In silico drug repurposing at the cytoplasmic surface of human aquaporin 1. by Aled R Lloyd, Karl Austin-Muttitt, Jonathan G L Mullins

“…The stability of the best docked conformations within the intrinsic water pore was assessed via short 15 nanosecond molecular dynamics (MD) simulations using the GROMACS-on-Colab utility. …”
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Molecular surface descriptors to predict antibody developability: sensitivity to parameters, structure models, and conformational sampling by Eliott Park, Saeed Izadi

“…Averaging the descriptor values over conformational distributions from molecular dynamics mitigates the systematic shifts and improves the consistency across different structure prediction methods, albeit with inconsistent improvements in correlations with biophysical data. …”
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Host-microbe computational proteomic landscape in oral cancer revealed key functional and metabolic pathways between Fusobacterium nucleatum and cancer progression by Camila Paz Muñoz-Grez, Mabel Angélica Vidal, Tamara Beatriz Rojas, Luciano Esteban Ferrada, Felipe Andrés Zuñiga, Agustin Andrés Vera, Sergio Andrés Sanhueza, Romina Andrea Quiroga, Camilo Daniel Cabrera, Barbara Evelyn Antilef, Ricardo Andrés Cartes, Milovan Paolo Acevedo, Marco Andrés Fraga, Pedro Felipe Alarcón-Zapata, Mauricio Alejandro Hernández, Alexis Marcelo Salas-Burgos, Francisco Tapia-Belmonte, Milly Loreto Yáñez, Erick Marcelo Riquelme, Wilfredo Alejandro González, Cesar Andrés Rivera, Angel Alejandro Oñate, Liliana Ivonne Lamperti, Estefanía Nova-Lamperti

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Linking machine learning and biophysical structural features in drug discovery by Armin Ahmadi, Shivangi Gupta, Vineetha Menon, Jerome Baudry

“…IntroductionMachine learning methods were applied to analyze pharmacophore features derived from four protein-binding sites, aiming to identify key features associated with ligand-specific protein conformations.MethodsUsing molecular dynamics simulations, we generated an ensemble of protein conformations to capture the dynamic nature of their binding sites. …”
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Structure-function analysis of carrier protein-dependent 2-sulfamoylacetyl transferase in the biosynthesis of altemicidin by Yuhao Zhu, Takahiro Mori, Masayuki Karasawa, Kohei Shirai, Wenjiao Cheng, Tohru Terada, Takayoshi Awakawa, Ikuro Abe

“…Furthermore, docking simulation, molecular dynamics simulation, and mutagenesis studies indicated the intimate structural details of the unique reaction mechanism of SbzI, which does not utilize a general base residue in contrast to other typical GNATs. …”
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Leiomodin creates a leaky cap at the pointed end of actin-thin filaments. by Dmitri Tolkatchev, Garry E Smith, Lauren E Schultz, Mert Colpan, Gregory L Helms, John R Cort, Carol C Gregorio, Alla S Kostyukova

“…Using nuclear magnetic resonance data and molecular dynamics simulations, we generated the first atomic structural model of the binding interface between the tropomyosin-binding site of cardiac leiomodin and the N-terminus of striated muscle tropomyosin. …”
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In Silico Study of Alkaloids: Neferine and Berbamine Potentially Inhibit the SARS-CoV-2 RNA-Dependent RNA Polymerase by Rishab Marahatha, Asmita Shrestha, Kabita Sharma, Bishnu P. Regmi, Khaga Raj Sharma, Pramod Poudel, Ram Chandra Basnyat, Niranjan Parajuli

“…Among the different alkaloids studied, neferine and berbamine were repurposed as potential drug candidates based on their binding affinity and interactions with RdRP. Further, molecular dynamics simulation of 90 ns revealed the conformational stability of the neferine-RdRP complex.…”
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Adsorption of Phenols from Different Solvents on Graphene: Semi-Empirical Quantum Mechanical Calculations by Pablo Húmpola, Héctor S. Odetti, Alberto G. Albesa, José L. Vicente

“…The adsorption of phenol from aqueous solutions on carbon surfaces is discussed from different theoretical points of view, such as Monte–Carlo simulations, semi-empirical calculations, density functional theory and molecular dynamics. We performed a quantitative analysis of the adsorption of aromatics in general, and phenolic compounds in particular, through semi-empirical quantum mechanical calculations using different approaches. …”
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The Stability of a Model Substrate for Topoisomerase 1-Mediated DNA Religation Depends on the Presence of Mismatched Base Pairs by William H. Gmeiner, Freddie Salsbury, Chris M. Olsen, Luis A. Marky

“…In the present study, we report that mismatched base pairs at the +1 position destabilize the duplex DNA components for a model Top1 cleavage complex formation even though one duplex component does not directly include a mismatched base pair. Molecular dynamics simulations reveal G-dU and G-FdU mismatched base pairs, but not a G-T mismatched base pair, increase flexibility at the Top1 cleavage site, and affect coupling between the regions required for the religation reaction to occur. …”
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Spermine Significantly Increases the Transfection Efficiency of Cationic Polymeric Gene Vectors by Yue Lv, Jiaoqin Xue, Pengfei Cui, Lin Qiu

“…Characterization of PEI/Spermine/DNA revealed that, compared to PEI/DNA, its particle size increased to approximately 150 nm. Molecular dynamics simulation results revealed that spermine can enhance the interaction between PEI and DNA, thereby forming a system with lower energy and greater stability. …”
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Insilico targeting of virus entry facilitator NRP1 to block SARS-CoV2 entry. by Nousheen Bibi, Maleeha Shah, Shahzad Khan, Muhammad Shahzad Chohan, Mohammad Amjad Kamal

“…The top two candidates, AZD3839 and LY2090314, were selected for molecular dynamics simulation studies over 100 ns to assess binding stability. …”
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Exosomal circRNAs: Deciphering the novel drug resistance roles in cancer therapy by Xi Li, Hanzhe Liu, Peiyu Xing, Tian Li, Yi Fang, Shuang Chen, Siyuan Dong

“…Their presence in bodily fluids positions them as potential non-invasive biomarkers, revealing the molecular dynamics of cancers. Research in exosomal circRNAs is reshaping our understanding of neoplastic intercellular communication. …”
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Amentoflavone from Selaginella bryopteris leaf extracts modulate MAPK signaling - Molecular modeling study for therapeutic target analysis by Praveen Mallari, Mashooq Ahmad Bhat

“…Interaction networks were built for the corresponding proteins, molecular docking, molecular dynamics, and molecular mechanics. Poisson–Boltzmann surface area (MMPBSA) binding free energy calculations were performed. …”
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Engineered crystalline polymers for effective contaminant removal from water by Hadiseh Heydari, Heidar Raissi, Afsaneh Ghahari

“…Abstract Herein, we discuss the structure-function of biomimetic imidazole-quartet substrates (I-quartets) obtained through the adaptive self-assembly of octyl-ureido-polyol structures in polyamide membranes designed as adsorbents. Molecular dynamics (MD) and well-tempered metadynamics simulations are utilized to examine ion contaminants’ adsorption process and dynamic behaviors onto alkylureido-ethylimidazoles with well-defined supramolecular structures. …”
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Curcumin mimics of potential chemoprevention with NQO1 induction properties by Dalia R. Aboshouk, Ahmed R. Hamed, Siva S. Panda, Mohamed S. Bekheit, M. Adel Youssef, Adel S. Girgis

“…Molecular modeling studies (including QSAR, molecular docking and molecular dynamics) were accessed supporting the observed biological profiles.…”
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Mechanism of Substrate Activation by Tryptophan Hydroxylase: A Computational Study by Dr. Thirakorn Mokkawes, Dr. Sam P. deVisser

“…In this work, we present a computational study ranging from molecular dynamics (MD) to quantum mechanics (QM) methods, focused on the mechanism of tryptophan hydroxylase. …”
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Machine learning configuration-dependent friction tensors in Langevin heatbaths by Matthias Sachs, Wojciech G Stark, Reinhard J Maurer, Christoph Ortner

“…We demonstrate the capabilities of the model approach by fitting a model of configuration-dependent tensorial electronic friction calculated from first principles that arises during reactive molecular dynamics at metal surfaces.…”
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Thiamine and Thiamine Pyrophosphate as Non-Competitive Inhibitors of Acetylcholinesterase—Experimental and Theoretical Investigations by Łukasz Szeleszczuk, Dariusz Maciej Pisklak, Błażej Grodner

“…The mechanisms of action of these compounds as potential inhibitors of AChE were evaluated using both experimental (enzymatic activity) as well as computational (molecular docking, molecular dynamics simulations, and MM-GBSA calculations) methods. …”
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Investigating Pb2 CAP-binding domain inhibitors from marine bacteria for targeting the influenza A H5N1. by Taha A Kumosani, Aymn T Abbas, Balogun Basheer, Ahmed M Hassan, Soonham S Yaghmoor, Areej H Alyahiby, Amer H Asseri, Vivek Dhar Dwivedi, Esam I Azhar

“…This process identified four potential inhibitors: CMNPD25830, CMNPD18675, CMNPD18676, and CMNPD27216. Subsequent molecular dynamics simulations, conducted using the Amber software suite, evaluated their binding affinities and dynamic interactions with the PB2 protein. …”
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Neutron imaging and molecular simulation of systems from methane and p-xylene by Martin Melčák, Tereza-Markéta Durďáková, Štěpán Tvrdý, Jonatan Šercl, Jong Min Lee, Pierre Boillat, Jan Heyda, Pavel Trtik, Ondřej Vopička

“…Abstract Bulk properties of two-phase systems comprising methane and liquid p-xylene were derived experimentally using neutron imaging and theoretically predicted using molecular dynamics (MD). The measured and predicted methane diffusivity in the liquid, Henry’s law constant, apparent molar volume, and surface tension compared well within the experimentally studied conditions (273.15 to 303.15 K, ≤ 100 bar). …”
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