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New and continuing developments at PROSITE
2012
Nucleic Acids Research
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PROSITE (http://prosite.expasy.org/) consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. ...
PROSITE signatures, together with ProRule, are used for the annotation of domains and features of UniProtKB/Swiss-Prot entries. ...
ACKNOWLEDGEMENTS The authors thank Fre´de´ric Bastian for helpful discussions regarding gene expression library databases and for the selection of multi-species tissues that are used in ScanProsite. ...
doi:10.1093/nar/gks1067
pmid:23161676
pmcid:PMC3531220
fatcat:wpxzlrpscfhbloaba56dxrvj4q
The PROSITE database, its status in 1999
1999
Nucleic Acids Research
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The PROSITE database consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of proteins ...
(if any) a new sequence belongs or which known domain(s) it contains. ...
Popular browsers available for most computer platforms include Mosaic™, developed at the National Center for Supercomputing Applications (NCSA) of the University of Illinois at Champaign (obtainable by ...
doi:10.1093/nar/27.1.215
pmid:9847184
pmcid:PMC148139
fatcat:5gsrgivtybgu7mregm3pyunbsm
The PROSITE database, its status in 1995
1996
Nucleic Acids Research
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The PROSITE database consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of proteins ...
(if any) a new sequence belongs or which known domain(s) it contains. ...
Popular browsers available for most computer platforms include Mosaic™, developed at the National Center for Supercomputing Applications (NCSA) of the University of Illinois at Champaign (obtainable by ...
doi:10.1093/nar/24.1.189
pmid:8594577
pmcid:PMC145570
fatcat:oifmuhfjnjgndnq5v2pucjdzwq
Managing the dynamics of mutual adaptation of technology and organisation in information systems development projects
2005
Software Process: Improvement and Practice
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The article builds on a longitudinal case study from a large public auditing organisation that developed a new audit process in parallel with the construction of a new information system to support it. ...
This article explores a strategy of mutual adaptation between the information system and the business process, facilitated by the iterative and incremental mechanisms of modern SW engineering frameworks ...
A special thanks to Liv Dreierstad at the Office of the Auditor General, who provided access to the PROSIT project, and also commented on the case description. ...
doi:10.1002/spip.234
fatcat:foa5kyj6knbd3gufaopjqhoo5u
pfsearchV3: a code acceleration and heuristic to search PROSITE profiles
2013
Bioinformatics
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We describe an improved and optimized implementation of the PROSITE search tool pfsearch that, combined with a newly developed heuristic, addresses this limitation. ...
PROSITE generalized profiles including the heuristic cut-off scores are available at the same address. ...
Funding: This work was funded by a Swiss National Science Foundation (SNSF) project grant (315230-116864) and the Swiss Federal Government through the State Secretariat for Education, Research and Innovation ...
doi:10.1093/bioinformatics/btt129
pmid:23505298
pmcid:PMC3634184
fatcat:vvnf3mckifbvhe33jcriytb26a
Clustering protein environments for function prediction: finding PROSITE motifs in 3D
2007
BMC Bioinformatics
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We found examples of clusters highly enriched for residues that share PROSITE sequence motifs. ...
As a preliminary validation, we asked whether known 3D environments associated with PROSITE motifs were "rediscovered". ...
Ng, and the Helix Group at Stanford http://helix-web.stanford.edu/ for helpful discussions. ...
doi:10.1186/1471-2105-8-s4-s10
pmid:17570144
pmcid:PMC1892080
fatcat:7qr5h7phynhkbbl352s5qng2ou
ProClass protein family database
2000
Nucleic Acids Research
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The ProClass motif collection contains ~72 000 motif sequences and >1300 multiple alignments for all PROSITE patterns, including >21 000 matches not listed in PROSITE and mostly detected from unique PIR ...
The database, now being implemented in an objectrelational database management system, is available for online sequence search and record retrieval from our WWW server at http://pir.georgetown.edu/gfserver ...
INTRODUCTION Molecular sequence data continue to grow at an accelerating pace due to the Human Genome Project and other large sequencing projects. ...
doi:10.1093/nar/28.1.273
pmid:10592245
pmcid:PMC102450
fatcat:jip4gszgpbdn3eir46o5folofe
ProClass Protein Family Database
1999
Nucleic Acids Research
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The ProClass motif collection contains ~72 000 motif sequences and >1300 multiple alignments for all PROSITE patterns, including >21 000 matches not listed in PROSITE and mostly detected from unique PIR ...
The database, now being implemented in an objectrelational database management system, is available for online sequence search and record retrieval from our WWW server at http://pir.georgetown.edu/gfserver ...
INTRODUCTION Molecular sequence data continue to grow at an accelerating pace due to the Human Genome Project and other large sequencing projects. ...
doi:10.1093/nar/27.1.272
pmid:9847199
pmcid:PMC148154
fatcat:447qhu5nbbf3nkozvg2rsdj6ry
PROSITE, a protein domain database for functional characterization and annotation
2009
Nucleic Acids Research
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ACKNOWLEDGEMENTS The authors thank Marco Pagni for helpful discussions and ideas and Andrea H. Auchincloss for critical reading of the manuscript. ...
Figure 2 . 2 Continued. ...
In collaboration with PeroxiBase (6), PROSITE has developed a strategy to construct profiles specific for the different subfamilies of the peroxidase family. ...
doi:10.1093/nar/gkp885
pmid:19858104
pmcid:PMC2808866
fatcat:3dk25oo67zgoteiueycrcyoimm
DomainViz: intuitive visualization of consensus domain distributions across groups of proteins
2021
Nucleic Acids Research
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Currently, DomainViz uses the well-established PFAM and Prosite databases for domain searching and assembles intuitive, publication-ready 'monument valley' plots (mv-plots) that display the extent of domain ...
The prediction of functional domains is typically among the first steps towards understanding the function of new proteins and protein families. ...
(University of Alberta) for troubleshooting, and Sukalp Muzumdar (Cold Spring Harbor Laboratory) for assistance with mathematical formulation. ...
doi:10.1093/nar/gkab391
pmid:34023887
fatcat:fuv5dniizvet7fauha23oaespe
InterPro in 2017—beyond protein family and domain annotations
2016
Nucleic Acids Research
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HAMAP and PROSITE annotation rules provide external users and the UniProt automatic annotation pipeline (UniRule) with annotations for functionally important residues (single residues as well as continuous ...
Patterns (10) , PROSITE Profiles (10) , SMART (11) , SUPERFAMILY (12) and TIGR-FAMs ( 13 )); two are new members, the Conserved Domains Database (CDD) (14) and Structure-Function Linkage Database ...
doi:10.1093/nar/gkw1107
pmid:27899635
pmcid:PMC5210578
fatcat:wa7z5pgpuffnrh5bf5ycimw7kq
Prediction and classification of aminoacyl tRNA synthetases using PROSITE domains
2010
BMC Genomics
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We developed a hybrid approach and achieved a maximum MCC of 0.72 with accuracy of 85.49%, where SVM model developed using selected dipeptide composition and information of four PROSITE domains. ...
The web-server based on the above study, is available at * The number of aaRSs/class-1 and non-aaRSs/class-2 having no hit (target) were considered as false negative and false positive respectively. ...
At the present time, genome sequencing projects continuously produce huge amounts of sequence data, but the function of several proteins is still unclear. ...
doi:10.1186/1471-2164-11-507
pmid:20860794
pmcid:PMC2997003
fatcat:w77imf7kcbde3eavbht6x46m74
PRINTS prepares for the new millennium
1999
Nucleic Acids Research
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Current efforts are focused on the design of more automated methods for database maintenance; implementation of an object-relational schema for efficient data management; and integration with PROSITE, ...
In addition to supporting its continued growth, recent enhancements to the resource include a BLAST server, and more efficient fingerprint search software, with improved statistics for estimating the reliability ...
ACKNOWLEDGEMENTS PRINTS is now built and maintained at the University of Manchester with support from the Royal Society (T.K.A. is a Royal Society University Research Fellow), having been hosted for the ...
doi:10.1093/nar/27.1.220
pmid:9847185
pmcid:PMC148140
fatcat:bn2qq3s7e5bfxgmguhvnws2bke
Integrated Computer-Aided Innovation: The PROSIT approach
2009
Computers in industry (Print)
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Acknowledgements The PROSIT project (Product development and systematic innovation http://www.kaemart.it/prosit) is co-funded by the Italian Ministry of University and Research. ...
Ingrassia from Università di Palermo for their contribution to the development of the PROSIT project. ...
In order to reduce development time and increase activities' effectiveness, design and Product Development Process have to be considered as a continuous iteration among these phases. ...
doi:10.1016/j.compind.2009.05.014
fatcat:mexprxbkujdjthk76lztlitpzi
Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations
1999
Bioinformatics
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The original Blocks Database, which contains ungapped multiple alignments for families documented in PROSITE, can be searched to classify new sequences. ...
Blocks+ consists of all blocks derived from PROSITE, blocks from Prints not present in PROSITE, blocks from Pfam-A not present in PROSITE or Prints, and so on for ProDom and Domo, for a total of 1995 protein ...
There are several programs for searching PROSITE patterns. Since early 1997, PROSITE has added only 18 new families with minimal documentation, for a total of 1015. ...
doi:10.1093/bioinformatics/15.6.471
pmid:10383472
fatcat:vmsyyoflqfeqxb3wbzxhuvyl5a
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