Article
Computer Science, Information Systems
Rage Uday Kiran, Pamalla Veena, Penugonda Ravikumar, Chennupati Saideep, Koji Zettsu, Haichuan Shang, Masashi Toyoda, Masaru Kitsuregawa, P. Krishna Reddy
Summary: Periodic pattern mining is an emerging technique for knowledge discovery. This paper proposes a novel model and algorithm to find partial periodic patterns in temporal databases, and demonstrates their effectiveness and scalability through comprehensive experiments.
Article
Chemistry, Analytical
Yuting Chen, Siming Yuan, Yangzhong Liu, Guangming Huang
Summary: The induced nanoelectrospray ionization method was developed to desalt protein samples in solutions with high concentrations of non-volatile salts, allowing for fast and direct identification of protein-ligand interactions in complex samples. This method has the potential to be a reliable approach for investigating proteins and protein complexes in biological samples.
ANALYTICA CHIMICA ACTA
(2021)
Article
Chemistry, Multidisciplinary
Long Li, Zhen Li, Ziying Wang, Shuyu Chen, Rongying Liu, Xuyang Xu, Zhi Zhang, Linfei Ye, Yu Ding, Quan Luo, Sheng Cao, Lei Zhang, Anne Imberty, Guosong Chen
Summary: By controlling the symmetry and number of supramolecular interactions on protein surfaces, nonspecific interactions between proteins can be induced to form various nanoscale assemblies, including coiling nanowires, nanotubes, and nanosheets, without manipulating the protein's native surfaces. These nanoscale assemblies can spontaneously evolve into more ordered architectures, crystals. These findings reveal a transformation mechanism of protein self-assembly that has not been exploited before and may provide an approach to generate complex and transformable biomacromolecular self-assemblies.
Review
Biochemical Research Methods
Lun Hu, Xiaojuan Wang, Yu-An Huang, Pengwei Hu, Zhu-Hong You
Summary: This paper reviews recent efforts towards developing effective computational models for predicting protein-protein interactions (PPIs). It introduces algorithms for learning computational models for PPI prediction and classifies these models into different categories. Different validation schemes and metrics for evaluating prediction performance are discussed, as well as the use of biological databases in extensive experiments to compare different prediction models. Finally, open issues in PPI prediction for future work are presented, discussing how tackling these issues can lead to improved performance.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Chemistry, Physical
Shouhang Li, Zhen Tong, Cheng Shao, Hua Bao, Thomas Frauenheim, Xiangjun Liu
Summary: The electrical transport properties of hexagonal close-packed noble metals are almost isotropic due to the complementary contributions of different bands. These metals have weak electron-phonon interactions, resulting in small electron-phonon scattering rates, which is beneficial for electron and thermal transport. This suggests that hexagonal close-packed noble metals have great potential in electronics and solar cells.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Margarita Colberg, Jeremy Schofield
Summary: This paper presents an adaptive method to evaluate the configurational entropy and the mean first passage times for linear chain models with discontinuous potentials. The approach uses event-driven dynamical sampling in a massively parallel architecture. The method can be applied to optimize the folding process of protein systems.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Xuemin Chen, Tuo Zhang, Hanxiong Liu, Jiachen Zang, Chenyan Lv, Ming Du, Guanghua Zhao
Summary: A protein engineering approach is used to design and construct shape-anisotropic protein arrays by utilizing multiple interaction sites and tunable features. The assembly of these arrays can be controlled by external stimuli and their anisotropic morphologies can be correlated with protein arrangement details through crystallography.
Article
Chemistry, Multidisciplinary
Genwei Zhang, Chengxi Li, Anthony J. Quartararo, Andrei Loas, Bradley L. Pentelute
Summary: The study introduces an automated BLI-assisted affinity selection platform that enables rapid discovery of new binders and affinity maturation of known peptide binders with high selectivity. This technology also offers real-time monitoring of peptide binding during the selection process, a feature not achievable by current methods.
Review
Chemistry, Multidisciplinary
Qiuran Wang, Sam H. Brooks, Tianchang Liu, Neil C. Tomson
Summary: Cluster complexes have recently been designed with ligand scaffolds specifically tailored to support multinuclear transition metal cores in order to facilitate cooperative small molecule activation. The incorporation of geometric flexibility and redox-active ligands in the ligand design allows for unique small molecule activation modes, providing significant analogies to heterogeneous and metalloenzyme catalysts.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Kurt P. P. Lindquist, Xianghan Xu, Robert J. J. Cava
Summary: Exploring metal-halide structures allows for studying structure-property relationships in magnetic solids. This study investigates the magnetism of Ba2CoCl6, as well as the previously unreported analogues Ba2FeCl6, Ba2MnCl6, and Ba2MgCl6. The magnetic ordering temperatures in Ba2CoCl6, Ba2FeCl6, and Ba2MnCl6 vary based on ionic radius and electronic configuration of the transition metal.
CHEMISTRY OF MATERIALS
(2023)
Editorial Material
Biochemistry & Molecular Biology
Anastassis Perrakis, Titia K. Sixma
Summary: AlphaFold is the most ground-breaking application of AI in science so far, promising to revolutionize structural biology, but caution is advised in its implementation.
Article
Crystallography
Abeer A. AlObaid, Ahmed Boshaala, Younis O. Ben Amer, Abrahem F. Abrahem, Nabil Al-Zaqri, Mohammed Suleiman, Abdelkader Zarrouk, Nawaf Al-Maharik, Hussien A. Khamees, Ismail Warad
Summary: Mixing the neutral 2,4,6-tri(pyridin-2-yl)-1,3,5-triazine (tptz) ligand with Ni(II) salt under room temperature ultrasonic conditions resulted in a high-yield complex with two different nickel(II) centers, as confirmed by crystal structure analysis and various analytical methods like FT-IR, UV-Vis, CHN-EA, TGA, and EDX. The thermal stability of the complex was evaluated up to ~400 degrees C with multistep thermal decomposition, demonstrating its stability. The existence of coordinated and uncoordinated water molecules in the crystal lattice was also examined, providing further insights into the complex structure.
Article
Chemistry, Physical
Xiang Li, Yu Wang, Meifeng Liu, Yunlong Xie, Jiahua Min, Xiyu Chen, Jingwen Gong, Leiyu Li, Min Zeng, Yiming Xu, Yiru Wang, Biwen Li, Xiuzhang Wang, Jun-Ming Liu
Summary: Co3NiNb2O9 demonstrates a significant magnetoelectric response below 32K, with a large ME coefficient, and can achieve stable mutual control by magnetic or electric fields.
JOURNAL OF MATERIOMICS
(2021)
Article
Multidisciplinary Sciences
Miriam Cipullo, Genis Valentin Gese, Anas Khawaja, B. Martin Haellberg, Joanna Rorbach
Summary: Mitochondrial ribosomes are crucial for synthesizing proteins essential for oxidative phosphorylation. This research provides insights into the structure and assembly process of mitoribosomes, highlighting the importance of factors involved in 16S rRNA folding, methylation, and PTC formation.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Jorge Novoa, Monica Chagoyen, Carlos Benito, F. Javier Moreno, Florencio Pazos
Summary: Scientific knowledge is rapidly accumulating in the biomedical literature, and PubMed is the go-to database for accessing biomedicine-related articles with over 36 million entries. To aid users in navigating through this vast amount of information, we have developed PMIDigest, an interactive tool that automatically summarizes large sets of PubMed articles. This tool allows for classification and sorting of articles based on various criteria, such as article type and citation-related figures. It also provides a visual representation of the distribution of MeSH terms and an interactive citation network for easy identification of article clusters and hub articles. Furthermore, this system can also process entries from other databases like Scopus or Web of Science.