CDD/SPARCLE: the conserved domain database in 2020
Shennan Lu,Jiyao Wang,Farideh Chitsaz,Myra K. Derbyshire,Renata C. Geer,Noreen R. Gonzales,Marc Gwadz,David I. Hurwitz,Gabriele H. Marchler,James S. Song,Narmada Thanki,Roxanne A. Yamashita,Mingzhang Yang,Dachuan Zhang,Chanjuan Zheng,Christopher J. Lanczycki,Aron Marchler-Bauer +16 more
TL;DR: As NLM's Conserved Domain Database (CDD) enters its 20th year of operations as a publicly available resource, curation staff continues to develop hierarchical classifications of widely distributed protein domain families, and to record conserved sites associated with molecular function, so that they can be mapped onto user queries in support of hypothesis-driven biomolecular research.
read more
Abstract: As NLM's Conserved Domain Database (CDD) enters its 20th year of operations as a publicly available resource, CDD curation staff continues to develop hierarchical classifications of widely distributed protein domain families, and to record conserved sites associated with molecular function, so that they can be mapped onto user queries in support of hypothesis-driven biomolecular research. CDD offers both an archive of pre-computed domain annotations as well as live search services for both single protein or nucleotide queries and larger sets of protein query sequences. CDD staff has continued to characterize protein families via conserved domain architectures and has built up a significant corpus of curated domain architectures in support of naming bacterial proteins in RefSeq. These architecture definitions are available via SPARCLE, the Subfamily Protein Architecture Labeling Engine. CDD can be accessed at https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Novel RAB3GAP1 Mutation in the First Tunisian Family With Warburg Micro Syndrome
TL;DR: Clinical and genetic characterization of a consanguineous Tunisian family with a WARBM phenotype presenting two pathogenic variations are presented and a novel variation in RAB3GAP1 is revealed that is most likely pathogenic and allowed the diagnosis of WARBM.
2
In silico targeting of SARS-CoV-2 spike receptor-binding domain from different variants with chaga mushroom terpenoids.
Faroque Amin,Abdo A. Elfiky +1 more
TL;DR: Sarma et al. as discussed by the authors examined the association of chaga mushroom terpenoids with the RBD of various SARS-CoV-2 variants, including alpha, beta, gamma, delta, and omicron.
2
A relaxin receptor gene RpGPCR41 is involved in the resistance of Rhopalosiphum padi to pyrethroids
Hongcheng Tang,Xi Liu,Suji Wang,Yixuan Wang,Longchuan Bai,Xiong Peng,Maohua Chen +6 more
TL;DR: The relaxin receptor gene RpGPCR41 is involved in the resistance of Rhopalosiphum padi to pyrethroids.
2
A new type of phasin characterized by the presence of a helix‐hairpin‐helix domain is required for normal polyhydroxybutyrate accumulation and granule organization in Caulobacter crescentus
Ana Laura Salinas,Aurora Osorio,Tonatiuh Legorreta-Hissner,Reyna Lara-Martínez,Luis Felipe Jiménez-García,Laura Camarena,Sebastian Poggio +6 more
TL;DR: An initial proteomic characterization of the PHB granules is shown and a new type of phasin (PhaH) characterized by the presence of an N‐terminal hydrophobic helix followed by a helix‐hairpin‐helix (HhH) domain is described.
2
Knowledge-guided data mining on the standardized architecture of NRPS: subtypes, novel motifs, and sequence entanglements
Vanessa Opassinis
- 17 Mar 2022
TL;DR: In this article , the motif-and-intermotif standardization of NRPS sequences was proposed to provide a consistent standard for annotating NRPS domains and modules, which has made data-driven discoveries challenging.
2
References
The Pfam protein families database in 2019.
Sara El-Gebali,Jaina Mistry,Alex Bateman,Sean R. Eddy,Aurelien Luciani,Simon C. Potter,Matloob Qureshi,Lorna Richardson,Gustavo A. Salazar,Alfredo Smart,Erik L. L. Sonnhammer,Layla Hirsh,Layla Hirsh,Lisanna Paladin,Damiano Piovesan,Silvio C. E. Tosatto,Robert D. Finn +16 more
TL;DR: A significant comparison to the structural classification database that led to the creation of 825 new families based on their set of uncharacterized families (EUFs) was carried out and Pfam entries were connected to the Sequence Ontology (SO) through mapping of the Pfam type definitions to SO terms.
4.7K
CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.
Aron Marchler-Bauer,Yu Bo,Lianyi Han,Jane He,Christopher J. Lanczycki,Shennan Lu,Farideh Chitsaz,Myra K. Derbyshire,Renata C. Geer,Noreen R. Gonzales,Marc Gwadz,David I. Hurwitz,Fu Lu,Gabriele H. Marchler,James S. Song,Narmada Thanki,Zhouxi Wang,Roxanne A. Yamashita,Dachuan Zhang,Chanjuan Zheng,Lewis Y. Geer,Stephen H. Bryant +21 more
TL;DR: NCBI's Conserved Domain Database (CDD) aims at annotating biomolecular sequences with the location of evolutionarily conserved protein domain footprints, and functional sites inferred from such footprints.
2.6K
CD-Search: protein domain annotations on the fly
TL;DR: The Conserved Domain Search service (CD-Search), a web-based tool for the detection of structural and functional domains in protein sequences, uses BLAST(R) heuristics to provide a fast, interactive service, and searches a comprehensive collection of domain models.
The COG database: new developments in phylogenetic classification of proteins from complete genomes
Roman L. Tatusov,Darren A. Natale,Igor Garkavtsev,Tatiana Tatusova,Uma Shankavaram,Bachoti S. Rao,Boris Kiryutin,Michael Y. Galperin,Natalie D. Fedorova,Eugene V. Koonin +9 more
TL;DR: The new features added to the COG database include information pages with structural and functional details on each COG and literature references, improvements of the COGNITOR program that is used to fit new proteins into the COGs, and classification of genomes and COGs constructed by using principal component analysis.
20 years of the SMART protein domain annotation resource.
Ivica Letunic,Peer Bork +1 more
TL;DR: In its 20th year, the SMART analysis results pages have been streamlined again and its information sources have been updated, and the internal full text search engine has been redesigned and updated, resulting in greatly increased search speed.