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. …”
Get full text

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.…”
Get full text

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. …”
Get full text

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. …”
Get full text

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.…”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

Influence of aluminium distribution on the diffusion mechanisms and pairing of [Cu(NH3)2]+ complexes in Cu-CHA by Joachim D. Bjerregaard, Martin Votsmeier, Henrik Grönbeck

“…Performing unbiased and constrained molecular dynamics simulations, we obtain unique information inaccessible to first-principle calculations and experiments. …”
Get full text

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. …”
Get full text

Lignin alkali regulated interfacial polymerization towards ultra-selective and highly permeable nanofiltration membrane by Wentian Zhang, Shanshan Zhao, Haiyun Li, Cunxian Lai, Shangwei Zhang, Wu Wen, Chuyang Y. Tang, Fangang Meng

“…Various characterizations and molecular dynamics simulations revealed that LA can promote the diffusion and partition of aqueous phase monomer piperazine (PIP) molecules into organic phase and their uniform dispersion on substrate, accelerating the IP reaction and promoting greater interfacial instabilities, thus endowing formation of TFC NF membrane with an ultrathin, highly cross-linked, and crumpled PA layer. …”
Get full text

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. …”
Get full text

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). …”
Get full text

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. …”
Get full text

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. …”
Get full text

Subsurface amorphization-induced ultrasmooth and ultrahard surface during the diamond turning of polycrystalline pure copper by Shuqi Wang, Chunlei He, Zhanfeng Wang, Jiwang Yan

“…By using a large-nose-radius (10 mm) diamond tool with a sharp cutting edge (10.3 nm) at a low feed rate (0.5 μm/rev), an ultrasmooth and ultrahard surface with a 0.61 nm roughness Sa and 5.0 GPa nanohardness was achieved. Molecular dynamics simulations revealed that the high shear strain was responsible for the amorphization and lattice structure transformation during pure copper diamond turning. …”
Get full text

Integrative determination of atomic structure of mutant huntingtin exon 1 fibrils implicated in Huntington disease by Mahdi Bagherpoor Helabad, Irina Matlahov, Raj Kumar, Jan O. Daldrop, Greeshma Jain, Markus Weingarth, Patrick C. A. van der Wel, Markus S. Miettinen

“…Atomic-resolution perspectives are enabled by an integrative analysis and unrestrained all-atom molecular dynamics (MD) simulations incorporating experimental data from electron microscopy (EM), solid-state NMR, and other techniques. …”
Get full text

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. …”
Get full text