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The InterPro protein families database: the classification resource after 15 years

Alex Mitchell, Hsin-Yu Chang, Louise Daugherty, Matthew Fraser, Sarah Hunter, Rodrigo Lopez, Craig McAnulla, Conor McMenamin, Gift Nuka, Sebastien Pesseat, Amaia Sangrador-Vegas, Maxim Scheremetjew (+24 others)
2014 Nucleic Acids Research  
InterPro integrates these signatures, capitalizing on the respective strengths of the individual databases, to produce a powerful protein classification resource.  ...  The InterPro database (http://www.ebi.ac.uk/ interpro/) is a freely available resource that can be used to classify sequences into protein families and to predict the presence of important domains and  ...  The resource has not only managed to keep track with the massive growth of UniProtKB in recent years, but has actually increased its coverage (from 79.6% of proteins in the database in 2011 to 83.5% in  ... 
doi:10.1093/nar/gku1243 pmid:25428371 pmcid:PMC4383996 fatcat:4asvzb32obgwhlvdkrfhiokvme

The InterPro protein families and domains database: 20 years on

Matthias Blum, Hsin-Yu Chang, Sara Chuguransky, Tiago Grego, Swaathi Kandasaamy, Alex Mitchell, Gift Nuka, Typhaine Paysan-Lafosse, Matloob Qureshi, Shriya Raj, Lorna Richardson, Gustavo A Salazar (+21 others)
2020 Nucleic Acids Research  
The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites.  ...  Founded in 1999, InterPro has become one of the most widely used resources for protein family annotation.  ...  ACKNOWLEDGEMENTS The authors would like to thank former members of the InterPro team: Sara El-Gebali, Matthew Fraser, Aurélien Luciani, Sebastien Pesseat, Simon Potter, Neil Rawlings, Amaia Sangrador-Vegas  ... 
doi:10.1093/nar/gkaa977 pmid:33156333 pmcid:PMC7778928 fatcat:vfs7k3dxr5bcpbpvxbptj6r46m

PCAS--a precomputed proteome annotation database resource

Yong Zhang, Yanbin Yin, Yunjia Chen, Ge Gao, Peng Yu, Jingchu Luo, Ying Jiang
2003 BMC Genomics  
We mapped SUPERFAMILY and COGs to InterPro, so the motif or domain databases are integrated through InterPro.  ...  Motif or domain based algorithms play a pivotal role in functional classification of proteins.  ...  The authors also would like to thank the anonymous reviewers for their helpful comments. This project is supported by Chinese National "863" Program (Grant No. 2001AA231011).  ... 
doi:10.1186/1471-2164-4-42 pmid:14594458 pmcid:PMC293463 fatcat:oiysgeeuczgelmf52rcas7yuwm

The 2015 Nucleic Acids Research Database Issue and Molecular Biology Database Collection

Michael Y. Galperin, Daniel J. Rigden, Xosé M. Fernández-Suárez
2015 Nucleic Acids Research  
Following the classification that has been introduced last year in order to simplify navigation of the entire issue, these articles are divided into eight subject categories.  ...  The size of NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/a/, remained approximately the same, following the addition of 74 new resources and removal of 77  ...  ACKNOWLEDGEMENTS We thank Dr Martine Bernardes-Silva and the Oxford University Press team led by Jennifer Boyd and Caoimhe Ní Dhónaill for their help in compiling this issue.  ... 
doi:10.1093/nar/gku1241 pmid:25593347 pmcid:PMC4383995 fatcat:rpqeohyapre5rijy7vfn7r2p7a

The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection

Daniel J Rigden, Xosé M Fernández
2018 Nucleic Acids Research  
Major returning nucleic acid databases include RNAcentral, miRBase and LncRNA2Target. Protein sequence databases include UniProtKB, InterPro and Pfam, while wwPDB and RCSB cover protein structure.  ...  The NAR online Molecular Biology Database Collection has been updated, reviewing 506 entries, adding 66 new resources and eliminating 147 discontinued URLs, bringing the current total to 1613 databases  ...  ACKNOWLEDGEMENTS We thank Dr Martine Bernardes-Silva, especially, and the rest of the Oxford University Press team led by Joanna Ventikos and Elisabeth Waelkens for their help in compiling this issue.  ... 
doi:10.1093/nar/gky1267 pmid:30626175 pmcid:PMC6323895 fatcat:6ihilznuizgodfgkja5zsmy3mm

PIRSitePredict for protein functional site prediction using position-specific rules

2019 Database: The Journal of Biological Databases and Curation  
Methods focused on predicting 'global' annotations for proteins (such as molecular function, biological process and presence of domains or membership in a family) have reached a relatively mature stage  ...  We demonstrate the use of PIRSitePredict for functional annotation of de novo assembled genome/transcriptome by annotating uncharacterized proteins from Trinity RNA-seq assembly of embryonic transcriptomes  ...  We also thank our colleagues at the UniProt Consortium for their support.  ... 
doi:10.1093/database/baz026 pmid:30805646 pmcid:PMC6389862 fatcat:pthry2g4wjbjdlro7kysxmdoxe

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts

2007 Nucleic Acids Research  
ACKNOWLEDGEMENTS We acknowledge all the members of the H-Invitational 2 consortium and Genome Information Integration Project (GIIP), especially the staffs of JBIRC for construction of H-InvDB, Ryo Aono  ...  NEW ANNOTATED FEATURES IN H-InvDB Classification of ncRNA We annotated the transcripts that do not have homology to known protein-coding genes or InterPro-domain-containing genes as non-protein-coding  ...  COMPREHENSIVE ANNOTATION RESOURCES IN H-InvDB The current H-InvDB annotation resources consist of two main views, Transcript view and Locus view, and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL  ... 
doi:10.1093/nar/gkm999 pmid:18089548 pmcid:PMC2238988 fatcat:q4zm6oxqwfgifbvf74ce3543ma

PhytoTypeDB: a database of plant protein inter-cultivar variability and function

Marco Necci, Damiano Piovesan, Diego Micheletti, Lisanna Paladin, Alessandro Cestaro, Silvio C E Tosatto
2018 Database: The Journal of Biological Databases and Curation  
Most existing databases focus on DNA/RNA data or specific gene families, with less emphasis on protein structure, function and variability.  ...  The database content is generated by an integrated pipeline, exploiting state-of-the-art methods for protein characterization requiring only the proteome reference sequence and variant calling files.  ...  Acknowledgements The authors are grateful to Tomas Di Domenico and Emilio Potenza for initial help with the database.  ... 
doi:10.1093/database/bay125 pmid:30576486 pmcid:PMC6301341 fatcat:amao2zkbd5a2rjve2644tqz63i

The human DEPhOsphorylation Database DEPOD: 2019 update

2019 Database: The Journal of Biological Databases and Curation  
The human Dephosphorylation Database (DEPOD) is a manually curated resource that harbors human phosphatases, their protein and non-protein substrates, dephosphorylation sites and the associated signaling  ...  With multiple significant improvements, DEPOD continues serving as a key resource for research on phosphatase-kinase networks. Database URL: www.depod.org.  ...  The authors would like to thank the users of DEPOD and colleagues for their feedback (see also the acknowledgments section online).  ... 
doi:10.1093/database/baz133 pmid:31836896 pmcid:PMC6911163 fatcat:gkmqr3epm5bfvb3zxkn3kp26ee

LEAPdb: a database for the late embryogenesis abundant proteins

Gilles Hunault, Emmanuel Jaspard
2010 BMC Genomics  
Results: LEAPdb gathers data about 8 LEAP sub-families defined by the PFAM, the Conserved Domain and the InterPro databases.  ...  Late Embryogenesis Abundant Proteins database (LEAPdb) contains resource regarding LEAP from plants and other organisms.  ...  Acknowledgements The authors thank Laurent Châtelain for his contribution to the initial development of LEAPdb, Dr. Jean-Michel Richer, Pr. Olivier Leprince and Pr.  ... 
doi:10.1186/1471-2164-11-221 pmid:20359361 pmcid:PMC2858754 fatcat:6eonag524befbbfo3vpdbyivsm

PTGBase: an integrated database to study tandem duplicated genes in plants

Jingyin Yu, Tao Ke, Sadia Tehrim, Fengming Sun, Boshou Liao, Wei Hua
2015 Database: The Journal of Biological Databases and Curation  
Tandem duplicated genes related to certain functions will lead to the expansion of gene families and bring increase of gene dosage in the form of gene cluster arrays.  ...  It delivers the most comprehensive resource available to date, spanning 39 plant genomes, including model species and newly sequenced species alike.  ...  Louis for the critical reading of the manuscript and three anonymous reviewers for their useful comments on the manuscript. Conflict of interest None declared.  ... 
doi:10.1093/database/bav017 pmid:25797062 pmcid:PMC4369376 fatcat:7wtpkejmsbejreoze7nhbtp75q

BambooGDB: a bamboo genome database with functional annotation and an analysis platform

H. Zhao, Z. Peng, B. Fei, L. Li, T. Hu, Z. Gao, Z. Jiang
2014 Database: The Journal of Biological Databases and Curation  
Moreover, they also appreciate colleagues in different universities or institutes both inside and outside China who helped them test the database and provided the valuable suggestions.  ...  Acknowledgement The authors thank Bamboo Genome Project, our colleagues and friends in International Center for Bamboo and Rattan, National Center for Gene Research of Chinese Academy of Sciences and Chinese  ...  PANTHER: Protein ANalysis THrough Evolutionary Relationships (one classification system of protein).  ... 
doi:10.1093/database/bau006 pmid:24602877 pmcid:PMC3944406 fatcat:vbnynmoztjh6ldc5l7rtwltxam

Comparison Of Popular Bioinformatics Databases

Abdulganiyu Abdu Yusuf, Zahraddeen Sufyanu, Kabir Yusuf Mamman, Abubakar Umar Suleiman
2016 Zenodo  
, Structural Classification of Protein (SCOP) and Class Architecture Topology Homology (CATH) databases.  ...  They are GenBank, Protein Information Resource (PIR), DNA Data Bank of Japan (DDBJ), European Molecular Biology Laboratory (EMBL), Protein Data Bank (PDB), Universal Protein Resource (UniProt), Swiss-Prot  ...  After studying details of the databases, it can be concluded thatmost of the databases have a webinterface to search for data.  ... 
doi:10.5281/zenodo.154757 fatcat:t3jt4miscvhnjoixghtpdyw63m

MGH: a genome hub for the medicinal plant maca (Lepidium meyenii)

Junhao Chen, Jiawei Zhang, Meigui Lin, Wei Dong, Xinyue Guo, Yang Dong, Zhengjia Wang, Liangsheng Zhang, Fei Chen
2018 Database: The Journal of Biological Databases and Curation  
After our previous release of the maca genome sequence, there's a growing need to store, query, analyze and integrate various maca resources efficiently.  ...  Currently, the MGH V1.0 harbors the genome sequence, predicted coding sequences and protein sequences, various annotations, markers and expression data.  ...  Acknowledgements We acknowledge the maca genome sequencing consortium for providing the genome sequence and annotations.  ... 
doi:10.1093/database/bay113 pmid:30339215 pmcid:PMC6195103 fatcat:l7glpjvqineqblrytanvffeq7i

PlantCAZyme: a database for plant carbohydrate-active enzymes

Alexander Ekstrom, Rahil Taujale, Nathan McGinn, Yanbin Yin
2014 Database: The Journal of Biological Databases and Curation  
downloading data of a specific CAZyme family or species and (iii) protein browse pages to provide an easy access to the most comprehensive sequence and annotation data.  ...  The current version contains data of 43 790 CAZymes of 159 protein families from 35 plants (including angiosperms, gymnosperms, lycophyte and bryophyte mosses) and chlorophyte algae with fully sequenced  ...  Acknowledgements A.E. computed most of the data and implemented the database and website. R.T. contributed to the data collection. N.M. developed an early version of the database.  ... 
doi:10.1093/database/bau079 pmid:25125445 pmcid:PMC4132414 fatcat:7n4duke7uzgqjmeerfdbfiqisu
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