Results 11 to 20 of about 18,469,580 (392)

BERT2DAb: a pre-trained model for antibody representation based on amino acid sequences and 2D-structure

mAbs, 2023
Prior research has generated a vast amount of antibody sequences, which has allowed the pre-training of language models on amino acid sequences to improve the efficiency of antibody screening and optimization.
Xiaowei Luo, Fan Tong, Wenbin Zhao, Xiangwen Zheng, Jiangyu Li, Jing Li, Dongsheng Zhao   +6 more
doaj   +1 more source

The 5′ and 3′ Untranslated Regions of the Japanese Encephalitis Virus (JEV): Molecular Genetics and Higher Order Structures

Frontiers in Microbiology, 2021
The untranslated region (UTRs) of viral genome are important for viral replication and immune modulation. Japanese encephalitis virus (JEV) is the most significant cause of epidemic encephalitis worldwide.
Hong Liu, Hong Liu, Jun Zhang, Yuzhen Niu, Guodong Liang   +4 more
doaj   +1 more source

RNA Secondary Structure Prediction [PDF]

Current Protocols in Nucleic Acid Chemistry, 2000
AbstractDetails for predicting secondary structure of RNA sequences using free energy minimization are given. Protocols present the use of the RNAstructure computer program (for PCs) and the mfold server (for Unix platforms). The minimum free energy structure and a set of suboptimal structures with similar free energies are predicted.
Mathews, David H., Turner, Douglas H., Zuker, Michael   +2 more
openaire   +6 more sources

Conservation of Differential Animal MicroRNA Processing by Drosha and Dicer

Frontiers in Molecular Biosciences, 2022
In complex biochemical systems, an enzyme, protein, or RNA, symbolized as E, has hundreds or thousands of substrates or interacting partners. The relative specificity hypothesis proposes that such an E would differentially interact with and influence its
Xiaoxiao Zhang, Fanming Yang, Fanzou Liu, Qiuhuan Tian, Min Hu, Peng Li, Yan Zeng   +6 more
doaj   +1 more source

RNA secondary structure prediction using deep learning with thermodynamic integration

Nature Communications, 2020
Accurate predictions of RNA secondary structures can help uncover the roles of functional non-coding RNAs. Although machine learning-based models have achieved high performance in terms of prediction accuracy, overfitting is a common risk for such highly
Kengo Sato, Manato Akiyama, Y. Sakakibara   +2 more
semanticscholar   +1 more source

Effects of Chemical Post-treatments on Structural and Physicochemical Properties of Silk Fibroin Films Obtained From Silk Fibrous Waste

Frontiers in Bioengineering and Biotechnology, 2020
Silk fibroin (SF) is a protein polymer claimed to have outstanding potential for medical applications. However, because of the manufacturing process, materials from regenerated SF exhibit a higher percentage of amorphous structures.
Melissa Puerta, Maria S. Peresin, Adriana Restrepo-Osorio, Adriana Restrepo-Osorio   +3 more
doaj   +1 more source

UFold: fast and accurate RNA secondary structure prediction with deep learning

bioRxiv, 2020
For many RNA molecules, the secondary structure is essential for the correction function of the RNA. Predicting RNA secondary structure from nucleotide sequences is a long-standing problem in genomics, but the prediction performance has reached a plateau
Laiyi Fu, Yingxin Cao, Jie Wu, Qinke Peng, Q. Nie, Xiaohui S. Xie   +5 more
semanticscholar   +1 more source

Novel perspectives for SARS-CoV-2 genome browsing

Journal of Integrative Bioinformatics, 2021
SARS-CoV-2 has spread worldwide and caused social, economic, and health turmoil. The first genome assembly of SARS-CoV-2 was produced in Wuhan, and it is widely used as a reference.
Gültekin Visam, Allmer Jens
doaj   +1 more source

Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy

Nucleic Acids Research, 2020
The current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication.
A. Wacker, J. Weigand, Sabine R. Akabayov, N. Altincekic, J. Bains, Elnaz Banijamali, O. Binas, Jesús Castillo-Martínez, E. Çetiner, Betül Ceylan, Liang-Yuan Chiu, Jesse Davila-Calderon, K. Dhamotharan, E. Duchardt-Ferner, J. Ferner, L. Frydman, B. Fürtig, J. Gallego, J. T. Grün, C. Hacker, Christina Haddad, Martin Hähnke, M. Hengesbach, Fabian Hiller, Katharina F. Hohmann, Daniel Hymon, Vanessa de Jesus, H. Jonker, Heiko Keller, Božana Knezic, Tom Landgraf, F. Löhr, Le Luo, K. Mertinkus, C. Muhs, Mihajlo Novakovic, Andreas Oxenfarth, Martina Palomino-Schätzlein, Katja Petzold, S. A. Peter, D. Pyper, N. Qureshi, Magdalena Riad, C. Richter, K. Saxena, Tatjana Schamber, T. Scherf, Judith Schlagnitweit, A. Schlundt, Robbin Schnieders, Harald Schwalbe, Alvaro Simba-Lahuasi, S. Sreeramulu, E. Stirnal, Alexey Sudakov, Jan-Niklas Tants, B. Tolbert, Jennifer Vögele, Lena Weiß, Julia Wirmer‐Bartoschek, Maria A Wirtz Martin, J. Wöhnert, Heidi Zetzsche   +62 more
semanticscholar   +1 more source

Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins

Molecules, 2017
Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins.
Koichi Kato, Tomoki Nakayoshi, Shuichi Fukuyoshi, Eiji Kurimoto, Akifumi Oda   +4 more
doaj   +1 more source