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Molecular dynamics

Probing the substrate binding modes and catalytic mechanisms of BLEG-1, a promiscuous B3 metallo-β-lactamase with glyoxalase II properties

Shaw Xian Au, Azyyati Mohd Padzil, Noor Dina Muhd Noor, Hiroyoshi Matsumura, Raja Noor Zaliha Raja Abdul Rahman, Yahaya M. Normi

published 06 Sep 2023

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Interaction of biomolecules with anatase, rutile and amorphous TiO₂ surfaces: A molecular dynamics study

Tamás Tarjányi, Ferenc Bogár, János Minárovits, Márió Gajdács, Zsolt Tóth

published 05 Sep 2023

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A computational approach to fighting type 1 diabetes by targeting 2C Coxsackie B virus protein with flavonoids

Shahid Ullah, Zilong Zheng, Wajeeha Rahman, Farhan Ullah, Anees Ullah, Muhammad Nasir Iqbal, Naveed Iqbal, Tianshun Gao

published 30 Aug 2023

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Discovery of novel RARα agonists using pharmacophore-based virtual screening, molecular docking, and molecular dynamics simulation studies

Atefeh Ghorayshian, Mahshid Danesh, Tahereh Mostashari-Rad, Afshin fassihi

published 24 Aug 2023

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Exploring the potential of approved drugs for triple-negative breast cancer treatment by targeting casein kinase 2: Insights from computational studies

Tagyedeen H. Shoaib, Walaa Ibraheem, Mohammed Abdelrahman, Wadah Osman, Asmaa E. Sherif, Ahmed Ashour, Sabrin R. M. Ibrahim, Kholoud F. Ghazawi, Samar F. Miski, Sara A. Almadani, Duaa Fahad ALsiyud, Gamal A. Mohamed, Abdulrahim A. Alzain

published 14 Aug 2023

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SuperNatural inhibitors to reverse multidrug resistance emerged by ABCB1 transporter: Database mining, lipid-mediated molecular dynamics, and pharmacokinetics study

Mahmoud A. A. Ibrahim, Khlood A. A. Abdeljawaad, Alaa H. M. Abdelrahman, Mahmoud M. H. Abdelhamid, Mohamed Ahmed Naeem, Gamal A. H. Mekhemer, Peter A. Sidhom, Shaban R. M. Sayed, Paul W. Paré, Mohamed-Elamir F. Hegazy

published 26 Jul 2023

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Enhancing the thermostability of Streptomyces cyaneofuscatus strain Ms1 tyrosinase by multi-factors rational design and molecular dynamics simulations

Zhengtao Li, Chen Zhao, Duanhua Li, Lu Wang

published 20 Jul 2023

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Molecular insights into the inhibitory potential of anthocyanidins on glucokinase regulatory protein

Christian Kenneth, Daru Seto Bagus Anugrah, Jeffry Julianus, Sendy Junedi

published 19 Jul 2023

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Poria cocos compounds targeting neuropeptide Y1 receptor (Y₁R) for weight management: A computational ligand- and structure-based study with molecular dynamics simulations identified beta-amyrin acetate as a putative Y₁R inhibitor

Ann Rann Wong, Andrew Hung, Angela Wei Hong Yang, Harsharn Gill, George Binh Lenon

published 30 Jun 2023

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Computer simulation approach to the identification of visfatin-derived angiogenic peptides

Ji Myung Choi, Srimai Vuppala, Min Jung Park, Jaeyoung Kim, Myeong-Eun Jegal, Yu-Seon Han, Yung-Jin Kim, Joonkyung Jang, Min-Ho Jeong, Bo Sun Joo

published 29 Jun 2023

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The ribosome-inactivating proteins MAP30 and Momordin inhibit SARS-CoV-2

Norman R. Watts, Elif Eren, Ira Palmer, Paul L. Huang, Philip Lin Huang, Robert H. Shoemaker, Sylvia Lee-Huang, Paul T. Wingfield

published 29 Jun 2023

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Variability in phenylalanine side chain conformations facilitates broad substrate tolerance of fatty acid binding in cockroach milk proteins

Partha Radhakrishnan Santhakumari, KanagaVijayan Dhanabalan, Saniya Virani, Amber S. Hopf-Jannasch, Joshua B. Benoit, Gaurav Chopra, Ramaswamy Subramanian

published 29 Jun 2023

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M^propred: A machine learning (ML) driven Web-App for bioactivity prediction of SARS-CoV-2 main protease (M^pro) antagonists

Nadim Ferdous, Mahjerin Nasrin Reza, Mohammad Uzzal Hossain, Shahin Mahmud, Suhami Napis, Kamal Chowdhury, A. K. M. Mohiuddin

published 23 Jun 2023

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