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Download jmol5/26/2023 ![]() An ideal single crystal will exhibit a perfect ordered structure. The improved DeepSnap-DL system will be a powerful tool for computer-aided molecular design as a novel QSAR system.Ĭrystalline materials are known for their well-defined periodic structure and their properties have been widely applied in numerous fields. ![]() 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. Permute ions in a geometry to match another geometry.Ĭonvert a strain tensor to order parameters.Ĭonstruct a deformation tensor from a strain tensor.Ĭreate a supercell by replicating a geometry.Growth-regulating factors (GRFs) encode plant-specific transcription factors that play a vital role in regulation of plant growth, development, and stress response. Get the chemical symbol for an atomic number. Interpolate a chain of images between two POSCAR files.įind the distance along a path in k-space.Įvaluate the Murnaghan equation of state.Įxtract energies and hyperdistance from NEB calculation.įit energies and forces of a NEB calculation using a spline.ĭetermine number of images used in a NEB calculation. Interpolate_poscar(filename1,filename2,N) Import energies from a VASP OSZICAR file. Get the atomic number for a chemical symbol.Įxport a geometry struct as a VASP POSCAR file.Ĭalculate hyperdistance between two geometry structures. For more details, see documentation in source code (or use the help command, e.g. Usageīelow is a summary of VASPLAB functions. Then, from MATLAB, open File->Set Path, and add the VASPLAB folder to your path. To install VASPLAB, place the VASPLAB folder somewhere on your hard drive (such as in your MATLAB folder). MATLAB functions for processing data from the Vienna Ab initio Simulation Package (VASP) and performing other common tasks related to the atomistic modeling of solid-state systems.
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