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Molecular dynamics

Cu(II)-tyrosinase enzyme catalyst mediated synthesis of mosquito larvicidal active pyrazolidine-3,5-dione derivatives with molecular docking studies and their ichthyotoxicity analysis

Velmurugan Loganathan, SurendraKumar Radhakrishnan, Anis Ahamed, Raman Gurusamy, Omar H. Abd-Elkader, Akbar Idhayadhulla

published 19 Sep 2024

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Metadynamics simulations reveal mechanisms of Na⁺ and Ca²⁺ transport in two open states of the channelrhodopsin chimera, C1C2

Lindsey A. Prignano, Mark J. Stevens, Juan M. Vanegas, Susan B. Rempe, Robert E. Dempski

published 06 Sep 2024

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Exploration of alpha-glucosidase inhibitors: A comprehensive in silico approach targeting a large set of triazole derivatives

Oussama Abchir, Meriem Khedraoui, Imane Yamari, Hassan Nour, Abdelkbir Errougui, Abdelouahid Samadi, Samir Chtita

published 06 Sep 2024

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Network analysis retrieving bioactive compounds from Spirulina (Arthrospira platensis) and their targets related to systemic lupus erythematosus

Amnart Chaiprasert, Ping Han, Teeraphan Laomettachit, Marasri Ruengjitchatchawalya

published 29 Aug 2024

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Taenia solium TAF6 and TAF9 bind to a downstream promoter element present in the Tstbp1 gene core promoter

Oscar Rodríguez-Lima, Ponciano García-Gutiérrez, Lucía Jiménez, Laura A. Velázquez-Villegas, Angel Zarain-Herzberg, Roberto Lazzarini, Karel Estrada, Abraham Landa

published 29 Aug 2024

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Unveiling the anti-obesity potential of Kemuning (Murraya paniculata): A network pharmacology approach

Rizka Fatriani, Firda Agustin Kartika Pratiwi, Annisa Annisa, Dewi Anggraini Septaningsih, Sandra Arifin Aziz, Isnatin Miladiyah, Siska Andrina Kusumastuti, Mochammad Arfin Fardiansyah Nasution, Donny Ramadhan, Wisnu Ananta Kusuma

published 29 Aug 2024

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AlphaFold-SFA: Accelerated sampling of cryptic pocket opening, protein-ligand binding and allostery by AlphaFold, slow feature analysis and metadynamics

Shray Vats, Raitis Bobrovs, Pär Söderhjelm, Soumendranath Bhakat

published 27 Aug 2024

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Unveiling the potential of phytochemicals to inhibit nuclear receptor binding SET domain protein 2 for cancer: Pharmacophore screening, molecular docking, ADME properties, and molecular dynamics simulation investigations

Gamal A. Mohamed, Hossam M. Abdallah, Ikhlas A. Sindi, Sabrin R. M. Ibrahim, Abdulrahim A. Alzain

published 20 Aug 2024

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Substitution of acidic residues near the catalytic Glu131 leads to human HYAL1 activity at neutral pH via charge-charge interactions

Tu Anh Nguyen, Trang Hoang, Thu-Thuy Nguyen, ChanSu Jeong, Trang Van Tran, Mal-Gi Choi, ChangWoo Lee

published 09 Aug 2024

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In silico exploration of PD-L1 binding compounds: Structure-based virtual screening, molecular docking, and MD simulation

Abdullah Alanzi, Ashaimaa Y. Moussa, Ramzi A. Mothana, Munawar Abbas, Ijaz Ali

published 09 Aug 2024

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Elucidating the inhibitory mechanism of Zika virus NS2B-NS3 protease with dipeptide inhibitors: Insights from molecular docking and molecular dynamics simulations

Shahid Ullah, Farhan Ullah, Wajeeha Rahman, Anees Ullah, Sultan Haider, Cao Yueguang

published 08 Aug 2024

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Structure based screening and molecular docking with dynamic simulation of natural secondary metabolites to target RNA-dependent RNA polymerase of five different retroviruses

Muhammad Azeem, Ghulam Mustafa, Sibtain Ahmed, Amna Mushtaq, Muhammad Arshad, Muhammad Usama, Muhammad Farooq

published 05 Aug 2024

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In silico approaches to study the human asparagine synthetase: An insight of the interaction between the enzyme active sites and its substrates

Anam Riaz, Afshan Kaleem, Roheena Abdullah, Mehwish Iqtedar, Daniel C. Hoessli, Mahwish Aftab

published 02 Aug 2024

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