Article
Chemistry, Multidisciplinary
Faraz Shaikh, Hio Kuan Tai, Nirali Desai, Shirley W. I. Siu
Summary: LigTMap is an online server that can efficiently predict protein targets of chemical compounds, outperforming other servers in both top 10 and top 1 success rates. It also provides ligand docking structures for further structural studies in computer-aided drug design.
JOURNAL OF CHEMINFORMATICS
(2021)
Article
Computer Science, Artificial Intelligence
Rachid Guerraoui, Anne-Marie Kermarrec, Guilhem Niot, Olivier Ruas, Francois Taiani
Summary: GoldFinger is a compact and fast-to-compute binary representation of datasets that approximates Jaccard's index. It accelerates KNN algorithms, protects user privacy, and achieves significant speedup in KNN queries.
IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
(2023)
Article
Mathematics
Alina Barbulescu, Lucica Barbes, Cristian Stefan Dumitriu
Summary: This study aims to analyze the similarity degree of molecules belonging to two subgroups of Aminoalkylindoles through Cheminformatics methods. The Tanimoto coefficients were computed to reveal the level of similarity, and dendrograms and heatmaps were built. The study also found atom-pair similarities within the same group and validated the clustering using the Kruskal-Wallis test.
Article
Computer Science, Artificial Intelligence
Chengdong Dong, Ajay Kumar
Summary: This paper introduces a new approach to accurately synthesize multi-view contactless 3D fingerprints and addresses the challenges of match accuracy and privacy concerns. The experimental results demonstrate the effectiveness of the proposed method.
IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE
(2023)
Article
Chemistry, Multidisciplinary
Haoqi Wang, Nirmitee Mulgaonkar, Lisa M. Perez, Sandun Fernando
Summary: Pharmacophore modeling is crucial in computer-aided drug design, and our Python tool ELIXIR-A can refine pharmacophores between multiple ligands, contributing to virtual screening platforms.
Article
Plant Sciences
Caio Canella Vieira, Diego Jarquin, Emanuel Ferrari do Nascimento, Dongho Lee, Jing Zhou, Scotty Smothers, Jianfeng Zhou, Brian Diers, Dean E. Riechers, Dong Xu, Grover Shannon, Pengyin Chen, Henry T. Nguyen
Summary: This study analyzed the response of soybean to off-target dicamba exposure and identified genomic regions associated with this response. Most soybean accessions showed a moderate response, and no differences were found across maturity groups and centers of origin. Significant associations were identified in certain candidate genes, indicating the possibility of developing non-GM soybean cultivars with improved tolerance to off-target dicamba exposure.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Ang Li, Hitoshi Mitsunobu, Shin Yoshioka, Takahisa Suzuki, Akihiko Kondo, Keiji Nishida
Summary: In this study, the authors perform structure-based rational engineering of the cytosine base editing system Target-AID to minimize off-target effects and decrease its size. The resulting cytosine base editing system is effective in minimizing RNA-mediated editing and gRNA-dependent/independent DNA off-targets in human cells.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Kedan He
Summary: In this study, the pharmacological affinity fingerprints of NPS compounds were predicted using Random Forest classification models. The results suggest that using Morgan fingerprints as input for the construction of Ph-fp can achieve satisfactory clustering performance.
JOURNAL OF CHEMINFORMATICS
(2022)
Article
Spectroscopy
Behafarid Ghalandari, Kazem Asadollahi, Farnaz Ghorbani, Suzan Ghalehbaghi, Saharnaz Rafiee, Ali Komeili, Seyed Kamran Kamrava
Summary: Photothermal therapy using nanoparticles has emerged as a promising approach for cancer treatment. However, the non-specific interactions between nanoparticles and proteins hinder their efficient use as photothermal agents. In this study, the interaction between two types of nanoparticles and model proteins was investigated, revealing distinct modes of interaction for charged and neutral nanoparticles. Furthermore, our findings suggest that charge functionalization of nanoparticles is an effective strategy for modulating their interaction with proteins.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Chemistry, Multidisciplinary
Sangjin Ahn, Si Eun Lee, Mi-Hyun Kim
Summary: Virtual screening has improved early stage drug discovery success rates, with recent methods benefiting from advances in machine learning and chemical information. Creative extraction of drug features is crucial for predicting drug-target interactions, and the development of a feature-driven classification model has shown promise in this area.
JOURNAL OF CHEMINFORMATICS
(2022)
Article
Chemistry, Analytical
Wei Zhang, Rui Shi, Kejun Dong, Hao Hu, Wan Shu, Yaoqin Mu, Bei Yan, Longjie Li, Xianjin Xiao, Hongbo Wang
Summary: The CRISPR-Cas12a system is an efficient and targeted genome editing tool. It can recognize and cleave target dsDNA sequences with insertion or deletion compared to the crRNA sequence. The tolerance of CRISPR-Cas12a to bubbles is determined by their location, size, and the GC base content of crRNA. Additionally, a new method for detecting mutations using CRISPR-Cas12a has been invented.
ANALYTICAL CHEMISTRY
(2022)
Article
Medicine, Research & Experimental
Huanhuan Shan, Zhiquan Liu, Yingqi Jia, Siyu Chen, Mao Chen, Yuning Song, Tingting Sui, Liangxue Lai, Zhanjun Li
Summary: The recently developed high-fidelity base editor, NGHiFi, showed improved on-target activity while significantly reducing off-target effects compared to NG-BE4max in Hoxc13-ablated rabbits. This enhanced specificity and reduced off-target effects of SpCas9-NG in cytidine base editing with NGHiFi system offer a promising tool for precise modeling of human diseases in rabbits.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2021)
Article
Computer Science, Artificial Intelligence
Jorge Martinez-Gil, Jose Manuel Chaves-Gonzalez
Summary: This work focuses on the data-driven approach for designing semantic similarity controllers, aiming to offer a set of solutions to human operators in the form of a Pareto front for choosing the best configuration for a specific use case. Multi-objective evolutionary algorithms are explored to find trade-offs between accuracy and interpretability.
KNOWLEDGE-BASED SYSTEMS
(2021)
Article
Biochemical Research Methods
Christian Anthon, Giulia Ilaria Corsi, Jan Gorodkin
Summary: The effectiveness of CRISPR/Cas9-mediated genome editing experiments relies on the careful selection of guide RNA (gRNA) for target recognition and cleavage activation. This study presents a user-friendly webserver that incorporates both on- and off-target prediction tools, CRISPRon and CRISPRoff, to facilitate gRNA selection.
Article
Biochemical Research Methods
Bin Liu, Jin Wang, Kaiwei Sun, Grigorios Tsoumakas
Summary: The discovery of drug-target interactions (DTIs) is crucial in pharmaceutical development. Computational methods are promising in predicting novel DTIs. This study presents a Fine-Grained Selective similarity integration approach (FGS) that captures and exploits the importance of similarities at a finer granularity.
BRIEFINGS IN BIOINFORMATICS
(2023)