Enter Your Search:
Results 1-2 (2)
Go to page number:
Select a Filter Below
Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology (1)
Nucleic Acids Research (1)
Mottarella, Scott E. (2)
Bangura, Abdul (1)
Beglov, Dmitri (1)
Bernstein, Herbert J. (1)
Bohnuud, Tanggis (1)
Craig, Paul A. (1)
Hall, David R. (1)
Kozakov, Dima (1)
Ngan, Chi Ho (1)
Rosa, Mario (1)
Vajda, Sandor (1)
Villar, Elizabeth A. (1)
Year of Publication
Did you mean:
author:("mozzarella, Scott E.")
FTMAP: extended protein mapping with user-selected probe molecules
Ngan, Chi Ho
Villar, Elizabeth A.
Hall, David R.
Nucleic Acids Research
2012;40(Web Server issue):W271-W275.
Binding hot spots, protein sites with high-binding affinity, can be identified using X-ray crystallography or NMR by screening libraries of small organic molecules that tend to cluster at such regions. FTMAP, a direct computational analog of the experimental screening approaches, globally samples the surface of a target protein using small organic molecules as probes, finds favorable positions, clusters the conformations and ranks the clusters on the basis of the average energy. The regions that bind several probe clusters predict the binding hot spots, in good agreement with experimental results. Small molecules discovered by fragment-based approaches to drug design also bind at the hot spot regions. To identify such molecules and their most likely bound positions, we extend the functionality of FTMAP (http://ftmap.bu.edu/param) to accept any small molecule as an additional probe. In its updated form, FTMAP identifies the hot spots based on a standard set of probes, and for each additional probe shows representative structures of nearby low energy clusters. This approach helps to predict bound poses of the user-selected molecules, detects if a compound is not likely to bind in the hot spot region, and provides input for the design of larger ligands.
Bernstein, Herbert J.
Craig, Paul A.
Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology
The aim of the Structural Biology Extensible Visualization Scripting Language (SBEVSL) project is to allow users who are experts in one scripting language to use that language in a second molecular visualization environment without requiring the user to learn a new scripting language. ConSCRIPT, the first SBEVSL release, is a plug-in for PyMOL that accepts RasMol scripting commands either as premade scripts or as line-by-line entries from PyMOL's own command line. The plug-in is available for download at http://sourceforge.net/projects/sbevsl/files in the ConSCRIPT folder.
PyMOL; RasMol; ConSCRIPT; molecular visualization; structural bioinformatics
Results 1-2 (2)
Go to page number:
Remove citation from clipboard
Add citation to clipboard
This will clear all selections from your clipboard. Do you wish proceed?
Clipboard is full! Please remove an item and try again.
PubMed Central Canada is a service of the
Canadian Institutes of Health Research
(CIHR) working in partnership with the National Research Council's
Canada Institute for Scientific and Technical Information
in cooperation with the
National Center for Biotechnology Information
U.S. National Library of Medicine
(NCBI/NLM). It includes content provided to the
PubMed Central International archive
by participating publishers.