DichroCalc - circular and linear dichroism online
نویسندگان
چکیده
MOTIVATION Circular dichroism (CD) is widely used in studies of protein folding. The CD spectrum of a protein can be estimated from its structure alone, using the well-established matrix method. In the last decade, a related spectroscopy, linear dichroism (LD), has been increasingly applied to study the orientation of proteins in solution. However, matrix method calculations of LD spectra have not been presented before. DichroCalc makes both CD and LD calculations available in an easy-to-use fashion. RESULTS DichroCalc can be used without registration and calculates CD and LD spectra using a variety of matrix method parameters. PDB files can be uploaded as input or retrieved via their PDB code and a Perl-based parser is offered for easy handling of PDB files. AVAILABILITY http://comp.chem.nottingham.ac.uk/dichrocalc and http://comp.chem.nottingham.ac.uk/parsepdb.
منابع مشابه
Element Speci c Magnetometry Combining X-ray Circular with Linear Dichroism: Fundamentals and Applications
This article gives an overview of the use of X-ray absorption spectroscopy to characterize the magnetic properties for technologically important, low dimensional magnetic materials. An overview is given both for the experimental hardware, the measurements and the analysis of the spectra. The information obtained is discussed for metallic and semiconducting systems, using both the X-ray magnetic...
متن کاملLinear and circular dichroism in porphyrin J-aggregates probed by polarization modulated scanning near-field optical microscopy.
Polarization modulated scanning near-field optical microscopy (PM-SNOM) is effective in detecting circular and linear dichroism with sub-wavelength resolution. PM-SNOM investigation of the chiroptical properties of single ribbon-like nanosized J-aggregates formed by acid induced aggregation of tris-(4-sulfonatophenyl)phenylporphyrin is reported. Linear dichroism maps give evidence of well-organ...
متن کاملCharacterisation of LHC II in the aggregated state by linear and circular dichroism spectroscopy
Absorption, linear dichroism and circular dichroism spectroscopy at 293 and 77 K have been used in order to further explore the process of energy quenching in LHC IIb, the main light-harvesting complex of photosystem II. Upon aggregation there was an enhancement of linear dichroism bands in the Q absorption region of chlorophyll b. The y absorption spectrum at 77 K of aggregates revealed new ba...
متن کاملDichroMatch at the protein circular dichroism data bank (DM@PCDDB): A web‐based tool for identifying protein nearest neighbors using circular dichroism spectroscopy
Circular dichroism spectroscopy is a well-used, but simple method in structural biology for providing information on the secondary structure and folds of proteins. DichroMatch (DM@PCDDB) is an online tool that is newly available in the Protein Circular Dichroism Data Bank (PCDDB), which takes advantage of the wealth of spectral and metadata deposited therein, to enable identification of spectra...
متن کاملIn vitro study of drug-protein interaction using electronic absorption, fluorescence, and circular dichroism spectroscopy
In the near future, design of a new generation of drugs targeting proteins will be required. Considering the complex bond between the drug and protein, the structure and stability of the target protein should be considered. So far, a series of in vitro investigations have been conducted with the aim of predicting drug-biological medium interactions. In these studies, use of spectroscopic method...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- Bioinformatics
دوره 25 4 شماره
صفحات -
تاریخ انتشار 2009