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A homology model of Shigella-CS with the flavin mononucleotide (FMN) binding was constructed using the crystal structure of CS from other species.
In addition, a homology model of c-Src kinase with the activation loop resembling the active conformation was constructed using the crystal structure of the kinase domain of Lck.
In addition, a homology model of Raf-1 was also constructed using the crystal structure of the kinase domain of B-Raf isoform with one of the most active Raf-1 inhibitors (48) inside the active site.
Models of the transporter protein were constructed using the crystal structure of the Escherichia coli major facilitator family transporter-LacY and the X-ray structure of the neurotransmitter symporter family (NSS) transporter-LeuTAa as templates.
Homology models of the bifunctional P. falciparum dihydropterin pyrophosphokinase dihydropteroate synthase (PPPK DHPS) enzyme as well as the separate domains complete with bound substrates were constructed using the crystal structures of Saccharomyces cerevisiae (PPPK DHPS), Mycobacterium tuberculosis (DHPS), Bacillus anthracis (DHPS), and Escherichia coli (PPPK) as templates.
A three-dimensional structural model of ANTR1 was constructed using the crystal structure of glycerol 3-phosphate/phosphate antiporter from E. coli as a template.
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To gain molecular insights into the interactions of LvIA with the α3β2, α6β2, and α3β4 nAChR subtypes, homology models of the extracellular ligand binding domain of rat α3β2, α6β2, and α3β4 nAChRs bound to LvIA were constructed using the co-crystal structure of Ac-AChBP/LvIA as template.
A reliable homology model of Kv1.5 is constructed using the recently published crystal structure of the Kv1.2 channel as a template.
The homology modeling of the p68 RNA helicase structure was constructed using the homology-modeling server SWISS-MODEL based on X-ray crystal structure of Drosophila vasa [ 62], which has the highest alignment score with p68 RNA helicase core.
In order to understand the relationship between sequence and structure in greater depth, the 3-D structure of GAD500 585 was constructed using the homology modeling method (InsightII software (2005), Accelrys, San Diego, CA) based on the crystal structure of GAD65.
The structural model of HotAldO was constructed using the CPHmodels 3.0 server (Nielsen et al. 2010) (http://www.cbs.dtu.dk/services/CPHmodels/) and the crystal structure of AldO complexed with xylitol (Protein Data Bank, PDB id: 2VFS).
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