Structural Genomics

Mat-Sharani, Shuhaila; Quay, Doris H.X.; Ng, Chyan Leong; Firdaus-Raih, Mohd

doi:10.1016/b978-0-12-809633-8.20155-6

Cited by 3 publications

(2 citation statements)

References 28 publications

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“…The science of genomics can be divided into two broad groups namely: structural and functional genomics. Structural genomics seeks to gain an insight into the structural organization of the whole genome using computational modelling or experimental approaches for accurate identification and characterization of genes [17]. Structural genomics encompasses sequencing and mapping, genome organization and comparative genomics.…”

Section: Application Of Genomics In Plant Breeding For Climate Resilimentioning

confidence: 99%

Application of Genomics and Phenomics in Plant Breeding for Climate Resilience

Ndlovu

2020

APRJ

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Advances in the fields of genomics and phenomics are currently creating significant foundations for the sustainable intensification of plant breeding initiatives targeting climate resilience. Genomics is a biological study that focuses on architecture, function, editing, mapping, and evolution of genomes. It can be applied extensively in climate resilience breeding for cost-effective, rapid, and high-through put genotyping, phenotyping, and trait mapping. The efficacy of genomics-assisted breeding (GAB) is strongly hinged on the high resolution and robustness of Next Generation Sequencing (NGS) and CRISPR/Cas9-based Gene Editing systems. The integration of genomics and phenomics in crop improvement can upscale the efficiency of breeding systems targeting climate resilience and hasten cultivar release cycle. Phenomics is an interdisciplinary field that focuses on the enhanced measurement of plant performance, growth, and composition. Similarly, phenomics has revolutionized the efficacy of plant breeding off-trial initiatives established to phenotypically characterize and study diversity levels of collected germplasm. Field phenomics tools such as the phenonet, phenomobile, and phenonetwork have proven to be efficient in capturing large sums of multiscale and multidimensional experimental data. The main purpose of this review article is to present a summarized account of the probable applications of integrated systems of genomics and phenomics in plant breeding for climate resilience in major crops.

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Section: Application Of Genomics In Plant Breeding For Climate Resilimentioning

confidence: 99%

Application of Genomics and Phenomics in Plant Breeding for Climate Resilience

Ndlovu

2020

APRJ

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“…the increased throughput induced by the implementation of the structural genomics initiatives, the number of solved protein structures still lags far behind that of sequenced genes [1][2][3]. On the other hand, emerging computational techniques, including big data analysis and machine learning methods, are increasingly data-hungry and rely upon the availability of a large amount of data to perform optimally.…”

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confidence: 99%

ProtCHOIR: a tool for proteome-scale generation of homo-oligomers

Tôrres¹,

Rossi²,

Blundell³

2021

Briefings in Bioinformatics

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The rapid developments in gene sequencing technologies achieved in the recent decades, along with the expansion of knowledge on the three-dimensional structures of proteins, have enabled the construction of proteome-scale databases of protein models such as the Genome3D and ModBase. Nevertheless, although gene products are usually expressed as individual polypeptide chains, most biological processes are associated with either transient or stable oligomerisation. In the PDB databank, for example, ~40% of the deposited structures contain at least one homo-oligomeric interface. Unfortunately, databases of protein models are generally devoid of multimeric structures. To tackle this particular issue, we have developed ProtCHOIR, a tool that is able to generate homo-oligomeric structures in an automated fashion, providing detailed information for the input protein and output complex. ProtCHOIR requires input of either a sequence or a protomeric structure that is queried against a pre-constructed local database of homo-oligomeric structures, then extensively analyzed using well-established tools such as PSI-Blast, MAFFT, PISA and Molprobity. Finally, MODELLER is employed to achieve the construction of the homo-oligomers. The output complex is thoroughly analyzed taking into account its stereochemical quality, interfacial stabilities, hydrophobicity and conservation profile. All these data are then summarized in a user-friendly HTML report that can be saved or printed as a PDF file. The software is easily parallelizable and also outputs a comma-separated file with summary statistics that can straightforwardly be concatenated as a spreadsheet-like document for large-scale data analyses. As a proof-of-concept, we built oligomeric models for the Mabellini Mycobacterium abscessus structural proteome database. ProtCHOIR can be run as a web-service and the code can be obtained free-of-charge at http://lmdm.biof.ufrj.br/protchoir.

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