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There are few reports on the identification of templates that are amenable to development as potent inhibitors in vivo and large diverse collections have yet to be exploited for the discovery of demethylase inhibitors.
The identification of templates for each target achieved using the program FUGUE (19) on the TOCCATA database of profiles.
These improvements are mainly because of (i) the better identification of templates by LOMETS than that by PSI-BLAST or HMM searches and (ii) the sensitive calibration of gaps and alignments by the domain conservation score as designed by ThreaDom.
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To build a structure model for a target protein sequence, the TBM process consists of four major steps: identification of structural templates, alignment of target sequence to structural templates (or sequence-structure alignment), model building, and model quality evaluation.
However, for target sequences with low sequence similarity, the reliable identification of structural templates and accurate sequence-structure alignment requires a much more complex process called threading or fold recognition that integrates many other types of information with sequence profile information.
The following items are checked in the validation process of each conversion: 1. Identification of COSMIC templates and archetypes.
Identification of distinct template and product exit tunnels allows proposal of a detailed model for template-directed replication with minimal disruption to the circularised RNP.
These observations indicated that the presence of the initially biased sequence may interfere with the identification of individual template clusters.
The first step is the identification of a template protein of known structure.
Secondly, the identification of sub-templates has to be specific in COSMIC versus the dynamic inclusion criteria of archetype slots.
Other successful recent efforts have involved combinatorial synthesis and screening for identification of new inhibitor templates.
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