Research graph
References from Biochemical functional predictions for protein structures of unknown or uncertain function. Local targets link to admitted publications; unresolved targets remain external evidence.
Activities at the universal protein resource (UniProt)
10.1093/nar/gku469 · 2014 · External reference
The Protein Data Bank and structural genomics
10.1093/nar/gkg068 · 2003 · External reference
10.1021/bi201312u
10.1021/bi201312u · External reference
10.1016/s0969-2126(00)00193-3
10.1016/s0969-2126(00)00193-3 · External reference
10.1016/j.str.2007.12.002
10.1016/j.str.2007.12.002 · External reference
10.1126/science.1058040
10.1126/science.1058040 · External reference
10.1038/35057062
10.1038/35057062 · External reference
10.1371/journal.pcbi.1000605
10.1371/journal.pcbi.1000605 · External reference
10.1016/s0022-2836(02)00016-5
10.1016/s0022-2836(02)00016-5 · External reference
10.1016/j.jmb.2003.08.057
10.1016/j.jmb.2003.08.057 · External reference
Percolation of annotation errors through hierarchically structured protein sequence databases
10.1016/j.mbs.2004.08.001 · 2005 · External reference
Annotating proteins with generalized functional linkages
10.1073/pnas.0809583105 · 2008 · External reference
10.1152/ajpcell.00225.2006
10.1152/ajpcell.00225.2006 · External reference
Unresolved reference
2006 · External reference
10.1038/nrc2036
10.1038/nrc2036 · External reference
10.1038/nrm2281
10.1038/nrm2281 · External reference
Network-based prediction of protein function
10.1038/msb4100129 · 2007 · External reference
Protein function annotation by homology-based inference
10.1186/gb-2009-10-2-207 · 2009 · External reference
An overview of in silico protein function prediction
10.1007/s00203-010-0549-9 · 2010 · External reference
10.1093/nar/25.17.3389
10.1093/nar/25.17.3389 · External reference
10.1109/tcbb.2004.32
10.1109/tcbb.2004.32 · External reference
Using Dali for structural comparison of proteins
10.1002/0471250953.bi0505s14 · 2006 · External reference
10.1093/nar/gkq366
10.1093/nar/gkq366 · External reference
Mechanisms and structures of crotonase superfamily enzymes — how nature controls enolate and oxyanion reactivity
10.1007/s00018-008-8082-6 · 2008 · External reference
A gold standard set of mechanistically diverse enzyme superfamilies
10.1186/gb-2006-7-1-r8 · 2006 · External reference
10.1006/jmbi.1999.2661
10.1006/jmbi.1999.2661 · External reference
10.1371/journal.pcbi.1002403
10.1371/journal.pcbi.1002403 · External reference
10.1016/j.str.2007.02.005
10.1016/j.str.2007.02.005 · External reference
10.1016/s0022-2836(02)00649-6
10.1016/s0022-2836(02)00649-6 · External reference
10.1016/s1367-5931(02)00018-2
10.1016/s1367-5931(02)00018-2 · External reference
Protein informatics towards function identification
10.1016/s0959-440x(03)00074-5 · 2003 · External reference
Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution
10.1186/1745-6150-5-31 · 2010 · External reference
GenBank
10.1093/nar/gkn723 · 2009 · External reference
10.1093/nar/gkm882
10.1093/nar/gkm882 · External reference
An iterative approach of protein function prediction
10.1186/1471-2105-12-437 · 2011 · External reference
The use of evolutionary patterns in protein annotation
10.1016/j.sbi.2012.05.001 · 2012 · External reference
Predicting protein function from sequence and structural data
10.1016/j.sbi.2005.04.003 · 2005 · External reference
Structure-based function prediction: approaches and applications
10.1093/bfgp/eln030 · 2008 · External reference
10.1093/bib/bbp017
10.1093/bib/bbp017 · External reference
A method to predict functional residues in proteins
10.1038/nsb0295-171 · 1995 · External reference
10.1093/bioinformatics/19.1.163
10.1093/bioinformatics/19.1.163 · External reference
10.1006/jmbi.1996.0167
10.1006/jmbi.1996.0167 · External reference
10.1093/nar/gkp339
10.1093/nar/gkp339 · External reference
INTREPID—INformation-theoretic TREe traversal for Protein functional site IDentification
10.1093/bioinformatics/btn474 · 2008 · External reference
SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions
10.1016/0263-7855(95)00073-9 · 1995 · External reference
10.1093/nar/gkl282
10.1093/nar/gkl282 · External reference
LIGSITE: predicting protein binding sites using the Connolly surface and degree of conservation
10.1186/1472-6807-6-19 · 2006 · External reference
10.1074/mcp.m400159-mcp200
10.1074/mcp.m400159-mcp200 · External reference
A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites
10.1186/1471-2105-8-s4-s9 · 2007 · External reference
10.1016/s1093-3263(98)00002-3
10.1016/s1093-3263(98)00002-3 · External reference
Q-SiteFinder: an energy-based method for the prediction of protein–ligand binding sites
10.1093/bioinformatics/bti315 · 2005 · External reference
Computational solvent mapping reveals the importance of local conformational changes for broad substrate specificity in mammalian cytochromes P450
10.1021/bi060343v · 2006 · External reference
10.1073/pnas.211436698
10.1073/pnas.211436698 · External reference
Prediction of active sites for protein structures from computed chemical properties
10.1093/bioinformatics/bti1039 · 2005 · External reference
Selective prediction of interaction sites in protein structures with THEMATICS
10.1186/1471-2105-8-119 · 2007 · External reference
10.1002/prot.20660
10.1002/prot.20660 · External reference
Statistical criteria for the identification of protein active sites using theoretical microscopic titration curves
10.1002/prot.20418 · 2005 · External reference
High conservation of amino acids with anomalous protonation behavior
10.2174/157489310791268414 · 2010 · External reference
10.1016/s0022-2836(03)00515-1
10.1016/s0022-2836(03)00515-1 · External reference
10.1073/pnas.0404569101
10.1073/pnas.0404569101 · External reference
Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design
10.1093/nar/gki894 · 2005 · External reference
Prediction of catalytic residues using support vector machine with selected protein sequence and structural properties
10.1186/1471-2105-7-312 · 2006 · External reference
siteFiNDER|3D: a web-based tool for predicting the location of functional sites in proteins
10.1093/nar/gkm422 · 2007 · External reference
10.1110/ps.062523907
10.1110/ps.062523907 · External reference
ResBoost: characterizing and predicting catalytic residues in enzymes
10.1186/1471-2105-10-197 · 2009 · External reference
SitesIdentify: a protein functional site prediction tool
10.1186/1471-2105-10-379 · 2009 · External reference
10.1093/bioinformatics/btq008
10.1093/bioinformatics/btq008 · External reference
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure
10.1371/journal.pcbi.1000585 · 2009 · External reference
10.1016/s0022-2836(02)01036-7
10.1016/s0022-2836(02)01036-7 · External reference
Partial order optimum likelihood (POOL): maximum likelihood prediction of protein active site residues using 3D structure and sequence properties
10.1371/journal.pcbi.1000266 · 2009 · External reference
Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: computational prediction and experimental validation of phosphoesterase activity
10.1002/prot.23035 · 2011 · External reference
The role of the PHP domain associated with DNA polymerase X from Thermus thermophilus HB8 in base excision repair
10.1016/j.dnarep.2012.09.001 · 2012 · External reference
A structural role for the PHP domain in E. coli DNA polymerase III
10.1186/1472-6807-13-8 · 2013 · External reference
Histidinol phosphate phosphatase, catalyzing the penultimate step of the histidine biosynthesis pathway, is encoded by ytvP (hisJ) in Bacillus subtilis
10.1128/jb.181.10.3277-3280.1999 · 1999 · External reference
Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis
10.1016/s0092-8674(00)81968-6 · 1999 · External reference
Reaction mechanism of alkaline phosphatase based on crystal structures. Two-metal ion catalysis
10.1016/0022-2836(91)90724-k · 1991 · External reference
Crystal structure of monofunctional histidinol phosphate phosphatase from Thermus thermophilus HB8
10.1021/bi701204r · 2007 · External reference
High-resolution (1.5A) crystal structure of phospholipase C from Bacillus cereus
10.1038/338357a0 · 1989 · External reference
Engineering the enolase magnesium II binding site: implications for its evolution
10.1021/bi100954f · 2010 · External reference
Functional classification of protein 3D structures from predicted local interaction sites
10.1142/s0219720010005166 · 2010 · External reference
ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins
10.1093/nar/gks435 · 2012 · External reference
ProFunc: a server for predicting protein function from 3D structure
10.1093/nar/gki414 · 2005 · External reference
10.1006/jmbi.2001.5034
10.1006/jmbi.2001.5034 · External reference
10.1107/s0907444904026460
10.1107/s0907444904026460 · External reference
The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes
10.1093/nar/gkt1243 · 2014 · External reference
Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs)
10.1186/1471-2105-14-s3-s13 · 2013 · External reference
10.1093/nar/gkq1091
10.1093/nar/gkq1091 · External reference
10.1038/nprot.2007.324
10.1038/nprot.2007.324 · External reference
The structure–function linkage database
10.1093/nar/gkt1130 · 2014 · External reference
Prediction and assignment of function for a divergent N-succinyl amino acid racemase
10.1038/nchembio.2007.11 · 2007 · External reference
10.1038/nature05981
10.1038/nature05981 · External reference
10.1038/nmeth.2340
10.1038/nmeth.2340 · External reference
Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function
10.1186/gb-2009-10-9-r97 · 2009 · External reference
10.1093/bioinformatics/btl492
10.1093/bioinformatics/btl492 · External reference
Bayesian Markov Random Field analysis for protein function prediction based on network data
10.1371/journal.pone.0009293 · 2010 · External reference
10.1126/science.1099511
10.1126/science.1099511 · External reference
10.1016/j.str.2004.10.015
10.1016/j.str.2004.10.015 · External reference
Hierarchical classification of gene ontology terms using the GOstruct method
10.1142/s0219720010004744 · 2010 · External reference
10.1073/pnas.0832373100
10.1073/pnas.0832373100 · External reference
10.1089/106652703322756168
10.1089/106652703322756168 · External reference
Predicting protein function from protein/protein interaction data: a probabilistic approach
10.1093/bioinformatics/btg1026 · 2003 · External reference
Whole-proteome prediction of protein function via graph—theoretic analysis of interaction maps
10.1093/bioinformatics/bti1054 · 2005 · External reference
Global protein function prediction from protein–protein interaction networks
10.1038/nbt825 · 2003 · External reference
10.1002/prot.23029
10.1002/prot.23029 · External reference
Enhanced automated function prediction using distantly related sequences and contextual association by PFP
10.1110/ps.062153506 · 2006 · External reference
10.1016/s0022-2836(02)00379-0
10.1016/s0022-2836(02)00379-0 · External reference
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes
10.1186/1471-2105-5-178 · 2004 · External reference
ConFunc—functional annotation in the twilight zone
10.1093/bioinformatics/btn037 · 2008 · External reference
Phydbac “Gene Function Predictor”: a gene annotation tool based on genomic context analysis
10.1186/1471-2105-6-247 · 2005 · External reference
10.1371/journal.pcbi.0010045
10.1371/journal.pcbi.0010045 · External reference
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium
10.1093/bib/bbr042 · 2011 · External reference
10.1126/science.285.5428.751
10.1126/science.285.5428.751 · External reference
10.1073/pnas.96.8.4285
10.1073/pnas.96.8.4285 · External reference
10.1038/75556
10.1038/75556 · External reference
One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012
10.1007/978-1-62703-302-2_4 · 2013 · External reference
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools
10.1093/nar/gku902 · 2014 · External reference
10.1093/nar/gkt1196
10.1093/nar/gkt1196 · External reference
10.1093/nar/gkt1110
10.1093/nar/gkt1110 · External reference
Ensembl Genomes 2013: scaling up access to genome-wide data
10.1093/nar/gkt979 · 2014 · External reference
FlyBase 102—advanced approaches to interrogating FlyBase
10.1093/nar/gkt1092 · 2014 · External reference
Standardized description of scientific evidence using the Evidence Ontology (ECO)
10.1093/database/bau075 · 2014 · External reference
10.1093/nar/gkr948
10.1093/nar/gkr948 · External reference
10.1093/nar/gkt1115
10.1093/nar/gkt1115 · External reference
The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations
10.1093/nar/gkt1029 · 2014 · External reference
10.1093/nar/gkq869
10.1093/nar/gkq869 · External reference
Genetic resources for advanced biofuel production described with the Gene Ontology
10.3389/fmicb.2014.00528 · 2014 · External reference
10.1186/2046-2530-2-7
10.1186/2046-2530-2-7 · External reference
10.1093/nar/gkr1032
10.1093/nar/gkr1032 · External reference
The Mouse Tumor Biology Database (MTB): a central electronic resource for locating and integrating mouse tumor pathology data
10.1177/0300985810395726 · 2012 · External reference
10.1093/nar/gkt1225
10.1093/nar/gkt1225 · External reference
10.1093/nar/gkt954
10.1093/nar/gkt954 · External reference
10.1093/nar/gks1118
10.1093/nar/gks1118 · External reference
10.1093/nar/gkr853
10.1093/nar/gkr853 · External reference
The Rat Genome Database 2013—data, tools and users
10.1093/bib/bbt007 · 2013 · External reference
10.1093/nar/gkt1102
10.1093/nar/gkt1102 · External reference
10.1093/nar/gkr1029
10.1093/nar/gkr1029 · External reference
10.1093/nar/gkr1090
10.1093/nar/gkr1090 · External reference
10.1093/nar/gkn803
10.1093/nar/gkn803 · External reference
10.1093/nar/gkr954
10.1093/nar/gkr954 · External reference
ZFIN: enhancements and updates to the Zebrafish Model Organism Database
10.1093/nar/gkq1077 · 2011 · External reference
AgBase: supporting functional modeling in agricultural organisms
10.1093/nar/gkq1115 · 2011 · External reference
10.1093/nar/gkr945
10.1093/nar/gkr945 · External reference
Protein function prediction by massive integration of evolutionary analyses and multiple data sources
10.1186/1471-2105-14-s3-s1 · 2013 · External reference
Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms
10.1186/1471-2105-13-s4-s14 · 2012 · External reference
10.1371/journal.pcbi.1002195
10.1371/journal.pcbi.1002195 · External reference
10.1093/nar/gkr367
10.1093/nar/gkr367 · External reference
10.1111/j.1574-6976.2010.00242.x
10.1111/j.1574-6976.2010.00242.x · External reference
10.1016/j.cell.2010.06.035
10.1016/j.cell.2010.06.035 · External reference
10.1016/j.bbrc.2008.05.058
10.1016/j.bbrc.2008.05.058 · External reference
The COMBREX project: design, methodology, and initial results
10.1371/journal.pbio.1001638 · 2013 · External reference
10.1093/nar/gkq1168
10.1093/nar/gkq1168 · External reference
The archaeal COG1901/DUF358 SPOUT-methyltransferase members, together with pseudouridine synthase Pus10, catalyze the formation of 1-methylpseudouridine at position 54 of tRNA
10.1261/rna.030841.111 · 2012 · External reference
10.1093/nar/gkr1146
10.1093/nar/gkr1146 · External reference
Diversity of archaeosine synthesis in crenarchaeota
10.1021/cb200361w · 2012 · External reference
Selenomodification of tRNA in archaea requires a bipartite rhodanese enzyme
10.1016/j.febslet.2012.01.024 · 2012 · External reference
Characterization of type II and III restriction–modification systems from Bacillus cereus strains ATCC 10987 and ATCC 14579
10.1128/jb.06248-11 · 2012 · External reference
10.1093/nar/22.22.4673
10.1093/nar/22.22.4673 · External reference
The neighbor-joining method: a new method for reconstructing phylogenetic trees
1987 · External reference
10.1111/j.1365-2958.2011.07690.x
10.1111/j.1365-2958.2011.07690.x · External reference
The importance of porE and porF in the anabolic pyruvate oxidoreductase of Methanococcus maripaludis
10.1007/s00203-003-0629-1 · 2004 · External reference
