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
SARM suppresses TRIF, TRAF3, and IRF3/7 mediated antiviral signaling in large yellow croaker Larimichthys crocea
Jia Zhang,Ying Li,Jun-Chun Tang,K. Li,Juan Juan Shen,Chang Liu,Yong Jiang,Zihao Zhang,Yi Lei Wang,Peng Fei Zou +9 more
TL;DR: In this paper , the ortholog of SARM, named as Lc-SARM, was cloned and identified in large yellow croaker (Larimichthys crocea).
Molecular docking and simulation studies of synthetic protease inhibitors against COVID-19: a computational study.
TL;DR: Sarma et al. as mentioned in this paper used protein data bank to obtain the X-ray crystal structure of the most important COVID-19 proteases 3CL pro (PDB ID: 6M2N).
5
Chicken GLUT4 undergoes complex alternative splicing events and its expression in striated muscle changes dramatically during development
TL;DR: Wang et al. as mentioned in this paper obtained chicken GLUT4 mRNA sequences by combining conventional amplification, 5'- and 3'- rapid amplification of cDNA ends technique (RACE), then bioinformatics analysis on its genomic structure, splicing pattern, subcellular localization prediction and homologous comparisons were carried out.
5
An In Silico Approach for Function Prediction of Hypothetical Proteins of Listeria monocytogenes
Jibin Varghese,John J. Georrge +1 more
TL;DR: From this work, it is predicted that these bacteria are having protein called Aryldialkylphosphatase which can degrade agricultural pesticides such as parathion which would also be helpful to understand metabolism and another functional role of the organism.
5
Phased grapevine genome sequence of an Rpv12 carrier for biotechnological exploration of resistance to Plasmopara viticola
Bianca Frommer,S Müllner,Daniela Holtgräwe,Prisca Viehöver,Bruno Hüttel,Reinhard Töpfer,Bernd Weisshaar,Eva Zyprian +7 more
TL;DR: In this paper , a haplotype-separated genome sequence of the diploid Rpv12-carrier Gf.99-03 was created and annotated, revealing approximately 600 up-regulated Vitis genes during host-pathogen interaction.
5
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.