:

Foods, 2025, v. 14, n. 13, p. 2371, doi. 10.3390/foods14132371

By:

Marañés, Javier;
Berzosa, Alejandro;
Bergua, Fernando;
Marín-Sánchez, Javier;
Raso, Javier;
Artal, Manuela

Publication type:

Article

Application of Predictive Modeling and Molecular Simulations to Elucidate the Mechanisms Underlying the Antimicrobial Activity of Sage (Salvia officinalis L.) Components in Fresh Cheese Production.

Published in:

Foods, 2025, v. 14, n. 13, p. 2164, doi. 10.3390/foods14132164

By:

Vukić, Dajana;
Lončar, Biljana;
Pezo, Lato;
Vukić, Vladimir

Publication type:

Article

Molecular Simulations of Interface-Driven Crosslinked Network Formation and Mechanical Response in Composite Propellants.

Published in:

Polymers (20734360), 2025, v. 17, n. 13, p. 1863, doi. 10.3390/polym17131863

By:

Ling, Chen;
Zhang, Xinke;
Li, Xin;
Mou, Guozhu;
Guo, Xiang;
Yuan, Bing;
Yang, Kai

Publication type:

Article

Computer-Guided Development of Hyperbranched Modified Starch-Based Adhesives.

Published in:

Polymers (20734360), 2025, v. 17, n. 13, p. 1812, doi. 10.3390/polym17131812

By:

Yu, Hongjian;
Chang, Jiang;
Chi, Wenrui;
Gao, Shuzhen;
Liu, Jie;
Tang, Yin

Publication type:

Article

Molecular Dynamics Simulation of Hydrogen Permeation Behavior in Epoxy Resin Systems.

Published in:

Polymers (20734360), 2025, v. 17, n. 13, p. 1755, doi. 10.3390/polym17131755

By:

Gao, Chang;
Chen, Hongzhi;
Xu, Hao;
Wu, Zhanjun;
Dong, Xufeng

Publication type:

Article

The Molecular Dynamics of Signature Gas Diffusions in Synthetic-Ester-Based Oil Under a Range of Thermal Conditions.

Published in:

Energies (19961073), 2025, v. 18, n. 13, p. 3276, doi. 10.3390/en18133276

By:

Guo, Liping;
Wang, Hongliang;
Qi, Weiwei;
Zhang, Jun;
Lu, Wu

Publication type:

Article

Effect of Temperature on the Low-Cycle Fatigue Behavior of Polycrystalline TiAl Alloys.

Published in:

Materials (1996-1944), 2025, v. 18, n. 13, p. 3147, doi. 10.3390/ma18133147

By:

Zhou, Junyan;
Zhao, Haochuan;
Li, Pei;
Xiang, Henggao

Publication type:

Article

Adhesion Properties Between Rubber Asphalt Mastic and Aggregate: Verification from Surface Free Energy Theory and Molecular Dynamics.

Published in:

Materials (1996-1944), 2025, v. 18, n. 13, p. 3115, doi. 10.3390/ma18133115

By:

Yin, Huajia;
Cao, Shenyang;
Guo, Fucheng;
Wu, Xu

Publication type:

Article

Review of Molecular Dynamics Simulation of Bimetallic Interfacial Behavior.

Published in:

Materials (1996-1944), 2025, v. 18, n. 13, p. 3048, doi. 10.3390/ma18133048

By:

Wang, Xiaoqiong;
Wang, Yuejia;
Li, Guangyu;
Jiang, Wenming;
Wang, Jun;
Kang, Xing;
Zeng, Qiantong;
Yao, Shan;
Yao, Pingkun

Publication type:

Article

Substituent Effects on Crystal Engineering of DNBT-Based Energetic Cocrystals: Insights from Multiscale Computational Analysis.

Published in:

Materials (1996-1944), 2025, v. 18, n. 13, p. 2995, doi. 10.3390/ma18132995

By:

Shi, Lu;
Liu, Min;
Xie, Shangrui;
Li, Song;
Liu, Shuxin;
Yuan, Shen;
Duan, Xiaohui;
Li, Hongzhen

Publication type:

Article

Binding Properties of Methyltrimethoxysilane-Modified Silica Sol Particle Surfaces and Their Molecular Dynamics Simulations.

Published in:

Materials (1996-1944), 2025, v. 18, n. 13, p. 2974, doi. 10.3390/ma18132974

By:

Pang, Hongxing;
Wang, Zhoufu;
Liu, Hao;
Ma, Yan;
Wang, Xitang;
Jiang, Pengcheng

Publication type:

Article

Unveiling Vibrational Couplings in Model Peptides in Solution by a Theoretical Approach.

Published in:

Molecules, 2025, v. 30, n. 13, p. 2854, doi. 10.3390/molecules30132854

By:

Coppola, Federico;
Perrella, Fulvio;
Petrone, Alessio;
Donati, Greta;
Marinelli, Luciana;
Rega, Nadia

Publication type:

Article

Inversion Motion of Xanthene and Detection of Its Oxidation Product Xanthone from Gas-Phase Rotational Spectroscopy.

Published in:

Molecules, 2025, v. 30, n. 13, p. 2801, doi. 10.3390/molecules30132801

By:

Bermúdez, Celina;
Goubet, Manuel;
Neeman, Elias M.

Publication type:

Article

Molecular Insights into the Interaction of Orexin 1 Receptor Antagonists: A Comprehensive Study Using Classical and Quantum Computational Methods.

Published in:

Molecules, 2025, v. 30, n. 13, p. 2790, doi. 10.3390/molecules30132790

By:

Sena, Caio;
Albuquerque, Pedro;
Oliveira, Jonas;
Vieira, Davi

Publication type:

Article

Molecular Recognition and Modification Strategies of Umami Dipeptides with T1R1/T1R3 Receptors.

Published in:

Molecules, 2025, v. 30, n. 13, p. 2774, doi. 10.3390/molecules30132774

By:

Hu, Kaixuan;
Sun, Guangzhou;
Yu, Wentong;
Zhang, Mengyu;
Wang, Shuang;
Cao, Yujie;
Hu, Dongling;
Liang, Li;
He, Gang;
Hu, Jianping;
Liu, Wei

Publication type:

Article

Understanding Anti-Obesity Potential of Four Porphyrin Compounds by Investigating Pancreatic Lipase Inhibition.

Published in:

Molecules, 2025, v. 30, n. 13, p. 2701, doi. 10.3390/molecules30132701

By:

Zhou, Jie;
Wang, Xinrui;
Liu, Yangyuxin;
Li, Xiaochen;
Huang, Mingze;
Bai, Helong;
Mo, Jingang

Publication type:

Article

Disclosing Pathogenic Variant Effects on the Structural Dynamics of the VAPB MSP Domain Causing Familial ALS.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 13, p. 6489, doi. 10.3390/ijms26136489

By:

Bashar, Md Abul;
Dash, Nayan;
Mitra, Sarmistha;
Dash, Raju

Publication type:

Article

Potent Inhibition of Chikungunya Virus Entry by a Pyrazole–Benzene Derivative: A Computational Study Targeting the E1–E2 Glycoprotein Complex.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 13, p. 6480, doi. 10.3390/ijms26136480

By:

Rahman, Md. Mohibur;
Limon, Md. Belayet Hasan;
Saikat, Tanvir Ahmed;
Saha, Poulomi;
Nahid, Abdul Hadi;
Alam, Mohammad Mamun;
Rahman, Mohammed Ziaur

Publication type:

Article

Short-Term Probiotic Colonization Alters Molecular Dynamics of 3D Oral Biofilms.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 13, p. 6403, doi. 10.3390/ijms26136403

By:

Udawatte, Nadeeka S.;
Liu, Chun;
Staples, Reuben;
Han, Pingping;
Kumar, Purnima S.;
Arumugam, Thiruma V.;
Ivanovski, Sašo;
Seneviratne, Chaminda J.

Publication type:

Article

Microscopic Mechanism Study on Gas–Crude-Oil Interactions During the CO 2 Flooding Process in Water-Bearing Reservoirs.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 13, p. 6402, doi. 10.3390/ijms26136402

By:

Xia, Wei;
Wang, Yu-Bo;
Wu, Jiang-Tao;
Zhang, Tao;
Gong, Liang;
Zhu, Chuan-Yong

Publication type:

Article

Molecular Mechanisms and Regulatory Factors Governing Feed Utilization Efficiency in Laying Hens: Insights for Sustainable Poultry Production and Breeding Optimization.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 13, p. 6389, doi. 10.3390/ijms26136389

By:

Gao, Zhouyang;
Zheng, Jiangxia;
Xu, Guiyun

Publication type:

Article

New Molecular Mechanisms and Markers in Inflammatory Disorders, 2nd Edition.

Published in:

2025

By:

Galliera, Emanuela Rita;
Vianello, Elena

Publication type:

Editorial

Quantum Mechanics in Drug Discovery: A Comprehensive Review of Methods, Applications, and Future Directions.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 13, p. 6325, doi. 10.3390/ijms26136325

By:

Niazi, Sarfaraz K.

Publication type:

Article

Network Pharmacology, Molecular Dynamics Simulation, and Biological Validation Insights into the Potential of Ligustri Lucidi Fructus for Diabetic Nephropathy.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 13, p. 6303, doi. 10.3390/ijms26136303

By:

Liu, Manting;
Gu, Yuhao;
Yang, Yuchang;
Zhang, Ke;
Yang, Jingwen;
Wang, Wenqi;
Li, Wenjing;
Wang, Xinzhu;
Dong, Xiaoxv;
Yin, Xingbin;
Qu, Changhai;
Ni, Boran;
Ni, Jian

Publication type:

Article

FINCHES: A Computational Framework for Predicting Intermolecular Interactions in Intrinsically Disordered Proteins.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 13, p. 6246, doi. 10.3390/ijms26136246

By:

Niazi, Sarfaraz K.

Publication type:

Article

Conformational Remodeling and Allosteric Regulation Underlying EGFR Mutant-Induced Activation: A Multi-Scale Analysis Using MD, MSMs, and NRI.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 13, p. 6226, doi. 10.3390/ijms26136226

By:

Duan, Hui;
Zhao, De-Rui;
Liu, Meng-Ting;
Yang, Li-Quan;
Sang, Peng

Publication type:

Article

Structure-Based Discovery of Orthosteric Non-Peptide GLP-1R Agonists via Integrated Virtual Screening and Molecular Dynamics.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 13, p. 6131, doi. 10.3390/ijms26136131

By:

Alturki, Mansour S.;
Alkhodier, Reem A.;
Gomaa, Mohamed S.;
Hussein, Dania A.;
Tawfeeq, Nada;
Al Khzem, Abdulaziz H.;
Pottoo, Faheem H.;
Albugami, Shmoukh A.;
Aldawsari, Mohammed F.;
Rants'o, Thankhoe A.

Publication type:

Article

Deciphering the 3D Structural Characterization of Gonadotropin-Releasing Hormone in Tenualosa ilisha Using Homology Modeling, Molecular Dynamics, and Docking Approaches.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 13, p. 6098, doi. 10.3390/ijms26136098

By:

Panda, Soumya Prasad;
Das, Basanta Kumar;
Gadnayak, Ayushman;
Nandy, Saurav Kumar;
Kumar, Vikash;
Pradhan, Smruti Priyambada;
Raut, Subhashree Subhasmita;
Chakrabarty, Ratul;
Kunui, Arghya;
Sahoo, Amiya Kumar

Publication type:

Article

Modeling Possible G-Quadruplexes and i-Motifs at DNA–DNA Contact Sites: Strategy, Classification, and Examples.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 13, p. 5979, doi. 10.3390/ijms26135979

By:

Tsvetkov, Vladimir B.

Publication type:

Article

Design and Synthesis of a Novel Plasticizer for Starch.

Published in:

Polymer-Plastics Technology & Materials, 2025, v. 64, n. 12, p. 1920, doi. 10.1080/25740881.2025.2487890

By:

Yang, Jinhui;
Li, Yang;
Wang, Ziyi;
Zhang, Guowei;
Chen, Yanxue

Publication type:

Article

Atomistic Observation of Defect Generation and Microstructural Evolution in Polycrystalline FeCrAl Alloys Under Different Irradiation Conditions.

Published in:

Nanomaterials (2079-4991), 2025, v. 15, n. 13, p. 988, doi. 10.3390/nano15130988

By:

Yao, Huan;
Wu, Changwei;
Ye, Tianzhou;
Wang, Pengfei;
Wu, Junmei;
Wu, Yingwei;
Chen, Ping

Publication type:

Article

Mechanical Tensile Response of Ni–Graphene Nanocomposites in Hydrogen-Irradiation-Coupled Environments Using Molecular Dynamics Simulations.

Published in:

Nanomaterials (2079-4991), 2025, v. 15, n. 13, p. 970, doi. 10.3390/nano15130970

By:

Liu, Tonghe;
Yuan, Xiaoting;
Huang, Hai

Publication type:

Article

Design and screening of novel 1,2,4-Triazole-3-thione derivatives as DCN1 inhibitors for anticardiac fibrosis based on 3D-QSAR modeling and molecular dynamics.

Published in:

Frontiers in Pharmacology, 2025, p. 1, doi. 10.3389/fphar.2025.1590711

By:

Bian, Wengong;
Guo, Yaxin

Publication type:

Article

Interaction and structure-activity relationship characterization of hop-derived a-acid/xanthohumol and protein Z.

Published in:

Food & Machinery, 2025, n. 6, p. 9, doi. 10.13652/j.spjx.1003.5788.2025.80068

By:

WANG Limin;
PENG Mengyan;
MA Changwei;
WU Zijian

Publication type:

Article

Directional Explosion of Finite Volume Water Confined in a Single-End-Opened CNT.

Published in:

Computers, Materials & Continua, 2025, v. 84, n. 2, p. 2573, doi. 10.32604/cmc.2025.066249

By:

Liu, Jiahao;
Kang, Yuanyuan;
Cai, Kun;
Duan, Haiyan;
Shi, Jiao

Publication type:

Article

Fluidity and Structure of CaO–Al2O3–MgO–V2O3 Slag for Smelting Al–V Alloys: Influence of MgO Content.

Published in:

Metallurgical & Materials Transactions. Part B, 2025, v. 56, n. 4, p. 3835, doi. 10.1007/s11663-025-03603-x

By:

Zhou, Hanghang;
Hou, Yong;
Dang, Jie;
Wu, Yuedong;
Lv, Xuewei

Publication type:

Article

Unveiling the Mechanism of Aluminum Removing Vanadium from Crude Titanium Tetrachloride Via Deep Potential Molecular Dynamics Simulation.

Published in:

Metallurgical & Materials Transactions. Part B, 2025, v. 56, n. 4, p. 3454, doi. 10.1007/s11663-025-03530-x

By:

Zhou, Jie;
Feng, Yan;
Chen, Xiumin;
Zhang, Enhao;
Wu, Huapeng;
Chen, Yunmin;
Huang, Haiguang;
Li, Jianjun;
Yang, Qian

Publication type:

Article

Understanding the molecular basis of herbal medicines for cough variant asthma under the guidance of traditional herbal theories.

Published in:

Frontiers in Pharmacology, 2025, p. 1, doi. 10.3389/fphar.2025.1594308

By:

Liu, Rui;
Yao, Jiaqi;
Sui, Yihang;
Zhang, Yinnan;
Kho, Boon Seng;
Zhu, Yingli;
Tan, Ninghua;
Wang, Yinyin

Publication type:

Article

Coarse-grained molecular dynamics investigation on the interaction between κ- and β-casein aggregates and curcumin.

Published in:

PLoS ONE, 2025, v. 20, n. 7, p. 1, doi. 10.1371/journal.pone.0328010

By:

Gao, Jian;
Dong, Rong;
Yang, Shuailing;
Zhao, Zhengtao;
Zhang, Ye-Wang

Publication type:

Article

Disrupting tuberculosis pathogenesis by targeting DprE1 in cell wall biosynthesis: a structural dynamics perspective.

Published in:

Journal of Computer-Aided Molecular Design, 2025, v. 39, n. 1, p. 1, doi. 10.1007/s10822-025-00626-z

By:

Alamri, Abdulwahab;
Alafnan, Ahmed;
Hussein, Weiam A.;
Almansour, Khaled;
Dhham, Alrafidi Rafidi;
Abouzied, Amr S.

Publication type:

Article

基于分子动力学模拟的氧化石墨烯改性沥青界面力学性能研究.

Published in:

Journal of Wuhan University of Science & Technology, 2025, v. 48, n. 4, p. 279, doi. 10.3969/j.issn.1674-3644.2025.04.005

By:

黄立新;
苏广厦;
罗伟伦

Publication type:

Article

The C-terminus of the multi-drug efflux pump EmrE prevents proton leak by gating transport.

Published in:

eLife, 2025, p. 1, doi. 10.7554/eLife.105525

By:

Brousseau, Merissa;
Da Teng;
Thomas, Nathan E.;
Voth, Gregory A.;
Henzler-Wildman, Katherine A.

Publication type:

Article

Tunneling Splittings of the Protonated Water and Water Dimer.

Published in:

Croatica Chemica Acta, 2025, v. 97, n. 4, p. 217, doi. 10.5562/cca4132

By:

Babić, Tea;
Eraković, Mihael;
Cvitaš, Marko T.

Publication type:

Article

In vivo CRISPR screening identifies POU3F3 as a novel regulator of ferroptosis resistance in hepatocellular carcinoma via retinoic acid signaling.

Published in:

Cell Communication & Signaling, 2025, v. 23, n. 1, p. 1, doi. 10.1186/s12964-025-02285-x

By:

Tian, Yu;
Bao, Xin;
Lei, Shan;
Huang, Youcai;
Wang, Xiaoling;
Tu, Yanyang;
He, Qinglian;
Zhang, Feixiang;
Xu, Haicheng;
Ashrafizadeh, Milad;
Sethi, Gautam;
Wang, Furong;
Zeng, Zhirui

Publication type:

Article

Differential adsorption characteristics in the composite model of deep marine shale: Implication from molecular dynamics simulations.

Published in:

Petroleum Science (KeAi Communications Co.), 2025, v. 22, n. 6, p. 2247, doi. 10.1016/j.petsci.2025.03.017

By:

Yu-Ying Wang;
Jun-Qing Chen;
Fu-Jie Jiang;
Xiao-Bin Yang;
Xiao Zhang;
Hong Pang;
Dong-Xia Chen;
Bing-Yao Li;
Xin-Yi Niu;
Gui-Li Ma;
Kan-Yuan Shi

Publication type:

Article