Submission Form for the ViewMotions

A Method to Visualize Conformational Changes in Proteins

Submission Form

Version 2025-02-03

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.

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:

Five alignment methods are available

Sequoia	(Default) A global optimized alignment, see the Sequoia Website for more details.
ML	The maximum likelihood (ML) method is used for the superposition using the THESEUS algorithm. ML improves the accuracy of the superposition by down-weighting variable structural regions. For more details see, DL Theobald, DS Wuttke, THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures, Bioinformatics. 2006, 22, 2171–2172.
Fatcat2	Fatcat is a procedure for the "Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists. This method is an excellent approach to use for comparing flexible protein structures.(Li, et al, (2020) Nucleic Acid Res. 48, W60-64). A Fatcat Server is available
Profit	Based on the program by Professor Andrew C. R. Martin's group and used in the Profit Server.
RMSD	Standard least-squares RMSD fit (W. Kabsch, Acta Crystallogr, 2011, A32, 922-933.

Enter an email address & project name, then submit

Email Address (*):
Project Name (*):

Example figures generated using the ViewMotions Website

glucose binding protein	The glucose binding protein without glucose (blue, 2GBP) and the domain closure that occurs when glucose binds (red, 2FW0). Glucose not shown.
Aspartate Transcarbamoylase	Aspartate transcarbamoylase from many organisms undergoes an allosteric conformational change from a less active T-structure to a more active R-structure upon substrate binding. Here the catalytic subunit of aspartate transcarbamoyl-ase in the T (blue, 1ZA1) and R (blue, 1D09) allosteric states. In this case, the R allosteric state is induced by the binding of a bisubstrate analog.
Alcohol Dehydrogenase	The hinge bending motion of alcohol dehydro-genase (blue, 8ADH) and in the presence of a nicotinamide adenine dinucleotide (NAD) (red, 6ADH) The NAD is not shown.
Citrate Synthesis	The structural changes induced in the unliganded citrate synthesis (blue, 1CTS) to citrate synthesis in the presence of citrate and coenzymeA (red, 2CTS). Citrate and coenzymeA are not shown.

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