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Biophysical simulations

Structure-based identification of bioactive compounds as trace amine-associated receptor 1 agonists for the therapeutic management of major depressive disorder

Abdelbaset Mohamed Elasbali, Ahmed S. Ali, Mohd Adnan, Taj Mohammad, Anas Shamsi, Md. Imtaiyaz Hassan

published 05 Aug 2025

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Consensus structure prediction of A. thaliana’s MCTP4 structure using prediction tools and coarse grained simulations of transmembrane domain dynamics

Sujith Sritharan, Raphaelle Versini, Jules D Petit, Emmanuelle E Bayer, Antoine Taly

published 15 Jul 2025

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

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

published 10 Jul 2025

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Development and validation of mass reduction prediction model during torrefaction using biomass chemical composition analysis

Sunyong Park, Kyeong Sik Kang, Kwang Cheol Oh, Seok Jun Kim, Paudel Padam Prasad, Seon Yeop Kim, Ha Eun Kim, Jae Youl Shin, DaeHyun Kim

published 23 May 2025

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Comparison of SPH and CEL methods for simulating the soil cutting process of a biomimetic digging shovel

Yunning Dong, Liangfei Fang, Kuan Qin, Shoujun Sun, Yue Gong

published 22 May 2025

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Cooperation in the face of disaster

Marijane Luistro Jonsson, Markus Jonsson

published 03 Apr 2025

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SMND-309 activates Nrf2 signaling to alleviate acetaminophen-induced hepatotoxicity and oxidative stress

Yao Dong, Ru Jia, Yujie Jiang, Qing Li, Lei Wang, Wensi Ding, Rui Yan, Yujie Qiu, Zhengjie Shi, Wenying Liu, Jing Wang, Sen Xu, Na Li

published 31 Mar 2025

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Unveiling Cathepsin B inhibition with repurposed drugs for anticancer and anti-Alzheimer’s drug discovery

Mohammed Alrouji, Sabina Yasmin, Mohammed S. Alshammari, Fahad A. Alhumaydhi, Sharaf E. Sharaf, Moyad Shahwan, Anas Shamsi

published 19 Dec 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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Identification of potent inhibitors of HDAC2 from herbal products for the treatment of colon cancer: Molecular docking, molecular dynamics simulation, MM/GBSA calculations, DFT studies, and pharmacokinetic analysis

Madan Khanal, Arjun Acharya, Rajesh Maharjan, Kalpana Gyawali, Rameshwar Adhikari, Deependra Das Mulmi, Tika Ram Lamichhane, Hari Prasad Lamichhane

published 22 Jul 2024

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Islands of cooperation emerge by stigmergic interactions in iterated spatial games

Franco Zambonelli, Federico Bergenti, Stefano Mariani, Stefania Monica

published 12 Jul 2024

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Conformations of a highly expressed Z19 α-zein studied with AlphaFold2 and MD simulations

Niels Johan Christensen

published 08 May 2024

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MVMRmode: Introducing an R package for plurality valid estimators for multivariable Mendelian randomisation

Benjamin Woolf, Dipender Gill, Andrew J. Grant, Stephen Burgess

published 07 May 2024

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