Tag: Identifies

Shiftcor 1.3 – Compares, Identifies, Corrects and Re-referencs Protein Chemical Shifts

Shiftcor 1.3

:: DESCRIPTION

Shiftcor compares, identifies, corrects and re-referencs 1H, 13C and 15N backbone chemical shifts of peptides and proteins by comparing the observed chemical shifts with the predicted chemical shifts derived from the 3D structure (PDB corrdinates) of the protein(s)of interest.

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Haiyan Zhang, Stephen Neal and David Wishart (2003)
“RefDB: A database of uniformly referenced protein chemical shifts”
Journal of Biomolecular NMR, 25: 173-195

CCRXP – Identifies Clusters of Conserved Residues in Proteins using PDB files

CCRXP

:: DESCRIPTION

CCR XP tries to automate the detection and analysis of such clusters in protein structures.CCR XP is made of two input modules. CCR XP lite can be accessed directly (see query form on top), by uploading a PDB coordinate data or entering a PDB code and CCRs using default parameter settings for all protein chains in the coordinate file will be returned. The server will automatically (1) Extract fasta file from atom records (2) Find aligned sequences and calculate conservation scores (3) Cluster conserved residues and (4) Report several other structural properties of each residue as well as whole clusters, including their solvent accessibility that will allow to distinguish potential interface clusters from stabilizing core residues.

::DEVELOPER

Shandar Ahmad

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W398-401. doi: 10.1093/nar/gkq360. Epub 2010 May 10.
CCRXP: exploring clusters of conserved residues in protein structures.
Ahmad S, Keskin O, Mizuguchi K, Sarai A, Nussinov R.