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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Structure-guided identification of mitogen-activated protein kinase-1 inhibitors towards anticancer therapeutics. by Md Nayab Sulaimani, Shazia Ahmed, Farah Anjum, Taj Mohammad, Anas Shamsi, Ravins Dohare, Md Imtaiyaz Hassan

“…Finally, selected molecules underwent extensive all-atom molecular dynamics (MD) simulations for a time duration of 200 nanoseconds. …”
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Substituted piperazine conjugated to quinoline-thiosemicarbazide as potent α-glucosidase inhibitors to target hyperglycemia by Mehran Ghasemi, Mohammad Mahdavi, Maryam Dehghan, Mohammadreza Eftekharian, Somayeh Mojtabavi, Mohammad Ali Faramarzi, Aida Iraji, Ahmed Al-Harrasi

“…Molecular docking simulations demonstrated key interactions between compound 7j and the active site of α-glucosidase, while molecular dynamics simulations confirmed the stability of the enzyme-ligand complex, reflected in low RMSD and RMSF values.…”
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Effects of Li2O on Structure and Viscosity of CaO-Al2O3-Based Mold Fluxes by Lifeng Chen, Kun Liu, Peng Han, Bin Yang, Lianghua Feng

“…Since CaO-Al2O3-based mold fluxes are one of the most important mold flux systems in metallurgic processes, it is important to explore their structure characteristics and viscosity. Molecular dynamics simulation is performed to study the effect of w(CaO)/w(Al2O3) ratio on both the structural and viscosity properties of CaO-Al2O3-based mold fluxes. …”
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Investigation on Viscoelastic Poisson’s Ratio of Composite Materials considering the Effects of Dewetting by Huiru Cui, Weili Ma, Xuan Lv, Changyuan Li, Yimin Ding

“…Time-dependent longitudinal and transverse strains are considered in the calculation of time-dependent Poisson’s ratio under the relaxation test. The molecular dynamics (MD) packing algorithm is used to generate the high area fraction RVE model of solid propellants consisting of ammonium perchlorate (AP) particles whose radius follows lognormal distribution. …”
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Characterization of the algC Gene Expression Pattern in the Multidrug Resistant Acinetobacter baumannii AIIMS 7 and Correlation with Biofilm Development on Abiotic Surface by Praveen K. Sahu, Pavithra S. Iyer, Sagar H. Barage, Kailas D. Sonawane, Balu A. Chopade

“…Our observation on differential expression pattern of algC having strong correlation with important biofilm stages, scanning electron-microscopic evidence of biofilm augmentation taken together with predictive enzyme functions via molecular dynamic (MD) simulation, proposes a new basis of A. baumannii AIIMS 7 biofilm development on inanimate surfaces.…”
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Exploring the Pharmacological Potential of Carrageenan Disaccharides as Antitumor Agents: An In Silico Approach by Ohana Leticia Tavares Silva, Monique Gabriela das Chagas Faustino Alves, Hugo Alexandre Oliveira Rocha

“…Notably, six of the complexes formed exhibited interactions between the disaccharides and the zinc cofactor, which represents a primary mechanism of inhibition for these targets. Furthermore, molecular dynamics simulations conducted using GROMACS demonstrated a stable interaction between the disaccharides and carbonic anhydrases. …”
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Interaction studies unveil potential binding sites on bovine serum albumin for gut metabolite trimethylamine n-oxide (TMAO) by Awadhesh Kumar Verma, Payal Gulati, GBVS Lakshmi, Anand Mohan, Neeta Raj Sharma, Pratima R. Solanki, Anil Kumar

“…Computational studies, such as molecular docking, molecular dynamics simulation and, MM/GBSA, confirm a stable complex with a binding energy of − 3.6 kcal/mol. …”
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A comprehensive in silico analysis of structural and functional impacts of natural nonsynonymous SNPs in the ALDH2_HUMAN gene by Mehr Ali Mahmood Janlou

“…Furthermore, performing microsecond-timescale molecular dynamics simulations revealed that only the E487K mutation elevated the conformational instability and induced less compactness of the ALDH2. …”
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Structure and function of a near fully-activated intermediate GPCR-Gαβγ complex by Maxine Bi, Xudong Wang, Jinan Wang, Jun Xu, Wenkai Sun, Victor Ayo Adediwura, Yinglong Miao, Yifan Cheng, Libin Ye

“…Guided by a conformational landscape visualized via 19F quantitative NMR and molecular dynamics (MD) simulations, we determined the structure of an intermediate GPCR-mini-Gαsβγ complex at 2.6 Å using cryo-EM, by blocking its transition to the fully activated complex. …”
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Ferroptosis-Related Transcriptional Level Changes and the Role of CIRBP in Glioblastoma Cells Ferroptosis by Zijiang Yang, Ting Zhang, Xuanlin Zhu, Xiaobiao Zhang

“…Conclusion: Our research unravels the complex molecular dynamics of ferroptosis in glioblastoma and underscores CIRBP as a potential biomarker and therapeutic target. …”
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Understanding pectin cross-linking in plant cell walls by Irabonosi Obomighie, Iain J. Prentice, Peter Lewin-Jones, Fabienne Bachtiger, Nathan Ramsay, Chieko Kishi-Itakura, Martin W. Goldberg, Tim J. Hawkins, James E. Sprittles, Heather Knight, Gabriele C. Sosso

“…This study employs a multidisciplinary approach, combining molecular dynamics simulations, experimental investigations, and mathematical modelling, to elucidate the mechanism of pectin cross-linking and its effect on cell wall porosity. …”
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Influence of continuous Cu-rich phase on the deformation mechanism in as-cast CoCrFeNiCu high-entropy alloy by W.Z. Xiao, W.B. Wang, Y.K. Wu, J.Q. Ren, R. Yang, W. Li, Q. Wang

“…The experimental observations and molecular dynamics (MD) simulation demonstrated that, these superior tensile properties were caused by the coherent interface induced by the continues Cu-rich phase, which can not only effectively refine the FCC matrix size, but also alleviate the stress concentration at the interface. …”
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Identification of Flavonoid C-Glycosides as Promising Antidiabetics Targeting Protein Tyrosine Phosphatase 1B by Athika Rampadarath, Fatai Oladunni Balogun, Charlene Pillay, Saheed Sabiu

“…A further probe (in terms of stability, flexibility, and compactness) of the complexes over a molecular dynamics time study of 100 ns for the three compounds suggested orientin as the most outstanding inhibitor of PTP1B owing to its overall -34.47 kcal/mol binding energy score compared to ursolic acid (-19.24 kcal/mol). …”
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Comprehensive Analysis of microRNA Methylation Profiles and Determination of Their Functional Significance in Colorectal Cancer: A Study Protocol by Nurul Syakima Ab Mutalib, Imilia Ismail, Muhammad Redha Abdullah Zawawi, Nadiah Abu, Siti Aishah Sulaiman, Loh Teng-Hern Tan, Learn-Han Lee

“…To understand the biological significance of methylated microRNAs, we will perform pathway enrichment analysis and molecular dynamics simulations to examine the binding of argonaut protein to the differentially methylated microRNAs and the structural changes involved. …”
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Structural Properties of G,T-Parallel Duplexes by Anna Aviñó, Elena Cubero, Raimundo Gargallo, Carlos González, Modesto Orozco, Ramon Eritja

“…The structure of G,T-parallel-stranded duplexes of DNA carrying similar amounts of adenine and guanine residues is studied by means of molecular dynamics (MD) simulations and UV- and CD spectroscopies. …”
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Flavonoids as Strong Inhibitors of MAPK3: A Computational Drug Discovery Approach by Amir Taherkhani, Parita Khodadadi, Lida Samie, Zahra Azadian, Zeynab Bayat

“…A cross-validation study was executed using the Schrödinger Maestro docking tool. Molecular dynamics (MD) was executed to evaluate the stability of docked poses between the top-ranked compounds and the MAPK3 catalytic domain. …”
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In Silico Study of Coumarins: Wedelolactone as a Potential Inhibitor of the Spike Protein of the SARS-CoV-2 Variants by Saurav Katuwal, Siddha Raj Upadhyaya, Rishab Marahatha, Asmita Shrestha, Bishnu P. Regmi, Karan Khadayat, Saroj Basnet, Ram Chandra Basnyat, Niranjan Parajuli

“…Furthermore, coarse-grained molecular dynamics (MD) simulation studies of spike protein-wedelolactone complexes validated the stable binding of wedelolactone in the respective binding pockets. …”
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