> > > NAR Database Issue 2010

NAR Database Issue 2010

RSS Feed Compact View Sort by Links Directory Index
downloadList as XML List as JSON List as TSV List as CSV
journalList by Category Publisher Site

Found 133 links

Displaying 15 links

Resources (0)Hide Databases (132)Hide Tools (1)

3D-FootprintDatabase Content

http://floresta.eead.csic.es/3dfootprint [open in a new window]

Share This Link
DNA > Databases
Protein > Databases

3D-footprint provides estimates of binding specificity for all protein-DNA complexes available at the Protein Data Bank. The web interface allows the user to: (i) browse DNA-binding proteins by keyword; (ii) find proteins that recognize a similar DNA motif and (iii) BLAST similar DNA-binding proteins, highlighting interface residues in the resulting alignments. Comparisons with expert-curated databases RegulonDB and TRANSFAC support the quality of structure-based estimates of specificity.

This content is being maintained by brunocontreras.

links directory index: 13
TitlePublication YearGoogle Scholar Citation Count
3D-footprint: a database for the structural analysis of protein-DNA complexes.201013
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0

3DNALandscapesDatabase Content

http://dcp.rutgers.edu [open in a new window]

Share This Link
DNA > Databases

3DNALandscapes is a database for exploring the conformational features of DNA. 3DNALandscapes enables searches of conformational information across multiple structures. The database contains a wide variety of structural parameters and molecular images, computed with the 3DNA software package and known to be useful for characterizing and understanding the sequence-dependent spatial arrangements of the DNA sugar-phosphate backbone, sugar-base side groups, base pairs, base-pair steps, groove structure, etc. The data comprise all DNA-containing structures--both free and bound to proteins, drugs and other ligands--currently available in the Protein Data Bank.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
3DNALandscapes: a database for exploring the conformational features of DNA20103
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsanimals computational biology dna genetic databases humans ligands nucleic acid conformation nucleic acid databases protein databases

ACLAMEDatabase Content

http://aclame.ulb.ac.be/ [open in a new window]

Share This Link
DNA > Databases

The ACLAME database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids). Classifications are available at various levels of organization. At the gene/protein level, families group similar sequences that are expected to share the same function. Families of four or more proteins are manually assigned with a functional annotation using the GeneOntology and the locally developed ontology MeGO dedicated to MGEs. At the genome level, evolutionary cohesive modules group sets of protein families shared among MGEs. At the population level, networks display the reticulate evolutionary relationships among MGEs.

links directory index: 22
TitlePublication YearGoogle Scholar Citation Count
ACLAME: a CLAssification of Mobile genetic Elements, update 2010201022
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms bacterial genome bacteriophages computational biology genetic databases interspersed repetitive sequences nucleic acid databases nucleic acid repetitive sequences plasmids

AntigenDBDatabase Content

http://www.imtech.res.in/raghava/antigendb/ [open in a new window]

Share This Link
Human Genome > Databases

AntigenDB contains 500 antigens to pathogenic species curated from the literature and other immunological resources. In AntigenDB, a database entry contains information regarding the sequence, structure, origin, etc. of an antigen with additional information such as B and T-cell epitopes, MHC binding, function, gene-expression and post translational modifications, where available. AntigenDB also provides links to major internal and external databases.

This content is being maintained by raghavagps.

links directory index: 10
TitlePublication YearGoogle Scholar Citation Count
AntigenDB: an immunoinformatics database of pathogen antigens201010
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsantigens communicable diseases computational biology epitopes genetic databases humans immune system immunogenetics lymphocytes peptide mapping post-translational protein processing protein databases tertiary protein structure

AspGDDatabase Content

http://www.aspergillusgenome.org/ [open in a new window]

Share This Link
Model Organisms > Databases

The Aspergillus Genome Database (AspGD) is an online genomics resource for researchers studying the genetics and molecular biology of the Aspergilli. AspGD combines high-quality manual curation of the experimental scientific literature examining the genetics and molecular biology of Aspergilli, cutting-edge comparative genomics approaches to iteratively refine and improve structural gene annotations across multiple Aspergillus species, and web-based research tools for accessing and exploring the data.

links directory index: 21
TitlePublication YearGoogle Scholar Citation Count
The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community201021
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsaspergillus nidulans computational biology fungal genes fungal genome fungal proteins genetic databases genetic models genetics nucleic acid databases phenotype protein databases tertiary protein structure

BeetleBaseDatabase Content

http://beetlebase.org/ [open in a new window]

Share This Link
Model Organisms > Databases

BeetleBase (http://www.beetlebase.org) has been updated to provide more comprehensive genomic information for the red flour beetle Tribolium castaneum. The database contains genomic sequence scaffolds mapped to 10 linkage groups (genome assembly release Tcas_3.0), genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The database was reconstructed using the upgraded Generic Model Organism Database (GMOD) modules. Genome information is visualized as tracks in GBrowse. The updated genetic map is visualized using the comparative genetic map viewer CMAP. To enhance the database search capabilities, the BLAST and BLAT search tools have been integrated with the GMOD tools.

links directory index: 18
TitlePublication YearGoogle Scholar Citation Count
BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum201018
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsanimals computational biology expressed sequence tags genetic databases genetic models genome genomics nucleic acid databases protein databases tertiary protein structure tribolium

BioDrugScreenDatabase Content

http://www.biodrugscore.org [open in a new window]

Share This Link
Other Molecules > Databases

BioDrugScreen is a resource for ranking molecules docked against a large number of targets in the human proteome. Nearly 1600 molecules from the freely available NCI diversity set were docked onto 1926 cavities identified on 1589 human targets resulting in >3 million receptor-ligand complexes. The targets in BioDrugScreen originated from Human Cancer Protein Interaction Network, which we have updated, as well as the Human Druggable Proteome, which we have created for the purpose of this effort. This makes the BioDrugScreen resource highly valuable in drug discovery.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
BioDrugScreen: a computational drug design resource for ranking molecules docked to the human proteome20109
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagscomputational biology drug design genetic databases humans ligands nucleic acid databases pharmaceutical preparations preclinical drug evaluation protein binding proteome proteomics

BioNumbersDatabase Content

http://www.bionumbers.hms.harvard.edu [open in a new window]

Share This Link
Literature > Databases

BioNumbers (http://www.bionumbers.hms.harvard.edu) is a database of key numbers in molecular and cell biology--the quantitative properties of biological systems of interest to computational, systems and molecular cell biologists. Contents of the database range from cell sizes to metabolite concentrations, from reaction rates to generation times, from genome sizes to the number of mitochondria in a cell. All numbers are taken directly from a literature source and that reference is provided with the number.

links directory index: 20
TitlePublication YearGoogle Scholar Citation Count
BioNumbers--the database of key numbers in molecular and cell biology201020
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms animals biological models cell biology computational biology genetic databases humans molecular biology nucleic acid databases protein databases systems biology theoretical models

BioSystemsDatabase Content

http://www.ncbi.nlm.nih.gov/biosystems [open in a new window]

Share This Link
Protein > Databases

The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI's Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other BioSystem type.

links directory index: 34
TitlePublication YearGoogle Scholar Citation Count
The NCBI BioSystems database201034
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
setsNational Center for Biotechnology Information (NCBI)

CAMPDatabase Content

http://bicnirrh.res.in/antimicrobial [open in a new window]

Share This Link
Other Molecules > Databases

Collection of Anti-Microbial Peptides (CAMP) is a free online database that is manually curated and currently holds 3782 antimicrobial sequences. These sequences are divided into experimentally validated (patents and non-patents: 2766) and predicted (1016) datasets based on their reference literature. Information like source organism, activity (MIC values), reference literature, target and non-target organisms of AMPs are captured in the database. Prediction and sequence analysis tools, including BLAST, are integrated in the database.

links directory index: 36
TitlePublication YearGoogle Scholar Citation Count
CAMP: a useful resource for research on antimicrobial peptides201036
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms anti-infective agents antimicrobial cationic peptides bacterial genome computational biology genetic databases humans nucleic acid databases peptides protein databases reproducibility of results

Candida Genome DatabaseDatabase Content

http://www.candidagenome.org/ [open in a new window]

Share This Link
Model Organisms > Databases

The Candida Genome Database provides online access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. Two tools have been added to the DB. The Biochemical Pathways tool provides visualization of metabolic pathways and analysis tools that facilitate interpretation of experimental data, including results of large-scale experiments, in the context of Candida metabolism. Textpresso for Candida allows searching through the full-text of Candida-specific literature, including clinical and epidemiological studies.

links directory index: 40
TitlePublication YearGoogle Scholar Citation Count
The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata.20126
New tools at the Candida Genome Database: biochemical pathways and full-text literature search201034
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagscandida albicans computational biology fungal dna fungal genes fungal genome genetic databases nucleic acid databases open reading frames protein databases tertiary protein structure

ChEBIDatabase Content

http://www.ebi.ac.uk/chebi/ [open in a new window]

Share This Link
Other Molecules > Databases

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. The molecular entities in question are either natural products or synthetic products used to intervene in the processes of living organisms. In addition to molecular entities, ChEBI contains groups (parts of molecular entities) and classes of entities.

links directory index: 97
TitlePublication YearGoogle Scholar Citation Count
Chemical Entities of Biological Interest: an update201097
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
external linksLink on Wikipedia
tagsagrochemicals animals biological products chemical dictionaries computational biology controlled vocabulary factual databases humans pharmaceutical preparations
setsEuropean Bioinformatics Institute (EBI)

ChimerDBDatabase Content

http://ercsb.ewha.ac.kr/fusiongene [open in a new window]

Share This Link
DNA > Databases

ChimerDB is a knowledgebase of fusion genes identified from bioinformatics analysis of transcript sequences in the GenBank and various other public resources such as the Sanger cancer genome project (CGP), OMIM, PubMed and the Mitelman's database. A new algorithm that is more sensitive, has detected 2699 fusion transcripts with high confidence. Furthermore, it can identify interchromosomal translocations as well as the intrachromosomal deletions or inversions of large DNA segments. Results from the analysis of next-generation sequencing data in the short read archives are incorporated along with a new alignment viewer.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
ChimerDB 2.0--a knowledgebase for fusion genes updated20106
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
external linksLink on Wikipedia
tagsalgorithms animals chromosomes computational biology expressed sequence tags gene expression profiling gene fusion genetic databases genetic translocation genomics humans information storage and retrieval internet messenger rna mice mutant chimeric proteins nucleic acid databases protein databases pubmed rats software user-computer interface

Comprehensive Microbial Resource (CMR)Database Content

http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi [open in a new window]

Share This Link
Model Organisms > Databases

The Comprehensive Microbial Resource provides a web-based central resource for the display, search and analysis of the sequence and annotation for complete and publicly available bacterial and archaeal genomes. In addition to displaying the original annotation from GenBank, the CMR makes available secondary automated structural and functional annotation across all genomes to provide consistent data types necessary for effective mining of genomic data. Precomputed homology searches are stored to allow meaningful genome comparisons. The CMR supplies users with over 50 different tools to utilize the sequence and annotation data across one or more of the 571 currently available genomes. Genome level information includes whole genome graphical displays, biochemical pathway maps and genome summary data. Comparative tools display analysis between genomes with homology and genome alignment tools, and searches across the accessions, annotation, and evidence assigned to all genes/genomes are available.

links directory index: 33
TitlePublication YearGoogle Scholar Citation Count
The comprehensive microbial resource201033
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsbacteria bacterial genes bacterial genome computational biology genetic databases nucleic acid databases protein databases tertiary protein structure

ComSinDatabase Content

http://antares.protres.ru/comsin/. [open in a new window]

Share This Link
Protein > Databases

ComSin is a database of protein structures in bound (complex) and unbound (single) states. The developed server enables one to search for proteins in bound and unbound states with several options including sequence similarity between the corresponding proteins in bound and unbound states, and validation of interaction interfaces of protein complexes.

links directory index: 8
TitlePublication YearGoogle Scholar Citation Count
ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder20108
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsanimals bacterial proteins computational biology genetic databases humans molecular conformation molecular models protein binding protein conformation protein databases tertiary protein structure

Associated Tag Cloud