ExPASy: the proteomics server for in-depth protein knowledge and analysis

By Elisabeth Gasteiger, Alexandre Gattiker, C. Hoogland, I. Ivanyi, R. Appel, Amos Bairoch. Nucleic Acids Res., 2003

5,340 citations recorded by the source corpus.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/1c405ce3655515312cba508f6e8bb8c904d23d25

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Citations in the corpus

ExPASy: SIB bioinformatics resource portal (2012, background): “Historically, ExPASy (1,2) was one of the first web servers in the life sciences community, known as ‘Expert Protein Analysis System’.”
Omicron and Delta Variant of SARS-CoV-2: A Comparative Computational Study of Spike protein (2021, methodology): “The Omicron complete genome (R40B60 BHP 3321001247/2021) was obtained from GSAID(15) and the genome sequence was translated to protein sequence using the Expasy translate program.(16) The translated sequence was used to select the Omicron spike protein.”
Exploiting sequence and stability information for directing nanobody stability engineering (2017, methodology): “They were analyzed with respect to pI, aliphatic index, GRAVY score [53], number of positive and negative charges, charge ratio and sequence length using the ExPASy server [42].”
Structural and biophysical properties of FopA, a major outer membrane protein of Francisella tularensis (2022, methodology): “The extinction coefficient and theoretical pI were calculated using ExPASy ProtParam (37).”
3D Complex: A Structural Classification of Protein Complexes (2006, background): “Also, we will assess below to what extent this result, observed on the subset of proteins present in PDB, can be generalized to SwissProt proteins [29].”
Use ggbreak to Effectively Utilize Plotting Space to Deal With Large Datasets and Outliers (2021, methodology): “The protein sequence was downloaded from the NCBI database (PDB: 7MWE_A) and then the hydrophilicity/hydrophobicity scales were analyzed using Expasy-ProtScale with default parameters (Gasteiger et al., 2003).”
Identification and characterization of a novel family of Drosophilaβ‐adrenergic‐like octopamine G‐protein coupled receptors (2005, methodology): “The consensus cDNA sequence was translated in the 6 possible open reading frames using the Expasy translate tool (Gasteiger et al. 2003) and the structure of the longest open reading frame domain analysed.”
Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment (2016, methodology): “Trace files of Sanger sequences obtained from individual PCR amplifications were edited and trimmed to remove low quality bases (Q 30) using SeqTrace 0.9.0 (Stucky, 2012) and checked for frame shifts using EXPASY (Gasteiger et al., 2003).”
Applications of genome-scale metabolic reconstructions (2009, methodology): “First, an initial reconstruction is built from gene-annotation data coupled with information from online databases such as KEGG (Kanehisa et al, 2006) and EXPASY (Gasteiger et al, 2003), which link known genes to functional categories and help bridge the genotype–phenotype gap.”
Refined solution structure of the 82-kDa enzyme malate synthase G from joint NMR and synchrotron SAXS restraints (2008, methodology): “The protein concentration was measured on samples diluted 30-fold in a solution of 6 M GuHCl by UV absorption at 280 nm wavelength using an extinction coefficient calculated from the MSG sequence and free amino acid values by the ExPASy server (Gasteiger et al. 2003).”
Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medicinal plants (2020, positive): “Gene sequences of 3CLpro were extracted from the whole-genome sequences and translated into protein sequences using the translate tool of the ExPASy server [14].”