Structure Function Linkage Database Archive

Names
More detailed information about this field from each metasource.

Structure Function Linkage Database Archive
metasource: Fairsharing.org
version: None

SFLD
metasource: Fairsharing.org
version: None

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

Other names: SFLD

Structure Function Linkage Database (SFLD) is a database of enzymes classified by linking sequences to chemical function. A hierachical systems is used to classify enzymes by family or superfamily other category levels include functional domain, subgroup and suprafamily. The archive does not contain the interactive functionality found in the original SFLD, such as search capabilities. Instead, the archive is a static snapshot of the data in the SFLD as of April 2019, and will not be updated.

Webpage:

http://sfld.rbvi.ucsf.edu/

Publications:

Publications
More detailed information about this field from each metasource.

The Structure-Function Linkage Database
PMID: 24271399
metasource: Fairsharing.org
version: None

Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database
PMID: 16489747
metasource: Fairsharing.org
version: None

Using the Structure-function Linkage Database to characterize functional domains in enzymes
PMID: 18428763
metasource: Fairsharing.org
version: None

http://dx.doi.org/10.1093/nar/gkt1130
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

The Structure-Function Linkage Database PubMed citations: 110.

110 articles citing: The Structure-Function Linkage Database

Cobalamin-Dependent Radical S-Adenosylmethionine Enzymes: Capitalizing on Old Motifs for New Functions. PMID:35726326
Bioinformatic Analyses of Peroxiredoxins and RF-Prx: A Random Forest-Based Predictor and Classifier for Prxs. PMID:35696080
Three-dimensional Structure Databases of Biological Macromolecules. PMID:35507259
Multiple Profile Models Extract Features from Protein Sequence Data and Resolve Functional Diversity of Very Different Protein Families. PMID:35353898
The Atypical Cobalamin-Dependent S-Adenosyl-l-Methionine Nonradical Methylase TsrM and Its Radical Counterparts. PMID:35344653
Structure of a B12-dependent radical SAM enzyme in carbapenem biosynthesis. PMID:35110734
Characterization of Helianthus annuus Lipoic Acid Biosynthesis: The Mitochondrial Octanoyltransferase and Lipoyl Synthase Enzyme System. PMID:34868183
Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site. PMID:34737728
PANNZER-A practical tool for protein function prediction. PMID:34562305
Duo: A Signature Based Method to Batch-Analyze Functional Similarities of Proteins. PMID:34475860
Methods to Screen for Radical SAM Enzyme Crystallization Conditions. PMID:34292557
Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence. PMID:34135888
Computational Approaches: An Underutilized Tool in the Quest to Elucidate Radical SAM Dynamics. PMID:33946806
A Comprehensive Phylogenetic Analysis of the Serpin Superfamily. PMID:33744972
Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation. PMID:33711918
Genomic signatures of the evolution of defence against its natural enemies in the poisonous and medicinal plant Datura stramonium (Solanaceae). PMID:33441607
The InterPro protein families and domains database: 20 years on. PMID:33156333
Human SIRT1 Multispecificity Is Modulated by Active-Site Vicinity Substitutions during Natural Evolution. PMID:32956445
Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing. PMID:32917720
A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function. PMID:32449511
The hidden enzymology of bacterial natural product biosynthesis. PMID:32232178
Impact of sunflower (Helianthus annuus L.) plastidial lipoyl synthases genes expression in glycerolipids composition of transgenic Arabidopsis plants. PMID:32111914
First Step in Catalysis of the Radical S-Adenosylmethionine Methylthiotransferase MiaB Yields an Intermediate with a [3Fe-4S]0-Like Auxiliary Cluster. PMID:31899624
A global analysis of function and conservation of catalytic residues in enzymes. PMID:31796628
Biosynthesis of the nitrogenase active-site cofactor precursor NifB-co in Saccharomyces cerevisiae. PMID:31767756
The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways. PMID:31553576
Radical SAM enzymes: surprises along the path to understanding mechanism. PMID:31494759
Radical S-adenosylmethionine maquette chemistry: Cx3Cx2C peptide coordinated redox active [4Fe-4S] clusters. PMID:31486952
Environmental conditions shape the nature of a minimal bacterial genome. PMID:31308405
Functional Evolution of Proteins. PMID:30714210
InterPro in 2019: improving coverage, classification and access to protein sequence annotations. PMID:30398656
Mechanism of Radical Initiation in the Radical S-Adenosyl-l-methionine Superfamily. PMID:30346729
'Democratized' genomic enzymology web tools for functional assignment. PMID:30268904
Structural and spectroscopic analyses of the sporulation killing factor biosynthetic enzyme SkfB, a bacterial AdoMet radical sactisynthase. PMID:30217813
Methods for Studying the Radical SAM Enzymes in Diphthamide Biosynthesis. PMID:30097101
Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. PMID:30097089
Paradigm Shift for Radical S-Adenosyl-l-methionine Reactions: The Organometallic Intermediate Ω Is Central to Catalysis. PMID:29954180
Discovery of the Tiancilactone Antibiotics by Genome Mining of Atypical Bacterial Type II Diterpene Synthases. PMID:29806086
Comparison of Alicyclobacillus acidocaldarius o-Succinylbenzoate Synthase to Its Promiscuous N-Succinylamino Acid Racemase/ o-Succinylbenzoate Synthase Relatives. PMID:29767960
Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species. PMID:29700415
New computational approaches to understanding molecular protein function. PMID:29621256
Most yeast SH3 domains bind peptide targets with high intrinsic specificity. PMID:29470497
X-ray and EPR Characterization of the Auxiliary Fe-S Clusters in the Radical SAM Enzyme PqqE. PMID:29405700
Identification of the Autochaperone Domain in the Type Va Secretion System (T5aSS): Prevalent Feature of Autotransporters with a β-Helical Passenger. PMID:29375499
Informing Efforts to Develop Nitroreductase for Amine Production. PMID:29364838
Inferring joint sequence-structural determinants of protein functional specificity. PMID:29336305
A Radical Intermediate in Bacillus subtilis QueE during Turnover with the Substrate Analogue 6-Carboxypterin. PMID:29303575
Enhanced Solubilization of Class B Radical S-Adenosylmethionine Methylases by Improved Cobalamin Uptake in Escherichia coli. PMID:29298049
Diversity and Functional Analysis of the FeMo-Cofactor Maturase NifB. PMID:29250084
Characterization of auxiliary iron-sulfur clusters in a radical S-adenosylmethionine enzyme PqqE from Methylobacterium extorquens AM1. PMID:29226074
Mechanism of a Class C Radical S-Adenosyl-l-methionine Thiazole Methyl Transferase. PMID:29190095
A global view of structure-function relationships in the tautomerase superfamily. PMID:29184004
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. PMID:29106569
Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily. PMID:29078300
Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition. PMID:28893989
TsrM as a Model for Purifying and Characterizing Cobalamin-Dependent Radical S-Adenosylmethionine Methylases. PMID:28882204
Transition State Analogue Inhibitors of 5'-Deoxyadenosine/5'-Methylthioadenosine Nucleosidase from Mycobacterium tuberculosis. PMID:28836767
Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence-Function Space and Genome Context to Discover Novel Functions. PMID:28826221
An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences. PMID:28777078
The distribution and mechanism of iodotyrosine deiodinase defied expectations. PMID:28774660
BrEPS 2.0: Optimization of sequence pattern prediction for enzyme annotation. PMID:28750104
Community detection in sequence similarity networks based on attribute clustering. PMID:28738060
Substrate-Dependent Cleavage Site Selection by Unconventional Radical S-Adenosylmethionine Enzymes in Diphthamide Biosynthesis. PMID:28383907
Biocuration in the structure-function linkage database: the anatomy of a superfamily. PMID:28365730
An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. PMID:28187133
An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences. PMID:28054422
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
BciD Is a Radical S-Adenosyl-l-methionine (SAM) Enzyme That Completes Bacteriochlorophyllide e Biosynthesis by Oxidizing a Methyl Group into a Formyl Group at C-7. PMID:27994052
The evolution of function within the Nudix homology clan. PMID:27936487
InterPro in 2017-beyond protein family and domain annotations. PMID:27899635
Radical Reaction Control in the AdoMet Radical Enzyme CDG Synthase (QueE): Consolidate, Destabilize, Accelerate. PMID:27859789
DASP3: identification of protein sequences belonging to functionally relevant groups. PMID:27835946
Evaluating Functional Annotations of Enzymes Using the Gene Ontology. PMID:27812939
Mammalian Fe-S proteins: definition of a consensus motif recognized by the co-chaperone HSC20. PMID:27714045
Molecular Diversity of Terpene Synthases in the Liverwort Marchantia polymorpha. PMID:27650333
Functional Annotations of Paralogs: A Blessing and a Curse. PMID:27618105
Transformations of the FeS Clusters of the Methylthiotransferases MiaB and RimO, Detected by Direct Electrochemistry. PMID:27598886
Defining the Product Chemical Space of Monoterpenoid Synthases. PMID:27517297
Isofunctional Protein Subfamily Detection Using Data Integration and Spectral Clustering. PMID:27348631
Transition State Structure and Inhibition of Rv0091, a 5'-Deoxyadenosine/5'-methylthioadenosine Nucleosidase from Mycobacterium tuberculosis. PMID:27019223
The impact of structural genomics: the first quindecennial. PMID:26935210
Radical-mediated ring contraction in the biosynthesis of 7-deazapurines. PMID:26643180
The language of the protein universe. PMID:26451980
Diversity in protein domain superfamilies. PMID:26451979
PqqE from Methylobacterium extorquens AM1: a radical S-adenosyl-l-methionine enzyme with an unusual tolerance to oxygen. PMID:26188050
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation. PMID:26139634
Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity. PMID:26073648
Computational-guided discovery and characterization of a sesquiterpene synthase from Streptomyces clavuligerus. PMID:25901324
Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks. PMID:25900361
DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe. PMID:25888481
Biochemical functional predictions for protein structures of unknown or uncertain function. PMID:25848497
Panoramic view of a superfamily of phosphatases through substrate profiling. PMID:25848029
Expanding our understanding of sequence-function relationships of type II polyketide biosynthetic gene clusters: bioinformatics-guided identification of Frankiamicin A from Frankia sp. EAN1pec. PMID:25837682
Key challenges for the creation and maintenance of specialist protein resources. PMID:25820941
The Radical S-Adenosyl-L-methionine Enzyme QhpD Catalyzes Sequential Formation of Intra-protein Sulfur-to-Methylene Carbon Thioether Bonds. PMID:25778402
Evolutionary expansion of the amidohydrolase superfamily in bacteria in response to the synthetic compounds molinate and diuron. PMID:25636851
The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam. PMID:25614388
Deletion of PHO13, encoding haloacid dehalogenase type IIA phosphatase, results in upregulation of the pentose phosphate pathway in Saccharomyces cerevisiae. PMID:25527558
Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases. PMID:25513739
Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. PMID:25503938
Using the structure-function linkage database to characterize functional domains in enzymes. PMID:25501940
Mechanistic diversity of radical S-adenosylmethionine (SAM)-dependent methylation. PMID:25477520
SPASM and twitch domains in S-adenosylmethionine (SAM) radical enzymes. PMID:25477505
EzCatDB: the enzyme reaction database, 2015 update. PMID:25324316
cddApp: a Cytoscape app for accessing the NCBI conserved domain database. PMID:25212755
New insights about enzyme evolution from large scale studies of sequence and structure relationships. PMID:25210038
Functional annotation and structural characterization of a novel lactonase hydrolyzing D-xylono-1,4-lactone-5-phosphate and L-arabino-1,4-lactone-5-phosphate. PMID:24955762
Evolution of enzymatic activities in the enolase superfamily: galactarate dehydratase III from Agrobacterium tumefaciens C58. PMID:24926996
Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere. PMID:24756107
The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection. PMID:24316579
Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database PubMed citations: 86.

86 articles citing: Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database

Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans. PMID:35484634
Novel Enzymes From the Red Sea Brine Pools: Current State and Potential. PMID:34777282
A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function. PMID:32449511
Whole Proteome Clustering of 2,307 Proteobacterial Genomes Reveals Conserved Proteins and Significant Annotation Issues. PMID:30873148
Biocuration in the structure-function linkage database: the anatomy of a superfamily. PMID:28365730
An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. PMID:28187133
An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences. PMID:28054422
Exploring Mouse Protein Function via Multiple Approaches. PMID:27846315
Radical new paradigm for heme degradation in Escherichia coli O157:H7. PMID:27791000
Molecular Diversity of Terpene Synthases in the Liverwort Marchantia polymorpha. PMID:27650333
Comparative Protein Structure Modeling Using MODELLER. PMID:27322406
PINGU: PredIction of eNzyme catalytic residues usinG seqUence information. PMID:26261982
Using the structure-function linkage database to characterize functional domains in enzymes. PMID:25501940
Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach. PMID:25299649
Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere. PMID:24756107
Parallel clustering algorithm for large-scale biological data sets. PMID:24705246
Radical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism. PMID:24362703
ModBase, a database of annotated comparative protein structure models and associated resources. PMID:24271400
The Structure-Function Linkage Database. PMID:24271399
Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis. PMID:24270792
Functional clustering of immunoglobulin superfamily proteins with protein-protein interaction information calibrated hidden Markov model sequence profiles. PMID:24246499
X-ray analysis of butirosin biosynthetic enzyme BtrN redefines structural motifs for AdoMet radical chemistry. PMID:24048029
Consequences of domain insertion on sequence-structure divergence in a superfold. PMID:23959887
Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function. PMID:23676670
Rapid catalytic template searching as an enzyme function prediction procedure. PMID:23675414
Functional site plasticity in domain superfamilies. PMID:23499848
Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily. PMID:23493556
Ballast: a ball-based algorithm for structural motifs. PMID:23383999
Seq2Ref: a web server to facilitate functional interpretation. PMID:23356573
Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking. PMID:23256477
Enzyme informatics. PMID:23116471
Relationships between kinetic constants and the amino acid composition of enzymes from the yeast Saccharomyces cerevisiae glycolysis pathway. PMID:22867018
Defining sequence space and reaction products within the cyanuric acid hydrolase (AtzD)/barbiturase protein family. PMID:22730121
Is EC class predictable from reaction mechanism? PMID:22530800
Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. PMID:22306579
clusterMaker: a multi-algorithm clustering plugin for Cytoscape. PMID:22070249
Divergent evolution in enolase superfamily: strategies for assigning functions. PMID:22069326
Inference of functional properties from large-scale analysis of enzyme superfamilies. PMID:22069325
MACiE: exploring the diversity of biochemical reactions. PMID:22058127
The Enzyme Function Initiative. PMID:21999478
The evolution of function in strictosidine synthase-like proteins. PMID:21948213
Pa0148 from Pseudomonas aeruginosa catalyzes the deamination of adenine. PMID:21710971
Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis. PMID:21605342
Constructing de novo biosynthetic pathways for chemical synthesis inside living cells. PMID:21591680
Toward mechanistic classification of enzyme functions. PMID:21489855
Topological variation in the evolution of new reactions in functionally diverse enzyme superfamilies. PMID:21458983
Protein function prediction: towards integration of similarity metrics. PMID:21353529
Analysis of the peroxiredoxin family: using active-site structure and sequence information for global classification and residue analysis. PMID:21287625
Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. PMID:21118823
ModBase, a database of annotated comparative protein structure models, and associated resources. PMID:21097780
Detailed analysis of function divergence in a large and diverse domain superfamily: toward a refined protocol of function classification. PMID:21070951
The LabelHash algorithm for substructure matching. PMID:21070651
Directed evolution of a thermostable quorum-quenching lactonase from the amidohydrolase superfamily. PMID:20980257
Chapter 4. Predicting and characterizing protein functions through matching geometric and evolutionary patterns of binding surfaces. PMID:20731991
Clustering of protein families into functional subtypes using Relative Complexity Measure with reduced amino acid alphabets. PMID:20718947
X-ray structure and mutational analysis of the atrazine Chlorohydrolase TrzN. PMID:20659898
Functional identification and structure determination of two novel prolidases from cog1228 in the amidohydrolase superfamily. PMID:20604542
Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction. PMID:20459833
Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function. PMID:20300652
Bacterial ammeline metabolism via guanine deaminase. PMID:20023034
Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PMID:20011109
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. PMID:19923231
An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations. PMID:19851441
Evolution of efficient pathways for degradation of anthropogenic chemicals. PMID:19620997
PSI-2: structural genomics to cover protein domain family space. PMID:19523904
Annotating enzymes of uncertain function: the deacylation of D-amino acids by members of the amidohydrolase superfamily. PMID:19518059
Exploiting structural classifications for function prediction: towards a domain grammar for protein function. PMID:19398323
Functional annotation of two new carboxypeptidases from the amidohydrolase superfamily of enzymes. PMID:19358546
Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. PMID:19219566
Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PMID:19190775
Toward accurate screening in computer-aided enzyme design. PMID:19161327
Functional annotation and three-dimensional structure of Dr0930 from Deinococcus radiodurans, a close relative of phosphotriesterase in the amidohydrolase superfamily. PMID:19159332
Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening. PMID:19000819
MODBASE, a database of annotated comparative protein structure models and associated resources. PMID:18948282
Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. PMID:18670595
Exploring the structure and function paradigm. PMID:18554899
Protein robustness promotes evolutionary innovations on large evolutionary time-scales. PMID:18430649
ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts. PMID:18325116
Automated protein subfamily identification and classification. PMID:17708678
Evolution of function in the "two dinucleotide binding domains" flavoproteins. PMID:17658942
Structure-based activity prediction for an enzyme of unknown function. PMID:17603473
N-Acetyl-D-glucosamine-6-phosphate deacetylase: substrate activation via a single divalent metal ion. PMID:17567047
Using reaction mechanism to measure enzyme similarity. PMID:17400244
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. PMID:17082206
Uronate isomerase: a nonhydrolytic member of the amidohydrolase superfamily with an ambivalent requirement for a divalent metal ion. PMID:16768441
A gold standard set of mechanistically diverse enzyme superfamilies. PMID:16507141
Using the Structure-function Linkage Database to characterize functional domains in enzymes PubMed citations: 1.

1 articles citing: Using the Structure-function Linkage Database to characterize functional domains in enzymes

From sequence to enzyme mechanism using multi-label machine learning. PMID:24885296
http://dx.doi.org/10.1093/nar/gkt1130

Tags:

Tags
More detailed information about this field from each metasource.

dna sequence data
metasource: Fairsharing.org
version: None

enzymatic reaction
metasource: Fairsharing.org
version: None

enzyme
metasource: Fairsharing.org
version: None

functional association
metasource: Fairsharing.org
version: None

hidden markov model
metasource: Fairsharing.org
version: None

protein domain
metasource: Fairsharing.org
version: None

protein structure
metasource: Fairsharing.org
version: None

metabolic and signaling pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

protein-protein interactions
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

dna sequences enzymatic reaction enzyme functional association hidden markov model protein domain protein structure metabolic and signaling pathways protein-protein interactions

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Enzyme Structure Function Ontology

Dockground

BRENDA

SCOPPI

HotSprint

SUPERFAMILY

InterDom

Conserved Domain Database

Life Science Database Archive

Structure Superposition Database

TCSBN

BioCarta Pathways

PIPs

Molecular Modeling Database

FunTree: A Resource For Exploring The Functional Evolution Of Structurally Defined Enzyme Superfamilies

PDZBase

PASS2

Model Archive

prePPI

Protein-protein interfaces