Review
Biochemistry & Molecular Biology
Clara Blanes-Mira, Pilar Fernandez-Aguado, Jorge De Andres-Lopez, Asia Fernandez-Carvajal, Antonio Ferrer-Montiel, Gregorio Fernandez-Ballester
Summary: The rapid advances in 3D techniques and computational methods have led to the identification of highly active compounds in computer drug design. Molecular docking is widely used in virtual screening to filter potential ligands targeted to proteins. Consensus scoring methods improve virtual screening outcomes by averaging the rank or score of individual molecules obtained from different docking programs.
Article
Biochemical Research Methods
Taj Mohammad, Yash Mathur, Md Imtaiyaz Hassan
Summary: InstaDock is a free and open access GUI program that efficiently performs molecular docking and high-throughput virtual screening. It is the easiest and more interactive interface for molecular docking and high-throughput virtual screening compared to existing GUIs.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Engineering, Multidisciplinary
Siwei Song, Yi Wang, Fang Chen, Mi Yan, Qinghua Zhang
Summary: This study presents a methodology that combines domain knowledge, machine learning algorithms, and experiments to accelerate the discovery of novel energetic materials. The established high-throughput virtual screening system allows for the rapid selection of candidate molecules with promising properties and desirable crystal packing modes from a large molecular space. Experimental results confirm the effectiveness of the proposed methodology.
Article
Chemistry, Multidisciplinary
Matz Liebel, Irene Calderon, Nicolas Pazos-Perez, Niek F. van Hulst, Ramon A. Alvarez-Puebla
Summary: Large-scale SERS particle screening (LSSPS) is a fast multiplexed widefield screening approach that quantifies both Raman and Rayleigh scattering simultaneously, allowing for direct quantification of the fraction of SERS-active particles and unprecedented correlation of SERS activity with particle size.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Chemistry, Medicinal
Nitesh Mani Tripathi, Anupam Bandyopadhyay
Summary: High-throughput virtual screening (HTVS) is an important biopharmaceutical technology that utilizes computational algorithms to discover biologically active compounds from large compound libraries, saving resources and time in drug discovery. Peptide-based drug discovery has gained momentum in recent years, highlighting the need for a high-fidelity HTVS platform for chemically versatile peptide libraries.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Matthew Rienzo, Shaina J. Jackson, Lawrence K. Chao, Timothy Leaf, Thomas J. Schmidt, Adam H. Navidi, Dana C. Nadler, Maud Ohler, Michael D. Leavell
Summary: Systems metabolic engineering is a challenging task that involves rewiring microbial metabolism to generate high-value molecules from inexpensive feedstocks. High-throughput screening of engineered organism variants for scalable manufacturing potential is necessary, requiring carefully controlled, parallel fermentations and precise analysis of complex mixtures. Strategies to design high-throughput, small-scale fermentation models for predicting improved strain performance at large commercial scale, including microplate and microfluidics-based screening systems, are essential for success.
METABOLIC ENGINEERING
(2021)
Article
Chemistry, Multidisciplinary
Yu-Ting Liu, Xian-Bin Li, Hui Zheng, Nian-Ke Chen, Xue-Peng Wang, Xu-Lin Zhang, Hong-Bo Sun, Shengbai Zhang
Summary: This study reports the largest scale PCM materials searching, starting with 124,515 candidate materials, and eventually screening 158 potential PCM materials using a rational high-throughput screening strategy. Further analyses revealed 52 materials with properties similar to the GST system, some of which show potential for low power consumption and suitability for optical/electrical PCM applications.
ADVANCED FUNCTIONAL MATERIALS
(2021)
Article
Chemistry, Physical
Matthew Bain, Jose L. Godinez Castellanos, Stephen E. Bradforth
Summary: High-repetition-rate lasers have the potential to revolutionize ultrafast spectroscopy by enabling routine analysis for machine learning models in the design of photochemical syntheses. In this study, we combine innovations in line scan cameras and micro-electro-mechanical grating modulators with high-pressure liquid chromatography pumps to develop a transient absorption spectrometer that can characterize photoreactions in minutes. Additionally, we demonstrate the utility of this technique in exploring the effects of conformational modification on excited-state processes.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Vei Wang, Gang Tang, Ya-Chao Liu, Ren-Tao Wang, Hiroshi Mizuseki, Yoshiyuki Kawazoe, Jun Nara, Wen Tong Geng
Summary: Two-dimensional materials have attracted attention for their unique physical properties and their ability to meet the demands of nanoscale devices. In this study, we conducted high-throughput calculations and screening to identify 73 direct-gap and 183 indirect-gap 2D nonmagnetic semiconductors based on criteria for thermodynamic, mechanical, dynamic, and thermal stabilities, as well as conductivity type. A database of these materials was created, providing a platform for computational modeling and design of new 2D semiconductors and heterostructures in applications such as photocatalysis and nanoscale devices. Additionally, a linear fitting model was proposed to accurately evaluate band gap, ionization energy, and electron affinity of 2D semiconductors with lower computational cost compared to hybrid DFT methods.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemical Research Methods
Madeline E. McCarthy, William B. Dodd, Xiaoming Lu, Daniel J. Pritko, Nishi D. Patel, Charlotte V. Haskell, Hugo Sanabria, Mark A. Blenner, Marc R. Birtwistle
Summary: We propose a theory for high-throughput genetic interaction screens, which extends the Multiplexing using Spectral Imaging and Combinatorics (MuSIC) approach to create 100,000 spectrally unique MuSIC barcodes. Experimental testing of this theory could revolutionize genetic perturbation technology and knowledge of genetic function. Additionally, a genome-scale spectral barcode library could have widespread applications in genetic screening and lineage tracing.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Engineering, Environmental
Min Cheng, Shihui Wang, Zhiyuan Zhang, Xu Ji, Chong Liu, Yiyang Dai, Yagu Dang, Li Zhou
Summary: This study proposes a high-throughput virtual screening strategy for the selection of metal-organic frameworks (MOFs) for Xe recovery from exhaled anesthetic gas mixture. Through pre-screening and simulation evaluation, ten top-performing MOFs for Xe recovery were identified, and three design strategies for developing high-performing new MOFs were proposed.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Chemistry, Physical
Mads Kruse, Urko Petralanda, Morten N. Gjerding, Karsten W. Jacobsen, Kristian S. Thygesen, Thomas Olsen
Summary: We performed a high throughput computational search in the C2DB and identified 63 ferroelectric materials, including 49 with in-plane polarization, 8 with out-of-plane polarization, and 6 with coupled in-plane and out-of-plane polarization. Most known 2D ferroelectrics were recovered and the predicted ones are accessible by direct exfoliation. About 25% of the materials showed a metastable state in the non-polar structure. We also discussed the case of VAgP2Se6, a magnetic pyroelectric material with switchable polarization coupled to magnetic excitation spectrum.
NPJ COMPUTATIONAL MATERIALS
(2023)
Article
Biotechnology & Applied Microbiology
Marshall S. Ma, Subramanian Sundaram, Lihua Lou, Arvind Agarwal, Christopher S. Chen, Thomas G. Bifano
Summary: Three dimensional engineered cardiac tissues (3D ECTs) are crucial in vitro models for assessing drug cardiotoxicity, but the low throughput of current assays limits their efficiency. To overcome this limitation, an innovative mosaic imaging system was developed to measure contractile force of 3D ECTs seeded on a 96-well plate, increasing throughput to 96 samples per measurement.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Review
Chemistry, Analytical
Lina Shi, Sutong Liu, Xue Li, Xiwei Huang, Hongzhi Luo, Qianwen Bai, Zhu Li, Lijun Wang, Xiaoxin Du, Cheng Jiang, Shan Liu, Chenzhong Li
Summary: High-throughput screening platforms are crucial for processing large amounts of experimental data rapidly and efficiently. The development of miniaturized high-throughput screening platforms is essential in the fields of biotechnology, medicine, and pharmacology. Droplet microarrays, as novel screening platforms, can effectively overcome the disadvantages of traditional microtiter plates, such as high reagent and cell consumption, low throughput, and cross-contamination. This article provides a brief overview of the preparation and compound addition methods of droplet microarrays, as well as their applications in biomedicine, drug development, and individualized medicine.
Article
Chemistry, Medicinal
Raitis Bobrovs, Iveta Kanepe, Nauris Narvaiss, Liene Patetko, Gints Kalnins, Mihails Sisovs, Anna L. Bula, Solveiga Grinberga, Martins Boroduskis, Anna Ramata-Stunda, Nils Rostoks, Aigars Jirgensons, Kaspars Tars, Kristaps Jaudzems
Summary: A study was conducted on high-throughput virtual screening against SARS-CoV-2 mRNA cap methyltransferases, leading to the identification of compounds with potential for developing efficient viral MTase inhibitors, although their selectivity and cell permeability need improvement.
Article
Multidisciplinary Sciences
Hironori Kaji, Hajime Suzuki, Tatsuya Fukushima, Katsuyuki Shizu, Katsuaki Suzuki, Shosei Kubo, Takeshi Komino, Hajime Oiwa, Furitsu Suzuki, Atsushi Wakamiya, Yasujiro Murata, Chihaya Adachi
NATURE COMMUNICATIONS
(2015)
Article
Materials Science, Multidisciplinary
Furitsu Suzuki, Katsuyuki Shizu, Hisafumi Kawaguchi, Shinya Furukawa, Tohru Sato, Kazuyoshi Tanaka, Hironori Kaji
JOURNAL OF MATERIALS CHEMISTRY C
(2015)
Article
Physics, Applied
Yoshimasa Wada, Katsuyuki Shizu, Shosei Kubo, Tatsuya Fukushima, Takuya Miwa, Hiroyuki Tanaka, Chihaya Adachi, Hironori Kaji
APPLIED PHYSICS EXPRESS
(2016)
Article
Polymer Science
Katsuyuki Shizu, Takuya Miwa, Yoshimasa Wada, Isamu Ogata, Hironori Kaji
JOURNAL OF PHOTOPOLYMER SCIENCE AND TECHNOLOGY
(2017)
Article
Multidisciplinary Sciences
Takuya Miwa, Shosei Kubo, Katsuyuki Shizu, Takeshi Komino, Chihaya Adachi, Hironori Kaji
SCIENTIFIC REPORTS
(2017)
Article
Chemistry, Multidisciplinary
Keita Tani, Toru Yashima, Kanae Miyanaga, Kazushige Hori, Kenta Goto, Fumito Tani, Yume Habuka, Katsuaki Suzuki, Katsuyuki Shizu, Hironori Kaji
Article
Multidisciplinary Sciences
Hiroki Uratani, Shosei Kubo, Katsuyuki Shizu, Furitsu Suzuki, Tatsuya Fukushima, Hironori Kaji
SCIENTIFIC REPORTS
(2016)
Article
Chemistry, Physical
Katsuyuki Shizu, Chihaya Adachi, Hironori Kaji
JOURNAL OF PHYSICAL CHEMISTRY A
(2020)
Article
Chemistry, Multidisciplinary
Katsuyuki Shizu, Chihaya Adachi, Hironori Kaji
Summary: Singlet fission materials have the potential to overcome traditional efficiency limits of OLEDs, with 55BT showing efficient SF in a locally excited singlet state. Its covalent bonding of tetracene units makes it a promising triplet sensitizer for near-infrared OLEDs, compared to other SF systems like the tetracene dimer.
Article
Chemistry, Physical
Yoshimasa Wada, Katsuyuki Shizu, Hironori Kaji
Summary: Efficient organic light-emitting diodes rely on well-balanced transition dipole moments and small energy splitting between excited singlet and triplet states, with some highly twisted donor-acceptor-type TADF molecules showing high performance despite sacrificing the former for the latter. Study suggests that the dynamics of excitons play a critical role in such TADF systems.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Chemistry, Physical
Katsuyuki Shizu, Hironori Kaji
Summary: An economical method for predicting electronic transition rate constants from excited states of molecules using density functional theory and the Fermi golden rule has been successfully applied to studying the excited-state decay mechanism of benzophenone. The calculated rate constants are consistent with experimental data, confirming the reliability of the method. Population kinetics calculations suggest that the predominant decay pathway for benzophenone is S-1 -> T-2 -> T-1 -> S-0.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Chemistry, Multidisciplinary
Yu Kusakabe, Yoshimasa Wada, Tomoya Misono, Katsuaki Suzuki, Katsuyuki Shizu, Hironori Kaji
Summary: Members of the imidazole family are widely used in the field of electron transporting, host, fluorescent, and phosphorescent materials. However, the emission color of imidazole-based organic light-emitting diodes (OLEDs) has been limited to blue to green. In this study, four acridan-imidazole systems are designed to achieve deep or pure-blue emission, and one of them exhibits a high external quantum efficiency (EQEMAX) in its application to OLEDs.
Article
Chemistry, Multidisciplinary
Chang-Ki Moon, Katsuaki Suzuki, Katsuyuki Shizu, Chihaya Adachi, Hironori Kaji, Jang-Joo Kim
ADVANCED MATERIALS
(2017)
Article
Polymer Science
Katsuyuki Shizu, Hironori Kaji
JOURNAL OF PHOTOPOLYMER SCIENCE AND TECHNOLOGY
(2016)
