Protein identification and analysis tools in the ExPASy server.

By M. Wilkins, Elisabeth Gasteiger, Amos Bairoch, Jean-Charles Sanchez, Keith L. Williams, R. Appel, D. Hochstrasser. 1999

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Citations in the corpus

Induction of Potent Neutralizing Antibody Responses by a Designed Protein Nanoparticle Vaccine for Respiratory Syncytial Virus (2019, methodology): “In vitro Assembly of DS-Cav1–I53-50 and I53-50 Concentrations of purified individual nanoparticle components were determined bymeasuring absorbance at 280 nm using a UV-Vis spectrophotometer (Agilent Cary 8454) and calculated extinction coefficients (Gasteiger et al., 2005).”
The Toxoplasma glucan phosphatase TgLaforin utilizes a distinct functional mechanism that can be exploited by therapeutic inhibitors (2022, methodology): “MW calculations of TgCBM and full-length TgLaforin recombinant protein was calculated using the ProtParam tool on the ExPASy server (88).”
Novel fold of rotavirus glycan-binding domain predicted by AlphaFold2 and determined by X-ray crystallography (2022, methodology): “The concentration of the puri ﬁ ed protein was determined by measuring the absorbance at 280nm and using an absorption coef ﬁ cient of 12,950M − 1 cm − 1 for VP8 * B calculated using ProtPraram on the ExPASy server 42 .”
Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses (2021, methodology): “Protein concentrations were determined with a NanoDrop spectrophotometer (ND 1000, Peqlab), using theoretical absorption coefficients calculated based upon the amino acid sequence by ProtParam on the ExPASy webserver [94].”
LEA (Late Embryogenesis Abundant) proteins and their encoding genes in Arabidopsis thaliana (2008, methodology): “To get more information about the nature of the gene products, the GRAVY (grand average of hydropathy), the molecular weight and the pI were predicted by the PROTPARAM [ 132 ,133] tool.”
Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0 (2018, methodology): “…amino acid classes in the sequence: Molecular weight Protein net charge Grand average of hydropathicity (GRAVY, Kyle and Doolittle, 1982) ProtParam (Gasteiger et al ., 2005) Average of surface exposure (Janin, 1979) Amino acid groupings and scales taken from Composition Profiler (Vacic et al .,…”