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MEROPS: the peptidase database

N. D. Rawlings
2006 Nucleic Acids Research  
The MEROPS database (http://merops.sanger.ac.uk) aims to fulfil the need for an integrated source of information about these proteins.  ...  The most important addition to the database has been newly written, concise text annotations for each peptidase family.  ...  ACKNOWLEDGEMENTS Funding to pay the Open Access publication charges for this article was provided by the Medical Research Council (UK) and the Wellcome Trust.  ... 
doi:10.1093/nar/gkj089 pmid:16381862 pmcid:PMC1347452 fatcat:x6xmawqzp5hhbl2cboctrocxru

MEROPS: the peptidase database

N. D. Rawlings, A. J. Barrett
1999 Nucleic Acids Research  
The MEROPS database (http://merops.sanger.ac.uk) aims to fulfil the need for an integrated source of information about these.  ...  Important additions to the database include newly written, concise text annotations for peptidase clans and the small molecule inhibitors that are outside the scope of the standard classification; displays  ...  ACKNOWLEDGEMENTS We wish to thank the Wellcome Trust and the Medical Research Council for financial support.  ... 
doi:10.1093/nar/27.1.325 pmid:9847218 pmcid:PMC148173 fatcat:pkhzo2q3efaefcvtbymh2xagbi

MEROPS: the peptidase database

N. D. Rawlings
2004 Nucleic Acids Research  
The MEROPS database (http://merops.sanger.ac.uk) aims to ®ll this need.  ...  The database has recently been expanded to include the protein inhibitors of peptidases, and these are classi®ed in much the same way as the peptidases.  ...  ACKNOWLEDGEMENTS The MEROPS database depends upon ®nancial support from the UK Medical Research Council and the Wellcome Trust.  ... 
doi:10.1093/nar/gkh071 pmid:14681384 pmcid:PMC308805 fatcat:2i6kk3fpg5fkpku46m3mkk3lxq

MEROPS: the peptidase database

Neil D. Rawlings, Alan J. Barrett, Alex Bateman
2009 Nucleic Acids Research  
The MEROPS database (http://merops .sanger.ac.uk) aims to fulfil the need for an integrated source of information about these.  ...  An important focus of the database has become distinguishing one peptidase from another through identifying the specificity of the peptidase in terms of where it will cleave substrates and with which inhibitors  ...  ACKNOWLEDGEMENTS We would like to thank Pfam and Rfam colleagues for helpful discussions, and Paul Bevan, Jody Clements and Matthew Waller from the Sanger Institute web team for all their help in maintaining  ... 
doi:10.1093/nar/gkp971 pmid:19892822 pmcid:PMC2808883 fatcat:u7vifdllxfbdpnebp6vqol3due

MEROPS: the peptidase database

N. D. Rawlings
2000 Nucleic Acids Research  
Important additions have been made to the MEROPS database (http://www.bi.bbsrc.ac.uk/Merops/Merops. htm ).  ...  These include sequence alignments and cladograms for many of the families of peptidases, and these have proved very helpful in the difficult task of distinguishing the sequences of peptidases that are  ...  INTRODUCTION The MEROPS database (http://www.bi.bbsrc.ac.uk/Merops/ Merops.htm) provides a catalogue and a structure-based classification of peptidases (i.e. all proteolytic enzymes) (1).  ... 
doi:10.1093/nar/28.1.323 pmid:10592261 pmcid:PMC102440 fatcat:d3ya5ijizbfofgl2ybm7o67zim

A large and accurate collection of peptidase cleavages in the MEROPS database

N. D. Rawlings
2009 Database: The Journal of Biological Databases and Curation  
At least one substrate cleavage is known for 45% of the 2415 different peptidases recognized in the MEROPS database.  ...  The MEROPS database is an Internet resource containing information on peptidases, their substrates and inhibitors.  ...  devising the specificity logo software, Dr Penelope Coggill for reading the manuscript and Dr Alex Bateman for guidance and useful discussions.  ... 
doi:10.1093/database/bap015 pmid:20157488 pmcid:PMC2790309 fatcat:6l5q7bndvzakbahx7uzckmo32e

Peptidase specificity from the substrate cleavage collection in the MEROPS database and a tool to measure cleavage site conservation

Neil D. Rawlings
2016 Biochimie  
Since 1996, the MEROPS database (http://merops.sanger.ac.uk) has accumulated a collection of cleavages in substrates that now amounts to 66,615 cleavages.  ...  sequence database.  ...  Acknowledgements The author would like to thank Dr Alan Barrett  ... 
doi:10.1016/j.biochi.2015.10.003 pmid:26455268 pmcid:PMC4756867 fatcat:guonr2yoevfebpqqpbnk3opjv4

The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database

Neil D Rawlings, Alan J Barrett, Paul D Thomas, Xiaosong Huang, Alex Bateman, Robert D Finn
2017 Nucleic Acids Research  
The MEROPS database (http://www.ebi.ac.uk/ merops/) is an integrated source of information about peptidases, their substrates and inhibitors.  ...  Cross-references have been established between MEROPS and the PANTHER database at both the family and proteinspecies level, which will help to improve curation and coverage between the resources.  ...  and Anna Foix from the EMBL-EBI web team for help with setting up this resource and the BLAST and FastA searches and Simon Potter from the Protein Families team for setting up HMMER searches.  ... 
doi:10.1093/nar/gkx1134 pmid:29145643 pmcid:PMC5753285 fatcat:swnt7wqlinewlgj2z7vyx45dte

Identification and prioritization of novel uncharacterized peptidases for biochemical characterization

Neil D. Rawlings
2013 Database: The Journal of Biological Databases and Curation  
The MEROPS database maintains large collections of sequences, references, substrate cleavage positions and inhibitor interactions of peptidases and their homologues.  ...  MEROPS also maintains a hierarchical classification of peptidase homologues, in which sequences are clustered as species variants of a single peptidase; homologous sequences are assembled into a family  ...  Acknowledgements The author thanks Dr Alan Barrett Conflict of interest. None declared.  ... 
doi:10.1093/database/bat022 pmid:23584835 pmcid:PMC3625958 fatcat:466dlsffwza5zbgonwyymmdh6q

The MEROPS Database

Neil Rawlings, Alan Barrett
2009 Nature Precedings  
The control of proteolysis is important because unchecked degradation can lead to pathological conditions, and the MEROPS database (Rawlings et al., 2008) includes not only peptidases but also their inhibitors  ...  The latest release of the database is 8.4 (April 2009).  ...  Peptidase and Substrate Interactions The MEROPS database also includes data on peptidase/substrate interactions, which are short-lived but fundamental.  ... 
doi:10.1038/npre.2009.3103.1 fatcat:6pwqglmwyndzragmb77xjj4smq

MEROPS: the protease database

N. D. Rawlings
2002 Nucleic Acids Research  
The MEROPS database (http://www.merops.ac.uk) has been redesigned to accommodate increased amounts of information still in pages of moderate size that load rapidly.  ...  Amongst these are CGI searches that allow the user to find a peptidase by name, its MEROPS identifier or its human or mouse chromosome location.  ...  INTRODUCTION The MEROPS database provides a catalogue and a structurebased classification of peptidases (i.e. all proteolytic enzymes).  ... 
doi:10.1093/nar/30.1.343 pmid:11752332 pmcid:PMC99100 fatcat:j72u6ojlgzc7tiosg4ct37mzji

Bioinformatic flowchart and database to investigate the origins and diversity of Clan AA peptidases

Carlos Llorens, Ricardo Futami, Gabriel Renaud, Andrés Moya
2009 Biology Direct  
The set of tools is work in progress we have organized in a database within the GyDB project, referred to as Clan AA Reference Database http://gydb.uv.es/gydb/phylogeny.php?tree=caard.  ...  Clan AA of aspartic peptidases relates the family of pepsin monomers evolutionarily with all dimeric peptidases encoded by eukaryotic LTR retroelements.  ...  We also thank Javier Ortiz and Isaac Fernandez of the SCSIE at University of Valencia for technical support to the GyDB project.  ... 
doi:10.1186/1745-6150-4-3 pmid:19173708 pmcid:PMC2642776 fatcat:7flcgg4fpjg33fnikd365l7alu

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors

Neil D. Rawlings, Matthew Waller, Alan J. Barrett, Alex Bateman
2013 Nucleic Acids Research  
The MEROPS database (http://merops .sanger.ac.uk) aims to fulfil the need for an integrated source of information about these.  ...  The database has been expanded to include proteolytic enzymes other than peptidases.  ...  ACKNOWLEDGEMENTS We would like to thank the following: Pfam and Rfam colleagues for helpful discussions, especially John Tate for help with displays; Paul Bevan and Matthew Waller from the Sanger Institute  ... 
doi:10.1093/nar/gkt953 pmid:24157837 pmcid:PMC3964991 fatcat:2vkn5nek5nembmnjpamlhjplv4

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors

N. D. Rawlings, A. J. Barrett, A. Bateman
2011 Nucleic Acids Research  
The MEROPS database (http://merops .sanger.ac.uk) aims to fulfil the need for an integrated source of information about these.  ...  The database has been expanded to include proteolytic enzymes other than peptidases.  ...  ACKNOWLEDGEMENTS We would like to thank the following: Pfam and Rfam colleagues for helpful discussions, especially John Tate for help with displays; Paul Bevan and Matthew Waller from the Sanger Institute  ... 
doi:10.1093/nar/gkr987 pmid:22086950 pmcid:PMC3245014 fatcat:lkdtveu44zaojfg5bxmrsnfznq

A comparison of Pfam and MEROPS: two databases, one comprehensive, and one specialised

David J Studholme, Neil D Rawlings, Alan J Barrett, Alex Bateman
2003 BMC Bioinformatics  
About half (89 out of 174) of the peptidase families in MEROPS overlapped single Pfam families. A further 32 MEROPS families overlapped multiple Pfam families.  ...  MEROPS is a catalogue and classification of enzymes with proteolytic activity (peptidases or proteases).  ...  Acknowledgements AB is funded by the Wellcome Trust. AJB, NDR and DJS are funded by the Medical Research Council, UK.  ... 
doi:10.1186/1471-2105-4-17 pmid:12740029 pmcid:PMC156619 fatcat:ixkjo3iew5fuzjacmz36oev5ve
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