Article
Chemistry, Medicinal
Thomas Seidel, Christian Permann, Oliver Wieder, Stefan M. Kohlbacher, Thierry Langer
Summary: Knowledge of bound-state conformation is crucial for computer-aided drug design methods. CONFORGE, an open-source conformer ensemble generator, delivers state-of-the-art performance for all types of organic molecules in drug-like chemical space. It outperforms other open-source generators for small molecules and achieves the highest accuracy among benchmarked generators for macrocyclic structures.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemical Research Methods
Luciano Kagami, Alan Wilter, Adrian Diaz, Wim Vranken
Summary: ACPYPE software and website facilitate the generation of parameter files for MD simulations of small molecules using force fields commonly used for proteins and nucleic acids. It can generate MD input files in Gromacs, AMBER, CHARMM, and CNS formats using OpenBabel and ANTECHAMBER. It now supports input of SMILES strings and includes GAFF2 and GLYCAM force field conversion.
Review
Agricultural Engineering
Mateus Berwaldt Santos, Leyre Sillero, Darci Alberto Gatto, Jalel Labidi
Summary: Bioactive molecules are substances capable of interacting with living organisms and causing changes in them. Wood extractives contain significant amounts of these molecules, some of which exhibit good antioxidant and antimicrobial activity and can be used as preservatives. Conventional extraction methods have drawbacks such as high solvent, energy, and time consumption. To overcome these issues, new extraction techniques are being developed to optimize the process. Separation techniques like chromatography and molecular distillation can purify extractives and obtain desired molecules. This review provides an overview of the extraction and purification methods used for wood bioactive molecules, discussing factors such as raw material, solvent type, solid/liquid ratio, temperature, pressure, and extraction time. The application of extractives as preservatives for low durability woods is also analyzed. The study concludes that the quality and quantity of bioactive molecules depend on the methods and solvents employed for extraction, making the choice of method and solvent fundamental for achieving desired results.
INDUSTRIAL CROPS AND PRODUCTS
(2022)
Article
Biochemistry & Molecular Biology
Ioannis Stylianakis, Nikolaos Zervos, Jenn-Huei Lii, Dimitrios A. Pantazis, Antonios Kolocouris
Summary: We conducted a study on 145 reference organic molecules used in computer-aided drug design. By using various force fields and computational methods, we calculated the conformational energies and barriers of these molecules. The results provide valuable insights into the stability of different conformers and can be utilized in drug design projects.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2023)
Article
Construction & Building Technology
Xizhen Xu, Xiaoxin Ding, Qun Wang, Tiebing Chen, Ronghui Deng
Summary: As an important part of the prefabricated building standard system, the evaluation standards for prefabricated buildings are crucial in guiding their construction and development. However, the existing national evaluation standards are too general and lack consideration, leading to confusion in the evaluation of prefabricated buildings and hindering their development. In order to improve the evaluation standard system, this study analyzes the calculation methods of the prefabrication rate in different regions, compares different standards, and identifies key factors affecting the total score.
Article
Chemistry, Physical
Milan Oncak, Rajko Cosic, Rene Kalus
Summary: A comparative study was conducted to evaluate the reliability of a diatomics-in-molecules (DIM) representation in calculating the photoabsorption spectra of charged helium clusters. The results showed that the DIM approach is suitable for simulating larger ionic helium clusters with good agreement with accurate ab initio methods.
Article
Biophysics
Banafsheh Safari, Ayuob Aghanejad, Leila Roshangar, Soodabeh Davaran
Summary: Bone tissue engineering is an alternative therapeutic approach that aims to replace lost tissue and restore function by recapitulating the natural regeneration process. By utilizing biocompatible materials, osteoprogenitor/stem cells, and bioactive factors to mimic the bone microenvironment, the goal is to promote bone regeneration effectively.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2021)
Article
Energy & Fuels
F. S. J. Hoekstra, M. C. F. Donkers, H. J. Bergveld
Summary: Battery overpotential model identification approaches based on local and global Linear Parameter-Varying (LPV) input-output models are developed in this paper. The LPVcore toolbox is used for global identification, and an iterative scheme is proposed to obtain a complete empirical battery model that includes both the ElectroMotive Force (EMF) and the overpotential model. This approach achieves a similar precision to the common cascaded approach but requires less measurement data, resulting in a reduction in experiment time by a factor of 7 to 35.
JOURNAL OF ENERGY STORAGE
(2023)
Review
Chemistry, Analytical
Andra Mihaela Onas, Constanta Dascalu, Matei D. Raicopol, Luisa Pilan
Summary: Nucleic acid aptamers have emerged as promising biorecognition elements for electrochemical biosensors in various fields. This article provides an overview of the thermodynamic and structural aspects of aptamer-target interaction, as well as the methods used for determining aptamer-binding affinity and structural characterization. It also discusses key aspects of aptamer-modified electrodes for electrochemical sensing and summarizes effective small molecule aptasensing platforms from recent literature.
Article
Gastroenterology & Hepatology
Heidi Pauer, Felipe Lopes Teixeira, Avery V. Robinson, Thiago E. Parente, Marilia A. F. De Melo, Leandro A. Lobo, Regina M. C. P. Domingues, Emma Allen-Vercoe, Rosana B. R. Ferreira, Luis Caetano M. Antunes
Summary: This study investigated the biological activity of small molecules produced by the human gut microbiota against the human pathogen Vibrio cholerae, and found that these molecules can inhibit the motility and mucin penetration of V. cholerae. RNA sequencing revealed that the gut metabolome has a significant impact on global gene expression in V. cholerae. This research suggests that small molecules from the gut metabolome may play a crucial role in microbe-microbe interactions in the gut environment.
Article
Chemistry, Physical
Iker Ortiz de Luzuriaga, Sawssen Elleuchi, Khaled Jarraya, Emilio Artacho, Xabier Lopez, Adria Gil
Summary: The computational study of DNA and its interaction with ligands is important for developing new therapeutic strategies. However, the complexity of such systems poses challenges in considering different types of interactions simultaneously. This study compares various computational methods and demonstrates the efficiency and accuracy of LS-DFT and DLPNO-CCSD(T) in describing the interaction of small molecules and cations with DNA.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Nanoscience & Nanotechnology
Sha Yang, Zhuyang Zhao, Binpan Wang, Liu Feng, Jie Luo, Ruijia Deng, Jing Sheng, Xueping Gao, Shuang Xie, Ming Chen, Kai Chang
Summary: Bioactive small molecules are important biomarkers for recognizing modulated organismal metabolism in correlation with diseases. This study presents a modular DNA tetrahedron-based nanomachine for ultrasensitive detection of intracellular small molecules, such as ATP. The nanomachine shows a linear response to ATP in the concentration range of 1 pM to 10 nM, with a low detection limit of 0.40 pM. The nanomachine can be used for intracellular ATP imaging and distinguishing tumor cells from normal cells based on ATP levels.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Medicinal
Chao Yang, Yingkai Zhang
Summary: A new scoring function Lin_F9 is introduced in this work, which achieves top scoring power among classical scoring functions in CASF-2016 benchmark test set. Parameters in Lin_F9 are obtained with a multistage fitting protocol, and it has been implemented in Smina for docking applications and further improvement of scoring functions.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Computer Science, Information Systems
Kazuki Takeuchi, Keito Sugawara, Ippei Nojima, Toshiaki Tsuji
Summary: This study compared and evaluated measurement methods for ankle joint torque, and proposed a method using a single 6-axis force sensor at the toe. The experimental results showed that the accuracy of this method was comparable to using two 6-axis force sensors, indicating its usefulness for both accuracy and sensor reduction.
Review
Food Science & Technology
Mahta Mirzaei, Amin Shavandi, Saeed Mirdamadi, Nazila Soleymanzadeh, Paria Motahari, Niloofar Mirdamadi, Muriel Moser, Gilles Subra, Houman Alimoradi, Stanislas Goriely
Summary: Yeast cells are a rich source of proteins and bioactive peptides with multiple functionalities. While research on yeast extract has increased, there is a lack of systematic review on the functional properties attributed to bioactive peptides content and production methods. Predicting and designing new peptide sequences can effectively transfer research findings into practical market applications.
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2021)
Article
Pharmacology & Pharmacy
Xiao-Yi Zeng, Hao Wang, Fang Bai, Xiu Zhou, Song-Pei Li, Lu-Ping Ren, Ruo-Qiong Sun, Charlie C. L. Xue, Hua-Liang Jiang, Li-Hong Hu, Ji-Ming Ye
BRITISH JOURNAL OF PHARMACOLOGY
(2015)
Article
Chemistry, Medicinal
Fang Bai, Sha Liao, Junfeng Gu, Hualiang Jiang, Xicheng Wang, Honglin Li
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2015)
Article
Multidisciplinary Sciences
Fang Bai, Faruck Morcos, Yang-Sung Sohn, Merav Darash-Yahana, Celso O. Rezende, Colin H. Lipper, Mark L. Paddock, Luhua Song, Yuting Luo, Sarah H. Holt, Sagi Tamir, Emmanuel A. Theodorakis, Patricia A. Jennings, Jose N. Onuchic, Ron Mittler, Rachel Nechushtai
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2015)
Article
Multidisciplinary Sciences
Kendrick H. Yim, Thomas L. Prince, Shiwei Qu, Fang Bai, Patricia A. Jennings, Jose N. Onuchic, Emmanuel A. Theodorakis, Leonard Neckers
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Article
Multidisciplinary Sciences
Fang Bai, Faruck Morcos, Ryan R. Cheng, Hualiang Jiang, Jose N. Onuchic
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Article
Chemistry, Medicinal
Wei Zhou, Xiaofeng Liu, Zhengchao Tu, Lianwen Zhang, Xin Ku, Fang Bai, Zhenjiang Zhao, Yufang Xu, Ke Ding, Honglin Li
JOURNAL OF MEDICINAL CHEMISTRY
(2013)
Article
Multidisciplinary Sciences
Fang Bai, Yechun Xu, Jing Chen, Qiufeng Liu, Junfeng Gu, Xicheng Wang, Jianpeng Ma, Honglin Li, Jose N. Onuchic, Hualiang Jiang
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2013)
Article
Chemistry, Medicinal
Yu Zhou, Yan Fu, Wanchao Yin, Jian Li, Wei Wang, Fang Bai, Shengtao Xu, Qi Gong, Tao Peng, Yu Hong, Dong Zhang, Dan Zhang, Qiufeng Liu, Yechun Xu, H. Eric Xu, Haiyan Zhang, Hualiang Jiang, Hong Liu
Summary: A novel kinetics-driven drug design strategy was employed to discover new-generation AChE inhibitors with longer drug-target residence time and larger safety window. Compound 12 was identified as a highly potent, selective, orally bioavailable, and brain preferentially distributed AChE inhibitor, showing significant cognitive improvement in different mouse models. Phase I trials demonstrated good safety, tolerance, and pharmacokinetic profiles of 12, supporting its further investigation in phase II trials for AD treatment.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Qian Wang, Lin Wang, Yumin Zhang, XiangLei Zhang, Leike Zhang, Weijuan Shang, Fang Bai
Summary: This study reveals the globally cooperative conformational dynamics of the S protein of SARS-CoV-2 through coarse-grained molecular dynamic simulations, and discovers an allosteric path that correlates the motion of the receptor-binding domain with the motion of the subdomains of the S protein. Based on this finding, non-RBD binding modulators were designed to inhibit the conformational change of the S protein and inhibit SARS-CoV-2. The inhibitory effect and function stages of these modulators were evaluated experimentally.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Shiwei Li, Sanan Wu, Lin Wang, Fenglei Li, Hualiang Jiang, Fang Bai
Summary: This article summarizes the major developments in computational methods for predicting protein-protein interactions (PPIs) using artificial intelligence algorithms. It covers the sources of experimental PPI data, PPI prediction methods based on sequential information, methods using structural information as input feature, and methods designed by combining different features. The state-of-the-art computational PPI prediction methods are reviewed for each category. The article also discusses the flaws in this field and future directions for next-generation algorithms.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Zhongneng Zhou, Zijing Chen, Xiu-Wen Kang, Yalin Zhou, Bingyao Wang, Siwei Tang, Shuhua Zou, Yifei Zhang, Qiaoyu Hu, Fang Bai, Bei Ding, Dongping Zhong
Summary: In this study, the photocycle of the FMN-Gln-Tyr motif in the BLUF domain of OaPAC was investigated using computational simulations. The results show that forward PCET is concerted, while only the wild-type protein proceeds with an ultrafast reverse PCET process.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Physical
Fang Bai, Hualiang Jiang
Summary: Traditional drug discovery focuses on binding affinity, but drug efficacy is also influenced by binding kinetics. The binding free energy landscape constructor can predict binding kinetics and provide insights into molecular mechanisms, aiding drug design.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Medicinal
Lin Wang, Feng-lei Li, Xin-yue Ma, Yong Cang, Fang Bai
Summary: Protein-protein interactions (PPIs) play crucial roles in biological processes. PPI-Miner is a computational method that utilizes protein motifs as queries to identify potential protein interacting partners. It matches motifs to proteins and builds PPI complex structures based on the binding mode of the discovered motifs. PPI-Miner has applications in discovering PPIs and can be used in the rational design of molecular glues and protein vaccines.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Review
Chemistry, Medicinal
Steve Agajanian, Mohammed Alshahrani, Fang Bai, Peng Tao, Gennady M. Verkhivker
Summary: Allosteric mechanisms play a crucial role in regulating complex biochemical processes and communication in cells. Understanding and characterizing these mechanisms require innovative computational and experimental approaches, empowered by artificial intelligence technologies, to obtain detailed knowledge of allosteric states and interactions. Recent developments in deep mutational scanning, structural prediction methods, machine learning, and structural biology have provided new insights into allosteric protein functions and their implications in viral infection.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Multidisciplinary
Anat Iosub-Amir, Fang Bai, Yang-Sung Sohn, Luhua Song, Sagi Tamir, Henri-Baptiste Marjault, Guy Mayer, Ola Karmi, Patricia A. Jennings, Ron Mittler, Jose N. Onuchic, Assaf Friedler, Rachel Nechushtai