Discovering structural cis‐regulatory elements by modeling the behaviors of mRNAs by Barrett C Foat, Gary D Stormo

“…Abstract Gene expression is regulated at each step from chromatin remodeling through translation and degradation. Several known RNA‐binding regulatory proteins interact with specific RNA secondary structures in addition to specific nucleotides. …”
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Transcriptomic and targeted metabolomic analysis identifies genes involved in differential anthocyanin accumulation in potato tubers by Rui Yang, Shuohan Huang, Dan Li, Yuan Sun, Guangdong Zhou, Duanrong Zhou, Binquan Huang

“…These genes were associated with ATP-binding cassette transporters and phytohormone pathways. …”
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The neurodevelopmental regulatory role and clinical value of hsa-circ-CORO1C–hsa-miR-708-3p–JARID2 + LNPEP axis in early-onset schizophrenia by Zexuan Li, Xinzhe Du, Xijin Wang, Jianzhen Hu, Meiqi Liu, Yao Gao, Zhifen Liu, Xiaohua Cao, Xinrong Li, Yong Xu, Sha Liu

“…Using these molecules to identify the disease is considered insufficient. MicroRNAs (miRNAs) binding to messenger RNAs (mRNAs) can lead to mRNA degradation, while circular RNAs (circRNAs), by binding to miRNAs as sponge, can reduce the inhibitory effect of miRNAs on mRNAs. …”
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An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions by Varshni Rajagopal, Jeanette Seiler, Isha Nasa, Simona Cantarella, Jana Theiss, Franziska Herget, Bianca Kaifer, Melina Klostermann, Rainer Will, Martin Schneider, Dominic Helm, Julian König, Kathi Zarnack, Sven Diederichs, Arminja N. Kettenbach, Maïwen Caudron-Herger

“…Abstract Ribonucleoprotein complexes are dynamic assemblies of RNA with RNA-binding proteins, which modulate the fate of RNA. …”
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Interaction Between Bovine Serum Albumin and <i>Trans</i>-Resveratrol: Multispectroscopic Approaches and Molecular Dynamics Simulation by Xiujuan Li, Mimi Guo, Chenxia Xie, Yalin Xue, Junhui Zhang, Dong Zhang, Zhangqun Duan

“…Recent studies have increasingly focused on molecular interactions between small molecules and proteins, especially binding mechanisms and thermodynamics, using multispectroscopic and molecular dynamics approaches. …”
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Affinity Peptide-Based Circularly Permuted Fluorescent Protein Biosensors for Non-Small Cell Lung Cancer Diagnosis by Dengyue Xu, Qingyun Jiang, Zhi Li, Angyang Shang, Jiaqi Liu, Chengyu Xue, Shuai Shao, Hangyu Zhang, Hong Yuan, Bin Wu, Bo Liu

“…Peptides with high affinity were then integrated as binding domains into biosensors by fusing them with circularly permuted fluorescent proteins (cpFPs) through genetic coding. …”
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Mitigating host microRNA interference to enhance mRNA vaccine efficacy in public health interventions by Tielong Xu, Ziqi Lin, Yicheng Yu, Muhammad Irfan, Munir Ahmed, Maya Septriana, Twinky Zebrina Cysta Sumantri, Anindini Winda Amalia, Bin Zheng

“…To decode these inhibitory interactions, the commentary proposes an integrated multi-omics framework combining Argonaute immunoprecipitation with crosslinking-based miR-mRNA interactome sequencing, enabling precise mapping of miR-vaccine mRNA binding events in vaccine-transfected APCs. …”
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Molecular Recognition of SARS-CoV-2 Mpro Inhibitors: Insights from Cheminformatics and Quantum Chemistry by Adedapo Olosunde, Xiche Hu

“…In this study, we present a systematic investigation into the molecular determinants of Mpro inhibition using an integrated approach combining large-scale data mining, cheminformatics, and quantum chemical calculations. …”
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DFT and dynamic simulations of OleuoPectin structures as a potential anticoagulant agent by Mona T. M. Ghanem, Heba D. Hassanein, Ahmed F. El-Sayed, Medhat A. Ibrahim, Ahmed M. Bayoumy

“…Furthermore, global reactivity descriptors were calculated to reveal the improved electronic features of Oleu-Pec structures upon adding Pec to Oleu, proposing it for further promising biomedical applications. The integrated approach of docking and molecular dynamics (MD) simulations applied to the P2Y12 receptor in conjunction with the ligands 2-Oleu(OH)-Pec(OH), Oleuropein, Pectin, compared with native inhibitor (AZJ) provides valuable insights into their binding characteristics. …”
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Structure guided functional analysis of the S. cerevisiae Mre11 complex by Marcel Hohl, You Yu, Vitaly Kuryavyi, Dinshaw J. Patel, John Petrini

“…The structure provided a foundation for detailed mutational analyses regarding homo and heterotypic protein interfaces, as well as DNA binding properties of Rad50. We define several conserved residues in Rad50 and Mre11 that are critical to complex assembly as well as for DNA binding. …”
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Identification of putative allosteric inhibitors of BCKDK via virtual screening and biological evaluation by Chunqiong Li, Quanjun Yang, Li Zhang

“…Here, we screened PPHN and POAB as novel putative allosteric inhibitors by integrating allosteric binding site prediction, large-scale ligand database virtual screening, and bioactivity evaluation assays. …”
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Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning. by Matheus V F Ferraz, W Camilla S Adan, Tayná E Lima, Adriele J C Santos, Sérgio O de Paula, Rafael Dhalia, Gabriel L Wallau, Rebecca C Wade, Isabelle F T Viana, Roberto D Lins

“…The design of proteins capable effectively binding to specific protein targets is crucial for developing therapies, diagnostics, and vaccine candidates for viral infections. …”
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Structural basis of voltage-dependent gating in BK channels by Gustavo F. Contreras, Rong Shen, Ramon Latorre, Eduardo Perozo

“…Abstract The allosteric communication between the pore domain, voltage sensors, and Ca2+ binding sites in the calcium- and voltage-activated K+ channel (BK) underlies its physiological role as the preeminent signal integrator in excitable systems. …”
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BIT: Bayesian Identification of Transcriptional regulators from epigenomics-based query region sets by Zeyu Lu, Lin Xu, Xinlei Wang

“…Leveraging a comprehensive library of TR ChIP-seq data, BIT offers a fully integrated Bayesian approach to assess genome-wide consistency between user-provided epigenomic profiling data and the TR binding library, enabling the identification of critical TRs while quantifying uncertainty. …”
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Post-transcriptional Control of Tumor Cell Autonomous Metastatic Potential by CCR4-NOT Deadenylase CNOT7. by Farhoud Faraji, Ying Hu, Howard H Yang, Maxwell P Lee, G Sebastian Winkler, Markus Hafner, Kent W Hunter

“…CNOT7 ribonucleoprotein-immunoprecipitation (RIP) and integrated transcriptome wide analyses reveal that CNOT7-regulated transcripts are enriched for a tripartite 3'UTR motif bound by RNA-binding proteins known to complex with CNOT7, TOB1, and CNOT1. …”
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Prediction of Translational Regulation by Network Interaction in Synaptic Plasticity Induced with Centella asiatica by Nurhadi Ibrahim, Ibrahim Nadian, Dimas R. Noor, Fadilah Fadilah

“…This study showed potentiality of Centella asiatica in AD through its binding to several proteins such as TSC1, Rheb, and FMRP. …”
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Theoretical Prediction of the Impact of Phosphorus Doping on the Elastic Constants of Silicon by Azadeh Jafari, Behraad Bahreyni

“…In this study, we investigate the influence of phosphorus doping on the elastic constants of silicon across a wide temperature range using a combination of tight-binding simulations and deformation potential theory. …”
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Interaction of the Spo20 membrane-sensor motif with phosphatidic acid and other anionic lipids, and influence of the membrane environment. by Habib Horchani, Maud de Saint-Jean, Hélène Barelli, Bruno Antonny

“…However, this response was not specific. The membrane binding of the probe depended on the presence of phosphatidylethanolamine and also integrated the contribution of other anionic lipids, including phosphatidylserine and phosphatidyl-inositol-(4,5)bisphosphate. …”
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Approaches to expand the conventional toolbox for discovery and selection of antibodies with drug-like physicochemical properties by Hristo L. Svilenov, Paolo Arosio, Tim Menzen, Peter Tessier, Pietro Sormanni

“…Therefore, it is attractive to integrate new methods that can optimize the process of selecting antibodies with both desired target-binding and drug-like biophysical properties. …”
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Repurposing drugs for the human dopamine transporter through WHALES descriptors-based virtual screening and bioactivity evaluation by Ding Luo, Zhou Sha, Junli Mao, Jialing Liu, Yue Zhou, Haibo Wu, Weiwei Xue

“…However, traditional hDAT-targeting drugs, which interact with the primary binding site, encounter significant limitations, including addictive potential and stimulant effects. …”
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