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Mateusz Kurcinski Aleksandra Badaczewska‐Dawid Michal Kolinski Andrzej Kolinski Sebastian Kmiecik 《Protein science : a publication of the Protein Society》2020,29(1):211-222
Molecular docking of peptides to proteins can be a useful tool in the exploration of the possible peptide binding sites and poses. CABS‐dock is a method for protein–peptide docking that features significant conformational flexibility of both the peptide and the protein molecules during the peptide search for a binding site. The CABS‐dock has been made available as a web server and a standalone package. The web server is an easy to use tool with a simple web interface. The standalone package is a command‐line program dedicated to professional users. It offers a number of advanced features, analysis tools and support for large‐sized systems. In this article, we outline the current status of the CABS‐dock method, its recent developments, applications, and challenges ahead. 相似文献
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Moises Exposito‐Alonso Hajk‐Georg Drost Hernn A. Burbano Detlef Weigel 《The Plant journal : for cell and molecular biology》2020,102(2):222-229
Sequencing them all. That is the ambitious goal of the recently launched Earth BioGenome project (Proceedings of the National Academy of Sciences of the United States of America, 115, 4325–4333), which aims to produce reference genomes for all eukaryotic species within the next decade. In this perspective, we discuss the opportunities of this project with a plant focus, but highlight also potential limitations. This includes the question of how to best capture all plant diversity, as the green taxon is one of the most complex clades in the tree of life, with over 300 000 species. For this, we highlight four key points: (i) the unique biological insights that could be gained from studying plants, (ii) their apparent underrepresentation in sequencing efforts given the number of threatened species, (iii) the necessity of phylogenomic methods that are aware of differences in genome complexity and quality, and (iv) the accounting for within‐species genetic diversity and the historical aspect of conservation genetics. 相似文献
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Model‐assisted identification of metabolic engineering strategies for Jatropha curcas lipid pathways
Sandra M. Correa Saleh Alseekh Lucía Atehortúa Yariv Brotman Rigoberto Ríos‐Estepa Alisdair R. Fernie Zoran Nikoloski 《The Plant journal : for cell and molecular biology》2020,104(1):76-95
Efficient approaches to increase plant lipid production are necessary to meet current industrial demands for this important resource. While Jatropha curcas cell culture can be used for in vitro lipid production, scaling up the system for industrial applications requires an understanding of how growth conditions affect lipid metabolism and yield. Here we present a bottom‐up metabolic reconstruction of J. curcas supported with labeling experiments and biomass characterization under three growth conditions. We show that the metabolic model can accurately predict growth and distribution of fluxes in cell cultures and use these findings to pinpoint energy expenditures that affect lipid biosynthesis and metabolism. In addition, by using constraint‐based modeling approaches we identify network reactions whose joint manipulation optimizes lipid production. The proposed model and computational analyses provide a stepping stone for future rational optimization of other agronomically relevant traits in J. curcas. 相似文献