ExPASy Proteomics

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Information about ExPASy Proteomics

Published on February 26, 2014

Author: amitkumarbiotech

Source: authorstream.com

ExPASy Proteomics server tools: ExPASy Proteomics server tools Amit Kumar M.Sc. Computational Biology Pondicherry University ExPASy: ExPASy A bioinformatics resource portal operated by the Swiss Institute of Bioinformatics (SIB). An extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics , etc. DeepView - Swiss-PdbViewer :  DeepView - Swiss- PdbViewer An application that provides a user friendly interface allowing to analyze several proteins at the same time. Proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. ProtParam :  ProtParam Computes various physico -chemical properties that can be deduced from a protein sequence. The protein can either be specified as a Swiss-Prot/ TrEMBL accession number or ID, or in form of a raw sequence. White space and numbers are ignored. The computed parameters include the molecular weight, theoretical pI , amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY) TMbase :  TMbase A database of transmembrane proteins and their helical membrane- spanning domains. TMbase was originally meant as a tool for analyzing the properties of transmembrane proteins. It is intended to facilitate the following tasks: finding positional preferences of certain amino acids deriving an improved method for the prediction of transmembrane domains testing of such prediction schemes statistical testing of general hypotheses concerning transmembrane proteins HAMAP: HAMAP High-quality Automated and Manual Annotation of Proteins. A system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated, manually created annotation rules that specify annotations that apply to family members. The criteria to assign initial membership to a family are sequence similarity and what is known in the literature about the protein in question. EasyProt :  EasyProt EasyProt is a complete graphical and user-friendly software platform for the analysis of MS/MS data. EasyProt is divided into two distinct parts: EasyProt EasyProtConv EasyProt is now available as a virtual machine, so no installation is required and it can run on any system. EasyProt and EasyProtConv are freely available AACompIdent Tool :  AACompIdent Tool AACompIdent tool can identify proteins by their AA composition. Program matches the percent empirically measured AA composition of an unknown protein against the theoretical percent AA compositions of proteins in the Swiss-Prot and/or TrEMBL databases. A score, which represents the degree of difference between the composition of the unknown protein and a protein in the database, is calculated for each database entry by the sum of the squared difference between the percent AA composition for all amino acids of the unknown protein and the database entry. Contd…: Contd … All proteins in the database are then ranked according to their score, from lowest (best match) to highest (worst match). Estimated protein pI and MW, as well as species and keyword of interest can also be used in the identification procedure. Ref: Ref Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E, Grosdidier A, Hernandez C, Ioannidis V, Kuznetsov D, Liechti R, Moretti S, Mostaguir K, Redaschi N, Rossier G, Xenarios I, and Stockinger H. ExPASy : SIB bioinformatics resource portal , Nucleic Acids Res , 40(W1):W597-W603, 2012. K. Hofmann & W. Stoffel (1993) TMbase - A database of membrane spanning proteins segments Biol. Chem. Hoppe- Seyler 374,166. Guex , N. and Peitsch , M.C. (1997) SWISS-MODEL and the Swiss- PdbViewer : An environment for comparative protein modeling. Electrophoresis 18 , 2714-2723. HAMAP in 2013, new developments in the protein family classification and annotation system Ivo Pedruzzi 1 , Catherine Rivoire 1 , Andrea H. Auchincloss 1 , Elisabeth Coudert 1 , Guillaume Keller 1 , Edouard de Castro 1 , Delphine Baratin 1 , Béatrice A. Cuche 1 , Lydie Bougueleret 1 , Sylvain Poux 1 , Nicole Redaschi 1 , Ioannis Xenarios 1 , Alan Bridge 1 , * , the UniProt Consortium 1 , 2 , 3 , 4 EasyProt — An easy-to-use graphical platform for proteomics data analysis Florent Gluck a , Christine Hoogland a , Paola Antinori a , b Xavier Robin b , Frederic Nikitin d , Anne Zufferey b , Carla Pasquarello c , Vanessa Fétaud b , c Loïc Dayon b , 2 Markus Müller d , Frederique Lisacek d , Laurent Geiser a , b Denis Hochstrasser a , b Jean -Charles Sanchez b , Alexander Scherl a , b , c Protein identification and analysis tools in the ExPASy server. Wilkins MR , Gasteiger E , Bairoch A , Sanchez JC , Williams KL , Appel RD , Hochstrasser DF .

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