scholarly journals CDD: specific functional annotation with the Conserved Domain Database

2009 ◽  
Vol 37 (Database) ◽  
pp. D205-D210 ◽  
Author(s):  
A. Marchler-Bauer ◽  
J. B. Anderson ◽  
F. Chitsaz ◽  
M. K. Derbyshire ◽  
C. DeWeese-Scott ◽  
...  
Keyword(s):  
Functional Annotation ◽  
Conserved Domain ◽  
Domain Database

scholarly journals CDD: a Conserved Domain Database for the functional annotation of proteins

2010 ◽  
Vol 39 (Database) ◽  
pp. D225-D229 ◽  
Author(s):  
A. Marchler-Bauer ◽  
S. Lu ◽  
J. B. Anderson ◽  
F. Chitsaz ◽  
M. K. Derbyshire ◽  
...  
Keyword(s):  
Functional Annotation ◽  
Conserved Domain ◽  
Domain Database

scholarly journals NCBI's Conserved Domain Database and Tools for Protein Domain Analysis

2019 ◽  
Vol 69 (1) ◽  
Author(s):  
Mingzhang Yang ◽  
Myra K. Derbyshire ◽  
Roxanne A. Yamashita ◽  
Aron Marchler‐Bauer
Keyword(s):  
Domain Analysis ◽  
Protein Domain ◽  
Conserved Domain ◽  
Domain Database

scholarly journals Does conserved domain SOD1 mutation has any role in ALS severity and therapeutic outcome?

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Surinder Pal ◽  
Abha Tiwari ◽  
Kaushal Sharma ◽  
Suresh Kumar Sharma
Keyword(s):  
Free Energy ◽  
Multiple Regression ◽  
Functional Annotation ◽  
Structural Changes ◽  
Tertiary Structure ◽  
Structural Annotation ◽  
Chi Square ◽  
Conserved Domain ◽  
Chi Square Analysis ◽  
Functional Components

Abstract Background Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative fatal disease that can affect the neurons of brain and spinal cord. ALS genetics has identified various genes to be associated with disease pathology. Oxidative stress induced bunina and lewy bodies formation can be regulated through the action of SOD1 protein. Hence, in the present study we aim to analyse the structural and functional annotation of various reported SOD1 variants throughout and their putative correlation with the location of mutation and degree of ALS severity by inferring the structural and functional alterations in different SOD1 variants. Methods We have retrieved around 69 SNPs of SOD1 gene from Genecards. Structural annotation of SOD1 variants were performed using SWISS Model, I-Mutant 2.0, Dynamut, ConSurf. Similarly, the functional annotation of same variants were done using SIFT, PHP-SNP, PolyPhen2, PROVEAN and RegulomeDB. Ramachandran plot was also obtained for six synonymous SNPs to compare the amino acid distribution of wild-type SOD1 (WT SOD1) protein. Frequency analysis, Chi square analysis, ANOVA and multiple regression analysis were performed to compare the structural and functional components among various groups. Results and conclusion Results showed the mutations in conserved domain of SOD1 protein are more deleterious and significantly distort the tertiary structure of protein by altering Gibb’s free energy and entropy. Moreover, significant changes in SIFT, PHP-SNP, PolyPhen2, PROVEAN and RegulomeDB scores were also observed in mutations located in conserved domain of SOD1 protein. Multiple regression results were also suggesting the significant alterations in free energy and entropy for conserved domain mutations which were concordant with structural changes of SOD1 protein. Results of the study are suggesting the biological importance of location of mutation(s) which may derive the different disease phenotypes and must be dealt accordingly to provide precise therapy for ALS patients.

scholarly journals S-Glutathionyl-(chloro)hydroquinone reductases: a novel class of glutathione transferases

2010 ◽  
Vol 428 (3) ◽  
pp. 419-427 ◽  
Author(s):  
Luying Xun ◽  
Sara M. Belchik ◽  
Randy Xun ◽  
Yan Huang ◽  
Huina Zhou ◽  
...  
Keyword(s):  
Disulfide Bond ◽  
Distinct Group ◽  
Degradation Pathway ◽  
Glutathione Transferases ◽  
Amino Acid Residues ◽  
Tblastn Search ◽  
Conserved Domain ◽  
Ping Pong ◽  
Sphingobium Chlorophenolicum ◽  
Domain Database

Sphingobium chlorophenolicum completely mineralizes PCP (pentachlorophenol). Two GSTs (glutathione transferases), PcpC and PcpF, are involved in the degradation. PcpC uses GSH to reduce TeCH (tetrachloro-p-hydroquinone) to TriCH (trichloro-p-hydroquinone) and then to DiCH (dichloro-p-hydroquinone) during PCP degradation. However, oxidatively damaged PcpC produces GS-TriCH (S-glutathionyl-TriCH) and GS-DiCH (S-glutathionyl-TriCH) conjugates. PcpF converts the conjugates into TriCH and DiCH, re-entering the degradation pathway. PcpF was further characterized in the present study. It catalysed GSH-dependent reduction of GS-TriCH via a Ping Pong mechanism. First, PcpF reacted with GS-TriCH to release TriCH and formed disulfide bond between its Cys53 residue and the GS moiety. Then, a GSH came in to regenerate PcpF and release GS–SG. A TBLASTN search revealed that PcpF homologues were widely distributed in bacteria, halobacteria (archaea), fungi and plants, and they belonged to ECM4 (extracellular mutant 4) group COG0435 in the conserved domain database. Phylogenetic analysis grouped PcpF and homologues into a distinct group, separated from Omega class GSTs. The two groups shared conserved amino acid residues, for GSH binding, but had different residues for the binding of the second substrate. Several recombinant PcpF homologues and two human Omega class GSTs were produced in Escherichia coli and purified. They had zero or low activities for transferring GSH to standard substrates, but all had reasonable activities for GSH-dependent reduction of disulfide bond (thiol transfer), dehydroascorbate and dimethylarsinate. All the tested PcpF homologues reduced GS-TriCH, but the two Omega class GSTs did not. Thus PcpF homologues were tentatively named S-glutathionyl-(chloro)hydroquinone reductases for catalysing the GSH-dependent reduction of GS-TriCH.

Protein Domain Annotations of the SARS-CoV-2 Proteomics as a Blue-Print for Mapping the Features for Drug and Vaccine Designs

2020 ◽  
Vol 25 (2) ◽  
pp. 26-32
Author(s):  
Arli Parikesit ◽  
Keyword(s):  
Drug Design ◽  
Vaccine Design ◽  
Causal Agent ◽  
Protein Domain ◽  
Potential Drug ◽  
Potential Target ◽  
Conserved Domain ◽  
Drug Lead ◽  
Blue Print ◽  
Domain Database

SARS-CoV-2 virus, as the causal agent for the COVID-19 pandemic, remains an enigma in the bioinformatics sense. Current efforts in drug and vaccine design in primarily targeting general devised protein domain while overlooking the specific features in the proteomics repertoire. However, the NCBI Conserved Domain Database (CDD) could annotate the specific features that are indispensable for a more advanced drug and vaccine design. In this regard, the annotation efforts were initiated with CDD database, and visualized with the 3D Protein Visualizer of Cn3D. The exsistence of the ATP and ADP binding protein with respected domains were found to be a very potential target for drug design. It is recommended that nucleoside inhibitor that could mimick the ATP molecule could serve as a potential drug lead agains SARS-CoV-2.

scholarly journals CDD: NCBI's conserved domain database

2014 ◽  
Vol 43 (D1) ◽  
pp. D222-D226 ◽  
Author(s):  
Aron Marchler-Bauer ◽  
Myra K. Derbyshire ◽  
Noreen R. Gonzales ◽  
Shennan Lu ◽  
Farideh Chitsaz ◽  
...  
Keyword(s):  
Conserved Domain ◽  
Domain Database

Protein domain hierarchy Gibbs sampling strategies

2014 ◽  
Vol 13 (4) ◽  
Author(s):  
Andrew F. Neuwald
Keyword(s):  
Gibbs Sampling ◽  
Sequence Alignment ◽  
Gibbs Sampler ◽  
Multiple Sequence Alignment ◽  
Protein Domain ◽  
Sampling Strategies ◽  
Multiple Sequence ◽  
Manual Curation ◽  
Conserved Domain ◽  
Domain Database

AbstractHierarchically-arranged multiple sequence alignment profiles are useful for modeling protein domains that have functionally diverged into evolutionarily-related subgroups. Currently such alignment hierarchies are largely constructed through manual curation, as for the NCBI Conserved Domain Database (CDD). Recently, however, I developed a Gibbs sampler that uses an approach termed

scholarly journals PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database

Database ◽  
2019 ◽  
Vol 2019 ◽  
Author(s):  
Rezarta Islamaj ◽  
W John Wilbur ◽  
Natalie Xie ◽  
Noreen R Gonzales ◽  
Narmada Thanki ◽  
...  
Keyword(s):  
Pearson Correlation ◽  
Information Access ◽  
Specific Protein ◽  
Reference List ◽  
Text Similarity ◽  
Multiple Sequence ◽  
Conserved Domain ◽  
Similarity Model ◽  
And Function ◽  
Domain Database

AbstractThis study proposes a text similarity model to help biocuration efforts of the Conserved Domain Database (CDD). CDD is a curated resource that catalogs annotated multiple sequence alignment models for ancient domains and full-length proteins. These models allow for fast searching and quick identification of conserved motifs in protein sequences via Reverse PSI-BLAST. In addition, CDD curators prepare summaries detailing the function of these conserved domains and specific protein families, based on published peer-reviewed articles. To facilitate information access for database users, it is desirable to specifically identify the referenced articles that support the assertions of curator-composed sentences. Moreover, CDD curators desire an alert system that scans the newly published literature and proposes related articles of relevance to the existing CDD records. Our approach to address these needs is a text similarity method that automatically maps a curator-written statement to candidate sentences extracted from the list of referenced articles, as well as the articles in the PubMed Central database. To evaluate this proposal, we paired CDD description sentences with the top 10 matching sentences from the literature, which were given to curators for review. Through this exercise, we discovered that we were able to map the articles in the reference list to the CDD description statements with an accuracy of 77%. In the dataset that was reviewed by curators, we were able to successfully provide references for 86% of the curator statements. In addition, we suggested new articles for curator review, which were accepted by curators to be added into the reference list at an acceptance rate of 50%. Through this process, we developed a substantial corpus of similar sentences from biomedical articles on protein sequence, structure and function research, which constitute the CDD text similarity corpus. This corpus contains 5159 sentence pairs judged for their similarity on a scale from 1 (low) to 5 (high) doubly annotated by four CDD curators. Curator-assigned similarity scores have a Pearson correlation coefficient of 0.70 and an inter-annotator agreement of 85%. To date, this is the largest biomedical text similarity resource that has been manually judged, evaluated and made publicly available to the community to foster research and development of text similarity algorithms.

scholarly journals Improving the consistency of domain annotation within the Conserved Domain Database

Database ◽  
2015 ◽  
Vol 2015 ◽  
Author(s):  
Myra K. Derbyshire ◽  
Noreen R. Gonzales ◽  
Shennan Lu ◽  
Jane He ◽  
Gabriele H. Marchler ◽  
...  
Keyword(s):  
Domain Annotation ◽  
Conserved Domain ◽  
Domain Database

scholarly journals CDD: a conserved domain database for interactive domain family analysis

2007 ◽  
Vol 35 (Database) ◽  
pp. D237-D240 ◽  
Author(s):  
A. Marchler-Bauer ◽  
J. B. Anderson ◽  
M. K. Derbyshire ◽  
C. DeWeese-Scott ◽  
N. R. Gonzales ◽  
...  
Keyword(s):  
Domain Family ◽  
Conserved Domain ◽  
Family Analysis ◽  
Domain Database
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