Consequently, we obtained that the three prediction models of agonists or antagonists of MIEs achieved high prediction-performance by optimizing the parameters of DeepSnap, such as the angle used in the depiction of the image of a 3D-chemical structure, data-split, and hyperparameters in DL. Therefore, in this study, we constructed an improved DeepSnap-DL system by combining the processes of generating an image from a 3D-chemical structure, DL using the image as input data, and statistical calculation of prediction-performance. However, there is room for improvement of this system’s time-consumption. This method can extract feature values from images generated on a three-dimensional (3D)-chemical structure as a novel QSAR analytical system. Previously, we have reported the high performance of prediction models molecular initiation events (MIEs) on the adverse toxicological outcome using a DL-based QSAR method, called DeepSnap-DL. Molecular design and evaluation for drug development and chemical safety assessment have been advanced by quantitative structure–activity relationship (QSAR) using artificial intelligence techniques, such as deep learning (DL). Further functional studies of kiwifruit GRFs in plant growth, development, and stress response will provide valuable insights for kiwifruit breeders. Taken together, we systematically analyzed the characterization of kiwifruit GRF family members for their potential role in kiwifruit development and Pseudomonas syringae pv. Protein-protein interaction analysis predicted AtGIF protein orthologs for AcGRFs and AeGRFs. The subcellular localization indicated the presence of kiwifruit GRFs in the nucleus of the plant cell. The presence of conserved protein structures and cis-regulatory elements caused functional divergence in duplicated gene pairs. We observed two genes in Ae (AeGRF6.1, AeGRF 6.2) and two genes in Ac (AcGRF 6.1, AeGRF 6.2) significantly upregulated in different RNA-seq datasets. The higher expression levels of kiwifruit GRFs in young tissues and under stress conditions indicated their regulatory role in kiwifruit growth and development. Synteny analysis showed that whole-genome duplication played a key role in the expansion of the GRF family in kiwifruit. Additionally, kiwifruit GRFs showed motif composition and gene structure similarities within the same group. Phy-logenetic analysis showed that kiwifruit GRF proteins were clustered into five distinct groups. eriantha are referred to as AeGRF) distributed on 21 chromosomes. eriantha is referred to as Ae, and GRF genes in A. chinensis are referred to as AcGRF) distributed on 17 chromosomes and one contig, and 26 GRF genes in A. chinensis is referred to as Ac, and GRF genes in A. In the present study, we identified 22 GRF genes on A. Although GRFs have been identified in various plants, there is no reported work available in Actinidia (commonly known as kiwifruit) so far. Although it cannot be considered as top product from its category, the tool does what it says and is suitable for beginners and professionals alike.Growth-regulating factors (GRFs) encode plant-specific transcription factors that play a vital role in regulation of plant growth, development, and stress response. The generated information can be printed, copied to the Clipboard, or exported it to JPG, PNG, or PPM.Īll things considered, Jmol comes packed with limited features for helping you analyze chemical data in a 3D environment. There are several configuration settings designed to help you pick a default atom size, specify the bonding distance, bond radius and tolerance, use a built-in script editor, as well as check a console for errors and history details. The application enables users to zoom in or out, move and rotate the selected object to different angles, select a group of atoms, measure the distance between atoms, enable the animation mode, create a list with atoms and modify their properties in terms of FPS, scale, amplitude, radius, and vibration, as well as undo or redo actions. Jmol sports a clean and straightforward layout that gives users the possibility to upload files with the following formats: ADF, MDL, PDB, CIF, or XYZ. You can copy it on any USB flash drive or other devices, and take it with you whenever you need to study chemical information on the breeze. Since this is a portable program, it is important to mention that it doesn’t leave any traces in the Windows Registry. This is a Java-based application, so before installing the application you should make sure you have the environment installed on the computer. Jmol is a Windows utility built specifically for helping you analyze chemical information in a 3D working environment.
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