The Pfam protein families database in 2019

The Pfam protein families database in 2019

2019, Vol. 47, Database issue | Sara El-Gebali, Jaina Mistry, Alex Bateman, Sean R. Eddy, Aurélien Luciani, Simon C. Potter, Matloob Qureshi, Lorna J. Richardson, Gustavo A. Salazar, Alfredo Smart, Erik L.L. Sonnhammer, Layla Hirsh, Lisanna Paladin, Damiano Piovesan, Silvio C.E. Tosatto and Robert D. Finn
The Pfam protein families database has seen significant updates in its latest release (version 32.0), released in September 2018. The database now contains 17,929 entries, with 77.2% of UniProtKB sequences and 53.2% of residues falling within Pfam entries. New additions and improvements include: 1. **Domain Boundary Refinement**: Pfam entries have been refined to improve domain boundaries, enhancing the accuracy of functional annotations. 2. **Clan Classification**: Pfam entries are classified into clans based on evolutionary relationships, with 628 clans in total, up from 5,282 in release 29.0. 3. **ECOD Integration**: Comparisons with the Evolutionary Classification of Protein Domains (ECOD) database led to the creation of 825 new entries, improving the consistency of Pfam domains with known structures. 4. **Sequence Ontology (SO) Mapping**: Pfam entries are now mapped to the Sequence Ontology (SO) terms, enhancing interoperability and data quality. 5. **Tandem Repeat Families**: Collaboration with RepeatsDB has improved the definition of tandem repeat families within Pfam. 6. **Author Credit**: Pfam now links authorship of entries to their ORCID identifiers, recognizing the contributions of the scientific community. Despite these improvements, the fraction of Pfam entries with no known function remains high, highlighting the need for more functional studies and high-throughput screening. The increased recognition of contributors aims to encourage broader participation in Pfam curation.The Pfam protein families database has seen significant updates in its latest release (version 32.0), released in September 2018. The database now contains 17,929 entries, with 77.2% of UniProtKB sequences and 53.2% of residues falling within Pfam entries. New additions and improvements include: 1. **Domain Boundary Refinement**: Pfam entries have been refined to improve domain boundaries, enhancing the accuracy of functional annotations. 2. **Clan Classification**: Pfam entries are classified into clans based on evolutionary relationships, with 628 clans in total, up from 5,282 in release 29.0. 3. **ECOD Integration**: Comparisons with the Evolutionary Classification of Protein Domains (ECOD) database led to the creation of 825 new entries, improving the consistency of Pfam domains with known structures. 4. **Sequence Ontology (SO) Mapping**: Pfam entries are now mapped to the Sequence Ontology (SO) terms, enhancing interoperability and data quality. 5. **Tandem Repeat Families**: Collaboration with RepeatsDB has improved the definition of tandem repeat families within Pfam. 6. **Author Credit**: Pfam now links authorship of entries to their ORCID identifiers, recognizing the contributions of the scientific community. Despite these improvements, the fraction of Pfam entries with no known function remains high, highlighting the need for more functional studies and high-throughput screening. The increased recognition of contributors aims to encourage broader participation in Pfam curation.
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