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

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.

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 CDD/SPARCLE: the conserved domain database in 2020

2019 ◽  
Vol 48 (D1) ◽  
pp. D265-D268 ◽  
Author(s):  
Shennan Lu ◽  
Jiyao Wang ◽  
Farideh Chitsaz ◽  
Myra K Derbyshire ◽  
Renata C Geer ◽  
...  
Keyword(s):  
Protein Domain ◽  
Molecular Function ◽  
Protein Families ◽  
Bacterial Proteins ◽  
Protein Architecture ◽  
Conserved Domain ◽  
Single Protein ◽  
Domain Database ◽  
User Queries

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.

scholarly journals Phylogenetic analysis of Na+/H+ (NuoL/MrpA) antiporters

2019 ◽  
pp. 8-15
Author(s):  
Lenin Sánchez-Calderón ◽  
Mauricio Nahuam Chávez-Avilés ◽  
Alma Laura Díaz-Pérez ◽  
Blanca Estela Gómez-Luna ◽  
Juan Carlos Ramírez-Granados ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Atp Synthesis ◽  
Domain Analysis ◽  
Phylogeny Reconstruction ◽  
Monovalent Cations ◽  
Minimum Evolution ◽  
Homologous Proteins ◽  
Conserved Domain ◽  
Low Concentrations ◽  
Eukaryotic Proteins

Objectives: Sodium/proton (Na+/H+) antiporters NuoL/MrpA-like proteins are important in monovalent cations homeostasis, ATP synthesis, are involved in growth using low concentrations of acetate, and in management of protons during methane production. To learn more about the evolutive origin and biological relevance of this protein, in this work a phylogenetic analysis of the NuoL/MrpA superfamily of proteins was done. Methodology: Phylogeny reconstruction was done with 596 NuoL/MrpA proteins and 39 MrpD-NuoM/N proteins. The algorithms used were minimum evolution and maximum likelihood, using MEGA program. Additionally, a conserved domain analysis was done. Contribution: NuoL/MrpA superfamily and their homologous proteins, MrpD-NuoM/N, form two paralogous groups. The NuoL/MrpA superfamily consists of two families. Family NuoL consist of arqueal, bacterial and eukaryotic proteins of around 600 aa in size. Family MrpA are formed by proteins from bacteria and archaea, with a 600 to 850 aa in size. Using the phylogenetic analysis and conserved domain analysis, a superfamily NuoL/MrpA evolution model was proposed.

scholarly journals d-Omix: a mixer of generic protein domain analysis tools

2009 ◽  
Vol 37 (Web Server) ◽  
pp. W417-W421 ◽  
Author(s):  
D. Wichadakul ◽  
S. Numnark ◽  
S. Ingsriswang
Keyword(s):  
Domain Analysis ◽  
Protein Domain ◽  
Analysis Tools

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 COVID-19:Attacks the 1-Beta Chain of Hemoglobin and Captures the Porphyrin to Inhibit Human Heme Metabolism

2020 ◽  
Author(s):  
liu wenzhong ◽  
Li hualan
Keyword(s):  
Molecular Docking ◽  
Cytochrome C ◽  
Viral Proteins ◽  
Domain Analysis ◽  
Heme Iron ◽  
The Novel ◽  
Beta Chain ◽  
Conserved Domain ◽  
Novel Coronavirus

<p>The novel coronavirus pneumonia (COVID-19) is an infectious acute respiratory caused by the novel coronavirus. The virus is the positive-strand RNA one with high homology to bat coronavirus. The pathogenic mechanism of the new coronavirus is still unclear, which is a significant obstacle to the development of drugs and patients' rescue. In this study, conserved domain analysis, homology modeling, and molecular docking were made to compare the biological roles of specific proteins belonging to the novel coronavirus. The conserved domain analysis showed envelope protein (E), nucleocapsid phosphoprotein (N) and ORF3a had heme linked sites, which Arg134 of ORF3a, Cys44 of E, Ile304 of N were the heme-iron linked site, respectively. ORF3a also possessed the conserved domains of human cytochrome C reductases and bacterial EFeB protein. These three domains were highly overlapping so that ORF3a could dissociate the iron of heme to form porphyrin. Heme linked sites of E protein may be relevant to the high infectivity, and the role of heme linked sites of N protein may be related to the virus replication. The docking results showed that orf1ab, ORF10, and ORF3a proteins coordinated to attack the 1-beta chain of hemoglobin, and some structural and non-structural viral proteins could bind porphyrin. Deoxyhemoglobin was more vulnerable to virus attacks than oxidized hemoglobin. But ORF3a was specific and would not attack blue blood protein, normal cytochrome C, and peroxidase. As for the attack, it would cause increasingly less hemoglobin that could carry oxygen and carbon dioxide, thus producing symptoms of respiratory distress and coagulation reaction, damaging many organs and tissues. The mechanism also interfered with the normal heme anabolic pathway of the human body, expecting to cause human diseases. Based on the small molecule drug library, drugbank, we searched for drugs bound to viral proteins by molecular docking. The results showed that some anticancer drugs could attach to the heme-iron linked site of ORF3a and N. Remdesivir was relatively more obvious than Hydroxychloroquine and Chloroquine in terms of the binding capacity of ORF3a, but the combined role of three drugs to ORF3a was lower. Unfortunately, no drug could bind to the heme-iron linked site of E. Besides, these higher binding energies may prevent all screened drugs from binding firmly to viral proteins. Since there were no clinical data, so inhibitory effects on ORF3a and N were still unclear. This theory is only for academic discussion and needed to be verified by other experiments. Please consult a qualified doctor for treatment details. Due to the toxicity and side effects of drugs, do not use medicines yourself. We expect these discoveries to bring more ideas to people to relieve patients' symptoms and save more lives.<br></p>

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