First, methods that use evolutionary conservation perform well on conserved miRNAs [ 25, 11] but fail to detect species-specific or fast evolving miRNAs [ 12].
LIGSITEcsc (csc = Conolly Surface and Conservation) performs a re-ranking of the top-three predicted pockets by the degree of conservation of the closest surface residues.
Thus, PPCheck is the only webserver, to the best of our knowledge, which can be reliably used for identifying non-covalent interactions, predicting hotspots at the interface, calculating residue conservation, performing computational alanine scanning, and differentiating native-like and non-native-like docking poses.
To investigate this conservation, we performed a genome-wide analysis of human microsatellites and measured their conservation using a binary character birth--death model on a mammalian phylogeny.
In order to decipher interactions between allele-specific DNA methylation of imprinted genes and evolutionary conservation, we performed a genome-wide comparative investigation of genomic sequences and highly conserved elements of imprinted genes in human and mouse.
Numerical solution of the equations of mass, species, and energy conservation are performed using a chemical kinetic mechanism recently developed at the National Institute of Standards and Technology.
For the identified microRNAs, the measurement of its evolutionary conservation was performed by similarity search against the currently known microRNAs in miRBase 19.0 in other plant species (Fig. 1).
The conservation score performed best, with 76.4 sensitivity and 82.5 specificity.
Quantitative assessment of sequence conservation was performed using phastCons with background (non-constrained) rates calculated from each locus alignment separately using phyloFit (HKY85+Gap substitution model), both from the PHASTCONS package [44] (version v0.9.9.6b).
