In its recently re-implemented version 2.0, EpiToolKit provides a range of new functionality and for the first time allows combining tools into complex workflows. It offers an array of immunoinformatics tools covering MHC genotyping, epitope and neo-epitope prediction, epitope selection for vaccine design, and epitope assembly. 31: 359-362).ĮpiToolKit - is a virtual workbench for immunological questions with a focus on vaccine design. Nucleic Acids Research 34: W202-W209.), and SDAP - Structural Database of Allergenic Proteins ( Reference: Ivanciuc, O. BMC Bioinformatics 14(Suppl 6): S4), AlgPred - prediction of allergenic proteins and mapping of IgE epitopes ( Reference: Saha, S.
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Biotech Software and Internet Report 2:198-200).Īntigenicity and allergenicity: a good place to start would be The Immune Epitope Database ( IEDB)Ībie Pro Peptide Antibody Design (Chang Bioscience)Īllergenicity servers: AllerTOP ( Reference: Dimitrov, I. Lyu Lab., National Tsing-Hua University, Taiwan) - calculates the theoretical protein melting temperature.Ĭomputation of size of DNA and Protein Fragments from Their Electrophoretic Mobility ( Reference: Raghava, G. Putnam, The Scripps Research Institute, U.S.A.) - calculates mass, pI, charge at a given pH, counts amino acid residues etc. Web Server issue ).Ĭomposition/Molecular Weight Calculation (Georgetown University Medical Center, U.S.A.) - the only problem with this site is that when run in batch mode it does not identify the sequence by name, merely sequential numberīatch Protein Isoelectric Point determination - part of the Sequence Manipulation Suite or ENDMEMOīatch Protein Molecular Weight determination - part of the Sequence Manipulation Suite or ENDMEMO The prediction accuracy (RMSD) of IPC 2.0 for proteins and peptides outperforms previous algorithms. Isoelectric Point Calculator 2.0 (IPC 2.0) - is a server for the prediction of isoelectric points and p K a values using a mixture of deep learning and support vector regression models. You can also specify post-translational modifications, such as N- and C- terminal modifications and positioning of disulfide bridges, to obtain more accurate outputs. Peptide Molecular Weight Calculator (GenScript) - the online calculator determines the chemical formula and molecular weight of your peptide of interest. Biochemistry-online (Vitalonic, Russia) gives one % composition, molecular weight, pI, and charge at any desired pH. Mass, pI, composition and mol% acidic, basic, aromatic, polar etc. If you want a plot of the relationship between charge and pH use ProteinChemist () or JVirGel Proteomic Tools (PRODORIC Net, Germany). Isoelectric Point - Compute pI/Mw tool (ExPASy, Switzerland). If you are specifically interested in antibodies I would recommend that you visit " The Antibody Resource Page."Īmino acid composition & Mass – ProtParam (ExPASy, Switzerland) For the biochemical properties of amino acids see PROWL, Amino Acid Hydrophobicity and Amino Acid Chart and Reference Table (GenScript). Online Analysis Tools - Protein ChemistryīACKGROUND INFORMATION: You might want to consult Robert Russell's Guide to Structure Prediction.
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