Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 Jul-Dec;7(2):124-6.
doi: 10.4103/0976-9668.184696.

PreFRP: Prediction and visualization of fluctuation residues in proteins

Konda Mani Saravanan  1 , Renganathan Senthil  2
Affiliations

PreFRP: Prediction and visualization of fluctuation residues in proteins

Konda Mani Saravanan et al. J Nat Sci Biol Med. 2016 Jul-Dec.

Abstract

Aim: The PreFRP web server extracts sequence and basic information of a protein structure and groups amino acid residues in a protein into three important types such as high, moderate, and weak fluctuating residues.

Materials and methods: The server takes a protein data bank file or an amino acid sequence as input and prints the probability of amino acid residues to fluctuate. The server also provides a link to Jmol, a molecular visualization program to visualize the high, moderate, and weak fluctuating residues in three different colors.

Results: Prediction and visualization of fluctuating amino acid residues in proteins may help to understand the complex three-dimensional structure of proteins and may further help in docking and mutation experiments.

Availability: The web server is freely accessible through the web page of the author's institution http://www.mpi.edu.in/prefrp/link.html.

Keywords: Binding site; carbon content; conformation change; fluctuation residues; intrinsic disorder.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Schematic design of webserver
Figure 2
Figure 2
Screenshot of the webserver
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Laurie AT, Jackson RM. Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites. Bioinformatics. 2005;21:1908–16. - PubMed
    1. Gromiha MM, Yokota K, Fukui K. Energy based approach for understanding the recognition mechanism in protein-protein complexes. Mol Biosyst. 2009;5:1779–86. - PubMed
    1. Jones S, Thornton JM. Analysis of protein-protein interaction sites using surface patches. J Mol Biol. 1997;272:121–32. - PubMed
    1. Ruvinsky AM, Kirys T, Tuzikov AV, Vakser IA. Structure fluctuations and conformational changes in protein binding. J Bioinform Comput Biol. 2012;10:1241002. - PMC - PubMed
    1. Koshland DE., Jr Enzyme flexibility and enzyme action. J Cell Comp Physiol. 1959;54:245–58. - PubMed

LinkOut - more resources