On dimension reduction of clustering results in structural bioinformatics

PDB_Amyloid: an extended live amyloid structure list from the PDB

The Protein Data Bank (PDB) contains more than 135 000 entries at present. From these, relatively few amyloid structures can be identified, since amyloids are insoluble in water. Therefore, most amyloid structures deposited in the PDB are in the form of solid state NMR data. Based on the geometric analysis of these deposited structures, we have prepared an automatically updated web server, which generates a list of the deposited amyloid structures, and also entries of globular proteins that have amyloid‐like substructures of given size and characteristics. We have found that by applying only appropriately selected geometric conditions, it is possible to identify deposited amyloid structures and a number of globular proteins with amyloid‐like substructures. We have analyzed these globular proteins and have found proof in the literature that many of them form amyloids more easily than many other globular proteins. Our results relate to the method of Stanković et al. [Stanković I et al. (2017) IPSI BgD Tran Int Res 13, 47–51], who applied a hybrid textual‐search and geometric approach for finding amyloids in the PDB. If one intends to identify a subset of the PDB for certain applications, the identification algorithm needs to be re‐run periodically, since in 2017 on average 30 new entries per day were deposited in the data bank. Our web server is updated regularly and automatically, and the identified amyloid and partial amyloid structures can be viewed or their list can be downloaded from the following website https://pitgroup.org/amyloid.

Significant differences found in short nucleotide sequences of human intestinal metagenomes of Northern-European and Chinese Origin

BACKGROUND

Metagenomic analysis of environmental and clinical samples is gaining considerable importance in today's literature. Changes in the composition of the intestinal microbial communities, relative to the healthy control, are reported in numerous conditions.

METHODS

We have carefully analyzed the frequencies of the short nucleotide sequences in the metagenomes of two different enterotypes; namely of Chinese and European origins.

RESULTS

We have identified 255 nucleotide sequences of length up to 9, such that their frequencies significantly differ in the two enterotypes examined.

CONCLUSIONS

We have demonstrated that short nucleotide sequences are capable of differentiating enterotypes, and not only metagenomes, originating from healthy and diseased subjects.

GENERAL SIGNIFICANCE

Our results may imply that the frequency-differences of certain short nucleotides have diagnostical value if properly applied for different clusters of metagenomes. "This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo".