title: The protein fluorescence and structural toolkit: Database and programs for the analysis of protein fluorescence and structural data.
abstract: Protein fluorescence is a powerful tool for studying protein structure and dynamics if we have a means to interpret the spectral data in terms of protein structural properties. Our previous research successfully provided this support through the development of individual software modules implementing the algorithms for fluorescence and structural analyses. Now we have integrated the developed software modules, introduced a new program for the assignment of tryptophan residues to spectral-structural classes, and created a web-based toolkit PFAST: protein fluorescence and structural toolkit: http://pfast.phys.uri.edu/. PFAST contains three modules: (1) FCAT is a fluorescence-correlation analysis tool, which decomposes protein fluorescence spectra to reveal the spectral components of individual tryptophan residues or groups of tryptophan residues located close to each other, and assigns spectral components to one of five previously established spectral-structural classes. (2) SCAT is a structural-correlation analysis tool for the calculation of the structural parameters of the environment of tryptophan residues from the atomic structures of the proteins from the Protein Data Bank (PDB), and for the assignment of tryptophan residues to one of five spectral-structural classes. (3) The last module is a PFAST database that contains protein fluorescence and structural data obtained from results of the FCAT and SCAT analyses.
authors.affiliation: Department of Computer Sciences and Statistics, University of Rhode Island, Kingston, Rhode Island 02881, USA.
authors.forename: Chi
authors.initials: C
authors.lastname: Shen
authors.forename: Rajiv
authors.initials: R
authors.lastname: Menon
authors.forename: Dipanwita
authors.initials: D
authors.lastname: Das
authors.forename: Nidhi
authors.initials: N
authors.lastname: Bansal
authors.forename: Neha
authors.initials: N
authors.lastname: Nahar
authors.forename: Neelima
authors.initials: N
authors.lastname: Guduru
authors.forename: Stephen
authors.initials: S
authors.lastname: Jaegle
authors.forename: Joan
authors.initials: J
authors.lastname: Peckham
authors.forename: Yana K
authors.initials: YK
authors.lastname: Reshetnyak
mesh_terms: D000465:Algorithms; D000818:Animals; D030562:Databases, Protein; D005453:Fluorescence; D005456:Fluorescent Dyes / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D008956:Models, Chemical; D011487:Protein Conformation; D011506:Proteins / Q000032:analysis / Q000737:chemistry* / Q000378:metabolism*; D020539:Sequence Analysis, Protein; D012984:Software; D013050:Spectrometry, Fluorescence; D014364:Tryptophan / Q000737:chemistry / Q000145:classification
chemical_list: D005456:Fluorescent Dyes; D011506:Proteins; D014364:Tryptophan