A Method to Visualize Conformational Changes in Proteins
Submission Form
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 a representation of a conformational change in a protein in a visually intuitive way using a spectrum of color in indicate the molecular motion (e.g. ViewMotion rainbow images). The Server can be used in one of two ways:
- Two PDB IDs from the Protein Data Bank corresponding to a protein conformational change. The appropriate chain letter must be indicated.
- Two PDB files can be uploaded representing the beginning and ending coordinates of a protein conformational change. The appropriate chain letter must be indicated.
General Usage: The two x-ray structures should have identical or almost identical sequences. The two pdb files should have the same number of residues. However, C-terminal or N-terminal deletions in one or the other chain is allowed, but internal deletions cannot be handed.
Fields designated by (*) are required.
Acknowledgements
CCP4 | MD Winn et al. "Overview of the CCP4 Suite and Current Developments" Acta. Cryst. D67, 235-242 (2011) |
CNS | AT Brunger, PD Adams, GM Clore, P Gros, RW Grosse-Kunstleve, J-S. Jiang, J Kuszewski, N Nilges, NS Pannu, RJ Read, LM Rice, T Simonson, GL Warren, "Crystallography & NMR System (CNS), A New Software Suite for Macromolecular Structure Determination", Acta Cryst.D54, 905-921(1998) |
Chimera | EF Pettersen, TD Goddard, CC Huang, GS Couch, DM Greenblatt, MC Meng, TE Ferrin, "UCSF Chimera: A Visualization System for Exploratory Research and Analysis" J. Comput. Chem. 2004 Oct;25(13):1605-12 |
ChimeraX | EC Meng, TD Goddard, EF Pettersen, GS Couch, ZJ Pearson, JH Morris, TE Ferrin,"UCSF ChimeraX: Tools for structure building and analysis" Protein Sci. 2023 Nov;32(11):e4792 |
Copyright 2012 & 2024 GM Cockrell & ER Kantrowitz
Email: evan.kantrowitz@bc.edu