MEROPS: the peptidase database
Reads0
Chats0
TLDR
The MEROPS database has added an analysis tool to the relevant species pages to show significant gains and losses of peptidase genes relative to related species, and has collected over 39 000 known cleavage sites in proteins, peptides and synthetic substrates.Abstract:
Peptidases (proteolytic enzymes) are of great relevance to biology, medicine and biotechnology. This practical importance creates a need for an integrated source of information about them, and also about their natural inhibitors. The MEROPS database (http://merops.sanger.ac.uk) aims to fill this need. The organizational principle of the database is a hierarchical classification in which homologous sets of the proteins of interest are grouped in families and the homologous families are grouped in clans. Each peptidase, family and clan has a unique identifier. The database has recently been expanded to include the protein inhibitors of peptidases, and these are classified in much the same way as the peptidases. Forms of information recently added include new links to other databases, summary alignments for peptidase clans, displays to show the distribution of peptidases and inhibitors among organisms, substrate cleavage sites and indexes for expressed sequence tag libraries containing peptidases. A new way of making hyperlinks to the database has been devised and a BlastP search of our library of peptidase and inhibitor sequences has been added.read more
Citations
More filters
Journal ArticleDOI
Asgard archaea capable of anaerobic hydrocarbon cycling
Kiley W. Seitz,Nina Dombrowski,Laura Eme,Laura Eme,Anja Spang,Jonathan Lombard,Jessica R. Sieber,Andreas P Teske,Thijs J. G. Ettema,Thijs J. G. Ettema,Brett J. Baker +10 more
TL;DR: It is suggested that members of the Helarchaeota have the potential to activate and subsequently anaerobically oxidize hydrothermally generated short-chain hydrocarbons.
Journal ArticleDOI
Plasmepsins as potential targets for new antimalarial therapy
TL;DR: It seems clear that in order to achieve high‐antiparasitic activities in P. falciparum‐infected erythrocytes it is necessary to inhibit several of the haemoglobin‐degrading plasmepsins, which represent all classes which, to the best of the authors' knowledge, have been disclosed in journal articles to date.
Journal ArticleDOI
Clostridium difficile toxins: mediators of inflammation
TL;DR: This review summarizes the current knowledge of the mechanisms by which glucosylating toxins and CDT disrupt target cell function, alter host physiology and stimulate immune responses.
Journal ArticleDOI
Architecture and function of metallopeptidase catalytic domains
TL;DR: Accumulated structural data from more than 300 deposited structures of the 12 currently characterized metzincin families provide detailed knowledge of the molecular features of their catalytic domains, help in the understanding of their working mechanisms, and form the basis for the design of novel drugs.
Journal ArticleDOI
The Wrickkened Pathways of FGF23, MEPE and PHEX
TL;DR: A global hypothesis is presented that attempts to explain the experimental and clinical observations in HYP, ADHR, and OHO, plus diverse mouse models that include the MEPE null mutant, HYP- PHEX transgenic mouse, and MEPE-PHEX double-null-mutant.
References
More filters
Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Book
Molecular Evolutionary Genetics
TL;DR: Recent developments of statistical methods in molecular phylogenetics are reviewed and it is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used.
Journal ArticleDOI
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
Wolfgang Kabsch,Chris Sander +1 more
TL;DR: A set of simple and physically motivated criteria for secondary structure, programmed as a pattern‐recognition process of hydrogen‐bonded and geometrical features extracted from x‐ray coordinates is developed.
Journal ArticleDOI
The Pfam protein families database
Marco Punta,Penny Coggill,Ruth Y. Eberhardt,Jaina Mistry,John Tate,Chris Boursnell,Ningze Pang,Kristoffer Forslund,Goran Ceric,Jody Clements,Andreas Heger,Liisa Holm,Erik L. L. Sonnhammer,Sean R. Eddy,Alex Bateman,Robert D. Finn +15 more
TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.