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New and continuing developments at PROSITE

Christian J. A. Sigrist, Edouard de Castro, Lorenzo Cerutti, Béatrice A. Cuche, Nicolas Hulo, Alan Bridge, Lydie Bougueleret, Ioannis Xenarios
2012 Nucleic Acids Research  
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

K. Hofmann, P. Bucher, L. Falquet, A. Bairoch
1999 Nucleic Acids Research  
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

A Bairoch
1996 Nucleic Acids Research  
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

Bendik Bygstad
2005 Software Process: Improvement and Practice  
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

T. Schuepbach, M. Pagni, A. Bridge, L. Bougueleret, I. Xenarios, L. Cerutti
2013 Bioinformatics  
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

Sungroh Yoon, Jessica C Ebert, Eui-Young Chung, Giovanni De Micheli, Russ B Altman
2007 BMC Bioinformatics  
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

H. Huang
2000 Nucleic Acids Research  
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

C. H. Wu, S. Shivakumar, H. Huang
1999 Nucleic Acids Research  
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

Christian J. A. Sigrist, Lorenzo Cerutti, Edouard de Castro, Petra S. Langendijk-Genevaux, Virginie Bulliard, Amos Bairoch, Nicolas Hulo
2009 Nucleic Acids Research  
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

Pascal Schläpfer, Devang Mehta, Cameron Ridderikhoff, R Glen Uhrig
2021 Nucleic Acids Research  
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

Robert D. Finn, Teresa K. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, Alan J. Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft (+35 others)
2016 Nucleic Acids Research  
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

Bharat Panwar, Gajendra PS Raghava
2010 BMC Genomics  
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

T. K. Attwood, D. R. Flower, A. P. Lewis, J. E. Mabey, S. R. Morgan, P. Scordis, J. N. Selley, W. Wright
1999 Nucleic Acids Research  
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

Umberto Cugini, Gaetano Cascini, Maurizio Muzzupappa, Vincenzo Nigrelli
2009 Computers in industry (Print)  
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

S. Henikoff, J. G. Henikoff, S. Pietrokovski
1999 Bioinformatics  
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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