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MODOMICS: a database of RNA modification pathways—2013 update
TLDR
New features are included: a census of human and yeast snoRNAs involved in RNA-guided RNA modification, a new section covering the 5′-end capping process, and a catalogue of ‘building blocks’ for chemical synthesis of a large variety of modified nucleosides. Expand
MODOMICS: a database of RNA modification pathways
MODOMICS is the first comprehensive database resource for systems biology of RNA modification. It integrates information about the chemical structure of modified nucleosides, their localization inExpand
Transcriptome Profile of Human Colorectal Adenomas
TLDR
Significant differences emerged not only between the expression profiles of normal and adenomatous tissues but also between those of small and large adenomas, and KIAA1199 was identified as a novel target of the Wnt signaling pathway and a putative marker of colorectal adenOMatous transformation. Expand
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases
TLDR
It is proposed that the Last Universal Common Ancestor of all extant organisms contained at least three SPOUT members, ancestors of contemporary RNA MTases that carry out m1G, m3U, and 2'O-ribose methylation, respectively. Expand
GeneSilico protein structure prediction meta-server
TLDR
This work has developed a novel WWW gateway for protein structure prediction, which combines the useful features of other meta-servers available, but with much greater flexibility of the input. Expand
MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins
TLDR
A series of disorder predictors were combined into a meta-meta predictor called GSmetaDisorderMD, which was the top scoring method in the subsequent CASP9 benchmark and also developed a disorder predictor GS metaDisorder3D that used no third-party Disorder predictors, but alignments to known protein structures, reported by the protein fold-recognition methods. Expand
MetaMQAP: A meta-server for the quality assessment of protein models
TLDR
MetaMQAP is a meta-predictor based on a multivariate regression model, which uses scores of the above-mentioned methods, but in which trivial parameters are controlled, and is the best among methods capable of evaluating just single models. Expand
Trm7p catalyses the formation of two 2′‐O‐methylriboses in yeast tRNA anticodon loop
TLDR
Evidence is presented that Trm7p methylates the 2′‐O‐ribose of nucleotides at positions 32 and 34 of the tRNA anticodon loop, both in vivo and in vitro, indicating that these tRNA modifications could be important for translation efficiency. Expand
ModeRNA: a tool for comparative modeling of RNA 3D structure
TLDR
ModeRNA can model post-transcriptional modifications, a functionally important feature analogous to post- translational modifications in proteins, and is equipped with many functions for merging fragments of different nucleic acid structures into a single model and analyzing their geometry. Expand
Structure of a multipartite protein-protein interaction domain in splicing factor prp8 and its link to retinitis pigmentosa.
TLDR
It is concluded that the expanded Prp8 Jab1/MPN domain represents a pseudoenzyme converted into a protein-protein interaction platform and that dysfunction of this platform underlies Retinitis pigmentosa. Expand
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