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SFLD specifications


Unique identifier OMICS_12043
Alternative name The Structure–Function Linkage Database
Restrictions to use None
Database management system MySQL
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes


  • person_outline Patricia Babbitt

Publication for The Structure–Function Linkage Database

SFLD citations


Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species

Sci Rep
PMCID: 5919931
PMID: 29700415
DOI: 10.1038/s41598-018-25016-4

[…] ring) thresholds. Furthermore, the predicted secretomes in Aspergillus species were annotated with protein family and domain information from TIGRFAM (http://www.jcvi.org/cgi-bin/tigrfams/index.cgi), SFLD (http://sfld.rbvi.ucsf.edu/django/), SMART (http://smart.embl-heidelberg.de/), CDD(https://www.ncbi.nlm.nih.gov/cdd), PROSITE, SUPERFAMILY (http://supfam.org/SUPERFAMILY/), PRINTS (http://130.88. […]


Identification of the Autochaperone Domain in the Type Va Secretion System (T5aSS): Prevalent Feature of Autotransporters with a β Helical Passenger

Front Microbiol
PMCID: 5767081
PMID: 29375499
DOI: 10.3389/fmicb.2017.02607

[…] P (Pedruzzi et al., ), PANTHER v11.1 (Mi et al., ), Pfam v30.0 (Finn et al., ), PIRSF (Wu et al., ), PRINTS (Attwood et al., ), ProDom v2012.1 (Servant et al., ), PROSITE v2017.01 (Sigrist et al., ), SFLD (Akiva et al., ), SMART v7.0 (Schultz et al., ), SUPERFAMILY v1.75 (Wilson et al., ), TIGRFAMs v15.0 (Haft et al., ). Besides structure modeling using Phyre v2, β-helix folds were predicted with […]


A global view of structure–function relationships in the tautomerase superfamily

PMCID: 5818174
PMID: 29184004
DOI: 10.1074/jbc.M117.815340
call_split See protocol

[…] erases in many of the major protein databases. InterPro () identifies the TSF by the following signatures: IPR028116, IPR001398, IPR015017, IPR004220, and IPR014347. These sequences were added to the SFLD () on August 16, 2016. Removal of redundant sequences produced a final, nonredundant set of 11,395 sequences for further analyses. […]


Diversity and Functional Analysis of the FeMo Cofactor Maturase NifB

Front Plant Sci
PMCID: 5715403
PMID: 29250084
DOI: 10.3389/fpls.2017.01947
call_split See protocol

[…] The 390 annotated NifB sequences retrieved from the Structure and Function Linkage Database (SFLD) () and UniProt are shown in Supplementary Table . To exclude potentially faulty annotated sequences, the following filtering procedure was applied to the dataset. First, amino acid sequences of […]


Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily

Proc Natl Acad Sci U S A
PMCID: 5692541
PMID: 29078300
DOI: 10.1073/pnas.1706849114

[…] .40.109.10 ()]. By using HMMSCAN () and Pfam sequence signatures, we verified that 94% of our superfamily members are single NTR domain sequences (). The resulting sequences were uploaded to the UCSF SFLD (). […]


Chemosensing of honeybee parasite, Varroa destructor: Transcriptomic analysis

Sci Rep
PMCID: 5638865
PMID: 29026097
DOI: 10.1038/s41598-017-13167-9

[…] the following domain search: BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, HAMAP, PatternScan, SuperFamily, SignalPHMM, TMHMM, HMMPanther, Gene3D, Phobius, Coils, CDD and SFLD. […]


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SFLD institution(s)
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA; Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biologicas, Santiago, Chile; Nodality, Inc., South San Francisco, CA, USA; Department of Electrical and Computer Engineering, College of Engineering, Boston University, Boston, MA, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, CA, USA; Center for Bioinformatics (ZBH), University of Hamburg, Hamburg, Germany; Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA; School of Medicine, University of California, San Francisco, San Francisco, CA, USA; UC Berkeley - UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA, USA; California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA, USA
SFLD funding source(s)
The National Institutes of Health [grant number R01GM60595], the National Science Foundation [DBI-0234768, DBI-0640476]; National Institute of General Medical Sciences [P41GM103311].

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