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194
Information resources at the National Center for Biotechnology Information
- Nucleic Acids Res
, 2009
"... In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made avail-able through the NCBI web site. NCBI resources include Entrez, the E ..."
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In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made avail-able through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene,
InterPro: the integrative protein signature database
, 2008
"... The InterPro database ..."
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et al: ChEBI: a database and ontology for chemical entities of biological interest
- Nucleic Acids Res
"... biological interest ..."
doi:10.1093/nar/gkr1088 The IntAct molecular interaction database in 2012
, 2011
"... IntAct is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. Two levels of curation are now available within the database, with both IMEx-level annotation and less detailed MIMIx-compatible entries currently ..."
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Cited by 100 (2 self)
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IntAct is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. Two levels of curation are now available within the database, with both IMEx-level annotation and less detailed MIMIx-compatible entries currently supported. As from September 2011, IntAct contains approximately 275 000 curated binary interaction evidences from over 5000 publications. The IntAct website has been improved to enhance the search process and in particular the graphical display of the results. New data download formats are also available, which will facilitate the inclusion of IntAct’s data in the Semantic Web. IntAct is an active contributor to the IMEx consortium
The European Bioinformatics Institute’s data resources. Nucleic Acids Res 2010;38:D17–25
"... ABSTRACT The wide uptake of next-generation sequencing and other ultra-high throughput technologies by life scientists with a diverse range of interests, ..."
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Cited by 91 (7 self)
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ABSTRACT The wide uptake of next-generation sequencing and other ultra-high throughput technologies by life scientists with a diverse range of interests,
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res
, 2014
"... Protein structure homology modelling has become a routine technique to generate 3D models for pro-teins when experimental structures are not available. Fully automated servers such as SWISS-MODEL with user-friendly web interfaces generate reliable mod-els without the need for complex software pack-a ..."
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Cited by 54 (1 self)
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Protein structure homology modelling has become a routine technique to generate 3D models for pro-teins when experimental structures are not available. Fully automated servers such as SWISS-MODEL with user-friendly web interfaces generate reliable mod-els without the need for complex software pack-ages or downloading large databases. Here, we de-scribe the latest version of the SWISS-MODEL ex-pert system for protein structure modelling. The SWISS-MODEL template library provides annotation of quaternary structure and essential ligands and co-factors to allow for building of complete structural models, including their oligomeric structure. The im-proved SWISS-MODEL pipeline makes extensive use of model quality estimation for selection of the most suitable templates and provides estimates of the ex-pected accuracy of the resulting models. The accu-racy of the models generated by SWISS-MODEL is continuously evaluated by the CAMEO system. The new web site allows users to interactively search for templates, cluster them by sequence similarity, structurally compare alternative templates and se-lect the ones to be used for model building. In cases where multiple alternative template structures are available for a protein of interest, a user-guided tem-plate selection step allows building models in differ-ent functional states. SWISS-MODEL is available at
Gene3D: merging structure and function for a Thousand genomes
- Nucleic Acids Res
, 2010
"... Over the last 2 years the Gene3D resource has been significantly improved, and is now more accurate and with a much richer interactive display via the Gene3D website ..."
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Cited by 21 (8 self)
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Over the last 2 years the Gene3D resource has been significantly improved, and is now more accurate and with a much richer interactive display via the Gene3D website
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education
- Nucleic Acids Res
, 2015
"... The RCSB Protein Data Bank (RCSB PDB, ..."
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Automated Detection of Conformational Epitopes Using Phage Display Peptide Sequences
"... Background: Precise determination of conformational epitopes of neutralizing antibodies represents a key step in the rational design of novel vaccines. A powerful experimental method to gain insights on the physical chemical nature of conformational epitopes is the selection of linear peptides that ..."
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Cited by 14 (1 self)
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Background: Precise determination of conformational epitopes of neutralizing antibodies represents a key step in the rational design of novel vaccines. A powerful experimental method to gain insights on the physical chemical nature of conformational epitopes is the selection of linear peptides that bind with high affinities to a monoclonal antibody of interest by phage display technology. However, the structural characterization of conformational epitopes from these mimotopes is not straightforward, and in the past the interpretation of peptide sequences from phage display experiments focused on linear sequence analysis to find a consensus sequence or common sequence motifs. Results: We present a fully automated search method, EpiSearch that predicts the possible location of conformational epitopes on the surface of an antigen. The algorithm uses peptide sequences from phage display experiments as input, and ranks all surface exposed patches according to the frequency distribution of similar residues in the peptides and in the patch. We have tested the performance of the EpiSearch algorithm for six experimental data sets of phage display experiments, the human epidermal growth factor receptor-2 (HER-2/neu), the antibody mAb Bo2C11 targeting the C 2 domain of FVIII, antibodies mAb 17b and mAb b12 of the HIV envelope protein gp120, mAb 13b5 targeting HIV-1 capsid protein and 80R of the SARS coronavirus spike protein. In all these examples the
NetCGlyc 1.0: Prediction of mammalian Cmannosylation sites Running Title: Prediction of C-mannosylation
, 2007
"... C-mannosylation is the attachment of an α-mannopyranose to a tryptophan via a C-C link. The sequence WXXW, in which the first Trp becomes mannosylated, has been suggested as a consensus motif for the modification, but only 2/3 of known sites follow this rule. We have gathered a data set of 69 experi ..."
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Cited by 13 (0 self)
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C-mannosylation is the attachment of an α-mannopyranose to a tryptophan via a C-C link. The sequence WXXW, in which the first Trp becomes mannosylated, has been suggested as a consensus motif for the modification, but only 2/3 of known sites follow this rule. We have gathered a data set of 69 experimentally verified C-mannosylation sites from literature. We analyzed these for sequence context and found that apart from Trp in position +3, Cys is accepted in the same position. We also find a clear preference in position +1, where a small and/or polar residue (Ser, Ala, Gly, and Thr) is preferred and a Phe or Leu discriminated against. The Protein Data Bank was searched for structural information and five structures of C-mannosylated proteins were obtained. We showed that modified tryptophan residues are at least partly solvent-exposed. A method predicting the location of C-mannosylation sites in proteins was developed using a neural network approach. The best overall network used a 21-residue sequence input window plus information on the presence/absence of the WXXW motif. NetCGlyc 1.0 correctly predicts 93 % of both positive and negative C-mannosylation sites. This is a significant improvement over the WXXW consensus motif itself, which only identifies 67 % of positive sites. NetCGlyc 1.0 is available at
