Research graph
References from Protein domain identification methods and online resources. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1007/978-1-4939-6622-6_7
10.1007/978-1-4939-6622-6_7 · 2017 · External reference
Improving protein function prediction using domain and protein complexes in PPI networks
10.1186/1752-0509-8-35 · 2014 · External reference
PANDA: protein function prediction using domain architecture and affinity propagation
10.1038/s41598-018-21849-1 · 2018 · External reference
10.1093/nar/gkv523
10.1093/nar/gkv523 · External reference
10.1002/prot.22588
10.1002/prot.22588 · External reference
CHOP: parsing proteins into structural domains
10.1093/nar/gkh481 · 2004 · External reference
10.1093/nar/gky1004
10.1093/nar/gky1004 · External reference
The Pfam protein families database in 2019
2018 · External reference
10.1093/nar/28.1.45
10.1093/nar/28.1.45 · External reference
10.1089/cmb.1995.2.9
10.1089/cmb.1995.2.9 · External reference
10.1038/nmeth.1818
10.1038/nmeth.1818 · External reference
Protein homology detection by HMM-HMM comparison
10.1093/bioinformatics/bti125 · 2005 · External reference
10.1371/journal.pcbi.1005038
10.1371/journal.pcbi.1005038 · External reference
A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling
10.1186/s40168-018-0532-2 · 2018 · External reference
10.1093/nar/gki410
10.1093/nar/gki410 · External reference
SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles
10.1093/bioinformatics/bti751 · 2006 · External reference
10.1142/9789812776303_0024
10.1142/9789812776303_0024 · 2002 · External reference
ThreaDom: extracting protein domain boundary information from multiple threading alignments
10.1093/bioinformatics/btt209 · 2013 · External reference
10.1002/prot.21702
10.1002/prot.21702 · External reference
10.1093/nar/gkm251
10.1093/nar/gkm251 · External reference
10.1073/pnas.1814684116
10.1073/pnas.1814684116 · External reference
10.1093/bioinformatics/btp560
10.1093/bioinformatics/btp560 · External reference
Using context to improve protein domain identification
10.1186/1471-2105-12-90 · 2011 · External reference
10.1093/bioinformatics/btv582
10.1093/bioinformatics/btv582 · External reference
Domain prediction with probabilistic directional context
10.1093/bioinformatics/btx221 · 2017 · External reference
Domain size distributions can predict domain boundaries
10.1093/bioinformatics/16.7.613 · 2000 · External reference
Sequence-based prediction of protein domains
10.1093/nar/gkh684 · 2004 · External reference
PPRODO: prediction of protein domain boundaries using neural networks
10.1002/prot.20442 · 2005 · External reference
10.1093/nar/25.17.3389
10.1093/nar/25.17.3389 · External reference
KemaDom: a web server for domain prediction using kernel machine with local context
10.1093/nar/gkl331 · 2006 · External reference
DOMpro: protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks
10.1007/s10618-005-0023-5 · 2006 · External reference
Unresolved reference
2008 · External reference
10.1186/1471-2105-7-s5-s6
10.1186/1471-2105-7-s5-s6 · External reference
DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning
10.1186/1471-2105-12-43 · 2011 · External reference
10.1007/s00726-010-0506-6
10.1007/s00726-010-0506-6 · External reference
AAindex: amino acid index database, progress report 2008
10.1093/nar/gkm998 · 2007 · External reference
DROP: an SVM domain linker predictor trained with optimal features selected by random forest
10.1093/bioinformatics/btq700 · 2011 · External reference
PDP-CON: prediction of domain/linker residues in protein sequences using a consensus approach
10.1007/s00894-016-2933-0 · 2016 · External reference
DomHR: accurately identifying domain boundaries in proteins using a hinge region strategy
10.1371/journal.pone.0060559 · 2013 · External reference
ConDo: protein domain boundary prediction using coevolutionary information
10.1093/bioinformatics/bty973 · 2019 · External reference
10.1142/9789813279827_0007
10.1142/9789813279827_0007 · External reference
10.1093/bioinformatics/btz464
10.1093/bioinformatics/btz464 · External reference
ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly
10.1093/nar/gkx410 · 2017 · External reference
FUpred: detecting protein domains through deep-learning based contact map prediction
10.1093/bioinformatics/btaa217 · 2020 · External reference
Extending protein domain boundary predictors to detect discontinuous domains
10.1371/journal.pone.0141541 · 2015 · External reference
10.1371/journal.pcbi.0030232
10.1371/journal.pcbi.0030232 · External reference
10.1093/nar/gky1097
10.1093/nar/gky1097 · External reference
DIAL: a web-based server for the automatic identification of structural domains in proteins
10.1093/nar/gki427 · 2005 · External reference
Protein domain decomposition using a graph-theoretic approach
10.1093/bioinformatics/16.12.1091 · 2000 · External reference
10.1093/bioinformatics/btg006
10.1093/bioinformatics/btg006 · External reference
10.1110/ps.062597307
10.1110/ps.062597307 · External reference
10.1093/nar/gkn326
10.1093/nar/gkn326 · External reference
10.1126/sciadv.1600552
10.1126/sciadv.1600552 · External reference
Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM
10.1002/prot.20737 · 2005 · External reference
10.1006/jmbi.2001.5387
10.1006/jmbi.2001.5387 · External reference
OPUS-Dom: applying the folding-based method VECFOLD to determine protein domain boundaries
10.1016/j.jmb.2008.10.093 · 2009 · External reference
Folding polypeptide α-carbon backbones by distance geometry methods
10.1002/bip.360340406 · 1994 · External reference
Global fold determination from a small number of distance restraints
10.1006/jmbi.1995.0436 · 1995 · External reference
Hierarchic inertial projection: a fast distance matrix embedding algorithm
10.1016/s0097-8485(96)00011-3 · 1997 · External reference
Protein structural domain identification
10.1093/protein/12.3.203 · 1999 · External reference
10.1093/nar/gkh131
10.1093/nar/gkh131 · External reference
10.1016/s0022-2836(03)00269-9
10.1016/s0022-2836(03)00269-9 · External reference
10.1073/pnas.95.11.5857
10.1073/pnas.95.11.5857 · External reference
10.1093/nar/gku949
10.1093/nar/gku949 · External reference
Activities at the universal protein resource (UniProt)
10.1093/nar/gkt1140 · 2014 · External reference
10.1093/nar/gkt1196
10.1093/nar/gkt1196 · External reference
10.1093/nar/gks1094
10.1093/nar/gks1094 · External reference
Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks
10.1073/pnas.91.25.12091 · 1994 · External reference
10.1093/nar/24.14.2730
10.1093/nar/24.14.2730 · External reference
PROSITE: a documented database using patterns and profiles as motif descriptors
10.1093/bib/3.3.265 · 2002 · External reference
New and continuing developments at PROSITE
10.1093/nar/gks1067 · 2012 · External reference
ProRule: a new database containing functional and structural information on PROSITE profiles
10.1093/bioinformatics/bti614 · 2005 · External reference
[21] progressive alignment of amino acid sequences and construction of phylogenetic trees from them
10.1016/s0076-6879(96)66023-6 · 1996 · External reference
10.1093/nar/gkz1064
10.1093/nar/gkz1064 · External reference
10.1016/s0969-2126(97)00260-8
10.1016/s0969-2126(97)00260-8 · External reference
SSAP: sequential structure alignment program for protein structure comparison
10.1016/s0076-6879(96)66038-8 · 1996 · External reference
webPRC: the Profile Comparer for alignment-based searching of public domain databases
10.1093/nar/gkp279 · 2009 · External reference
10.1093/nar/gku1243
10.1093/nar/gku1243 · External reference
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains
10.1093/nar/gks1266 · 2012 · External reference
CATH: an expanded resource to predict protein function through structure and sequence
10.1093/nar/gkw1098 · 2017 · External reference
SUPERFAMILY, HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments
10.1093/nar/30.1.268 · 2002 · External reference
FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
10.1006/jmbi.2001.4762 · 2001 · External reference
10.1002/prot.21688
10.1002/prot.21688 · External reference
pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination
10.1093/bioinformatics/btp302 · 2009 · External reference
