A5026383671- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
- Protein Structure and Dynamics
- Enzyme Structure and Function
- Genetics, Bioinformatics, and Biomedical Research
- Bioinformatics and Genomic Networks
- Advanced Proteomics Techniques and Applications
- Microbial Metabolic Engineering and Bioproduction
- Biomedical Text Mining and Ontologies
- Molecular Biology Techniques and Applications
- Glycosylation and Glycoproteins Research
- Gene expression and cancer classification
- COVID-19 Clinical Research Studies
- Heat shock proteins research
- Receptor Mechanisms and Signaling
- CRISPR and Genetic Engineering
- Bacterial Genetics and Biotechnology
- vaccines and immunoinformatics approaches
- SARS-CoV-2 and COVID-19 Research
- Chemical Synthesis and Analysis
- Scientific Computing and Data Management
- Manufacturing Process and Optimization
- Natural Language Processing Techniques
- Vector-borne infectious diseases
National Center for Biotechnology Information
2015-2024
National Institutes of Health
2015-2024
Medical University of Graz
2009-2011
Institut de génétique et de biologie moléculaire et cellulaire
2010
United States National Library of Medicine
1999
Bryant University
1997
Bauer Research Foundation
1997
Universitat de València
1996
University of Vienna
1996
Research Institute of Molecular Pathology
1994
NCBI's CDD, the Conserved Domain Database, enters its 15th year as a public resource for annotation of proteins with location conserved domain footprints. Going forward, we strive to improve coverage and consistency provided by CDD. We maintain live search system well an archive pre-computed sequences tracked in Entrez protein database, which can be retrieved single or bulk. also import procedures so that CDD contains models definitions several collections available domain, those produced...
NCBI’s Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with location conserved domain footprints, and functional sites inferred from these footprints. CDD includes manually curated models that make use 3D structure to refine provide insights into sequence/structure/function relationships. Manually are organized hierarchically if they describe families clearly related by common descent. As also imports family variety external sources, it partially...
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 widely distributed protein domain families, and record conserved sites associated with molecular function, so that they can be mapped onto user queries in support hypothesis-driven biomolecular research. offers both an archive pre-computed annotations well live search services for single or nucleotide...
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. An archive pre-computed annotation is maintained for proteins tracked by Entrez database, live search services are offered as well. CDD curation staff supplements a comprehensive collection family models, which have been imported external providers, representations selected families that...
We describe the Conserved Domain Search service (CD-Search), a web-based tool for detection of structural and functional domains in protein sequences. CD-Search uses BLAST® heuristics to provide fast, interactive service, searches comprehensive collection domain models. results are displayed as architecture cartoons pairwise alignments between query domain-model consensus may be visualized further detail by embedding sequence into multiple alignment displays mapping onto three-dimensional...
Abstract The National Center for Biotechnology Information (NCBI) produces a variety of online information resources biology, including the GenBank® nucleic acid sequence database and PubMed® citations abstracts published in life science journals. NCBI provides search retrieval operations most these data from 35 distinct databases. E-utilities serve as programming interface Resources receiving significant updates past year include PubMed, PMC, Bookshelf, RefSeq, SRA, Virus, dbSNP, dbVar,...
The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains conserved sites. InterProScan is the underlying software that allows nucleic acid to be searched against InterPro's signatures. Signatures are predictive models which describe or sites, provided by multiple databases. combines signatures representing equivalent additional information such as descriptions, literature...
Abstract The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains conserved sites. Here, we report recent developments with (version 90.0) its associated software, including updates to data content the website. These extend enrich information provided by InterPro, provide a more user friendly access data. Additionally, have worked on adding Pfam website features website, as...
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources biological information and data, including the GenBank® nucleic acid sequence database PubMed citations abstracts published life science journals. Entrez system search retrieval operations most these data from 39 distinct databases. E-utilities serve as programming interface system. Augmenting many Web applications are custom implementations BLAST program optimized to specialized sets. New...
InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and predict the presence of important domains sites. InterProScan underlying software that allows both nucleic acid be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with associated software, including addition two new databases (SFLD CDD), functionality include residue-level annotation...
The InterPro database (http://www.ebi.ac.uk/interpro/) classifies protein sequences into families and predicts the presence of functionally important domains sites. Here, we report recent developments with (version 70.0) its associated software, including an 18% growth in size terms on new entries, updates to content, inclusion additional entry type, refined modelling discontinuous domains, development a programmatic interface website. These extend enrich information provided by InterPro,...
The Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system. CDD linked to other databases such as Proteins, Taxonomy PubMed, can be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. CD-Search, which available http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi, a fast, interactive tool identify conserved domains in new sequences. CD-Search results for sequences are pre-computed provide links between proteins domain...
NCBI's Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. The can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml, also part Entrez query retrieval system, cross-linked to numerous other resources. CDD provides annotation domain footprints functional sites on sequences. Precalculated retrieved for sequences tracked CDD's models queried with...
The conserved domain database (CDD) is part of NCBI's Entrez system and serves as a primary resource for the annotation footprints on protein sequences in Entrez. Entrez's global query interface can be accessed at Author Webpage will search CDD many other databases. Domain proteins has been pre-computed readily available form 'Conserved Domain' links. Novel scanned against using CD-Search service; this service searches databases CDD-derived profile models with sequence queries BLAST...
CDD, the Conserved Domain Database, is part of NCBI's Entrez query and retrieval system also accessible via http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml. CDD provides annotation protein sequences with location conserved domain footprints functional sites inferred from these footprints. Pre-computed available Entrez, interactive search services accept single or nucleotide queries, as well batch submissions sequences, utilizing RPS-BLAST to rapidly identify putative matches....
The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) provides annotation over 95 000 prokaryotic genomes that meet standards sequence quality, completeness, and freedom from contamination. Genomes are annotated by a single Prokaryotic Genome Annotation Pipeline (PGAP) to provide users with resource is as consistent accurate possible. Notable recent changes include development of hierarchical evidence scheme, new focus on curating sources,...
The NCBI BioSystems database, found at http://www.ncbi.nlm.nih.gov/biosystems/, centralizes and cross-links existing biological systems databases, increasing their utility target audience by integrating pathways into resources. This integration allows users of NCBI's Entrez databases to quickly categorize proteins, genes small molecules metabolic pathway, disease state or other BioSystem type, without requiring time-consuming inference relationships from the literature multiple experimental datasets.
Abstract The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) contains nearly 200 000 bacterial and archaeal genomes 150 million proteins with up-to-date annotation. Changes in Prokaryotic Genome Annotation Pipeline (PGAP) since 2018 have resulted a substantial reduction spurious hierarchical collection of protein family models (PFMs) used by PGAP as evidence structural functional annotation was expanded to over 35 profile hidden Markov (HMMs),...
The Conserved Domain Database (CDD) is now indexed as a separate database within the Entrez system and linked to other databases such MEDLINE(R). This allows users search for domain types by name, example, or view architecture of any protein in Entrez's sequence database. CDD can be accessed on WorldWideWeb at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. Users may also employ CD-Search service identify conserved domains new sequences,...
The Conserved Domain Database (CDD) is a compilation of multiple sequence alignments representing protein domains conserved in molecular evolution. It has been populated with alignment data from the public collections Pfam and SMART, as well contributions colleagues at NCBI. current version CDD (v.1.54) contains 3693 such models. are linked to structure Entrez. viewer Cn3D serves tool interactively visualize three-dimensional structure, link residue coordinates descriptions evolutionary...
In addition to maintaining the GenBank® nucleic acid sequence database, National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources data in GenBank other biological made available through NCBI Web site. include Entrez, Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP,...
In addition to maintaining the GenBank® nucleic acid sequence database, National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources data in GenBank other biological made available through NCBI web site. include Entrez, Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Gene, Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, Reference Sequence, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes,...
In addition to maintaining the GenBank® nucleic acid sequence database, National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources data in GenBank other biological made available through NCBI Website. include Entrez, Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome related tools,...