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A Method to Visualize Conformational Changes in Proteins    

Submission Form    

Version 2.32      

Citation Info:
Cockrell, G. M. & Kantrowitz, E. R. "ViewMotions Rainbow: A New Method to Illustrate Molecular Motions in Proteins". J. Mol. Graph. Model. 40, 48-53 (2013).


The ViewMotions Server can produce ViewMotion rainbow images. The Server can be used in one of three ways:

  1. A morph ID can be entered from the Database of Macromolecular Motions corresponding to a protein conformational change.
  2. Two PDB IDs from the Protein Data Bank corresponding to a protein conformational change. The appropriate chain letter must be indicated.
  3. Two PDB files can be uploaded representing the beginning and ending coordinates of a protein conformational change. The appropriate chain letter must be indicated.

Fields designated by (*) are required.

MorphID:  
Enter Two PDB IDs:
        PDB ID #1:
Chain:  
        PDB ID #2:
Chain:  
Enter Two PDB files:
        PDB File #1: Chain:  
        PDB File #2: Chain:  
 
Alignment Method:

Four Alignment Methods are available when two pdb files are entered:

  1. Sieve-Fit (default): Same method as used by the Morph Server (Krebs & Gerstein, 2000). Iterative procedure, alpha carbons with largest RMSD are deleted, and process is continued until 50% of atoms are deleted.
  2. Gaussian-Weighted: Based on the algorithm of Damm & Carlson, 2006.
  3. Sequoia: Finds the global optimized alignment, see the Sequoia Website for more details.
  4. Standard RMSD: Standard least-squares RMSD fit (Kabsch, W. (1976) Acta Crystallogr. A32, 922-933).
Your E-mail Address (*):
Project Name (*):
 
    

Copyright 2012 GM Cockrell & ER Kantrowitz
Email: evan.kantrowitz@bc.edu