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This way a nonredundant taxonomy for all entries was generated.
A multisequence alignment of all 336 protein entries was generated using CLUSTALW.
* SHV-like: SHV variant with a mutation profile that is not in the SHV mutation table A multisequence alignment of all 200 protein entries was generated using CLUSTALW.
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In our experiments, all the missing entries are generated based on the general principle.
63260 (PubMed) and 126845 (WoS) entries were generated, respectively.
Models based on these PDB entries were generated using LigandScout software.
The first five entries were generated from a uniform distribution on the interval [-1.2, -0.8] and [0.8, 1.2].
It should be noted that the SOAPdenovo entry was generated at a time when some of the Illumina mate-pair libraries were temporarily mislabelled in the data instruction file (details of 4 Kbp and 10 Kbp libraries were mistakenly switched).
Up to 500 models for each heterodimer entry were generated by using our sampling method 39 in the bound bound docking where the structures of two protomers derived from the complex structure were used.
The HCV pseudoparticles (HCVpp), which reproduce HCV envelope-mediated entry, were generated by transfecting the expression plasmids for MLV Gag-Pol, HCV E1E2, and a luciferase that can be packaged into the virion (kindly provided by Dr. Francois-Loic Cosset at the University of Lyon) into 293T cells.
The pDonrP2rP3-SuperClomeleon entry vector was generated by PCR and Gateway cloning of the SuperClomeleon sequence from pUC19-SuperClomeleon (Grimley et al., 2013) into the pDonrP2rP3 Gateway entry vector.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com