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The generation of molecular conformations is an essential part of many computational analyses in chemistry, particularly in the field of computational drug design.
The presence of adapter chimeras and adapter sequences at the end of short-insert molecules, as well as increased error rates and short read lengths complicate many computational analyses.
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Many computational chemistry analyses require the generation of conformers, either on-the-fly, or in advance.
In many cases, computational analyses can provide useful guidance as to whether a candidate motif would be worth following up experimentally.
The syntax will facilitate many types of computational analyses of minimotifs.
Several methods involve many computational experiments to analyse the effects of uncertain parameters (e.g. 'Exploratory Modeling' Bankes (1993) ) to seek for robust decisions (Lempert et al., 2006; Lempert and Bankes, 2003 ) or optimal solutions ('Info Gap' theory Ben-Haim (2001) ).
Many of the previous computational analyses of this same dataset reported regions in the genome, coined eQTL hotspots, which control the expression level of gene clusters that are highly enriched for a common function [ 8, 9].
It also entails gathering key knowledge regarding the host architecture and translocation machinery and associated substrate recognition via experimentation and integration of diverse computational analyses from many proteins and, where possible, that are derived from different species within the same genus.
Accordingly, many similar instances (to that of Kiriakidou et al) of flawed computational analyses have been published (see [ 29], suggested by reviewer 1 and Reviewer 3 below).
All computational analyses were performed in a local computing environment.
And, let me add, the coolest – and most important – thing is that our computational analyses are fully validated in chemical practice.
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