institute for computational biomedicine: ProperTM

[ description ]

ProperTM calculates properties associated with positions in a sequence alignment. The methods employed in this program are designed to analyze membrane proteins (and G-protein coupled receptors (GPCRs) in particular) but some of the options (i.e the calculation of a conservation index) could be useful for the analysis of sequences of non-membrane proteins too.

[ about the method ]

Three-dimensional representations of G protein-coupled receptor structures and mechanisms. Visiers I, Ballesteros JA, Weinstein H. (2002) Methods Enzymol 343:329-371. [PubMed]

Integrated Methods for the Construction of Three-Dimensional Models and Computational Probing of Structure-Function Relations in G Protein-Coupled Receptors. Ballesteros JA, Weinstein H. (1995) Methods Neuroscience 25:366-428.

A knowledge-based scale for the analysis and prediction of buried and expose d faces of transmembrane domain proteins. Beuming T. and Weinstein H. Bioinformatics. 2004 Aug 12;20 (12):1822-35 [PubMed]

[ documentation ]

Visit the following help pages for more information about ProperTM:

Alignments

Generic Numbering Scheme (Reference Sequence)

Hydrophobicity

Volume

Conservation

Lipid Facing Probability

Fourier Transform

[ availability ]

ProperTM is web accessible: [ access ProperTM ]

News

Jul, 2009; ChIPseeqer, a comprehensive framework for analysis of ChIP-seq data developed in the Elemento lab, is now available for download. [More]
Apr, 2009; The BDVal program developed by the Campagne laboratory for MAQC-II is now available from http://bdval.org. The software supports the development and evaluation of predictive biomarker models from high-throughput data. The web site offers binary and source distributions. [More]
Jan, 2009; Twease now supports searching MEDLINE articles by Author, Journal, and Publication Year. Examples for performing these searches can be found in the updated Twease tutorial. [More]

[News Archives] [Mailing List]

Events

Dec 11th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Fabien Campagne; ICB Conference Room - Y.1301
Jan 15th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Lei Shi; ICB Conference Room - Y.1301
Feb 12th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Christopher E. Mason; ICB Conference Room - Y.1301
Mar 12th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Olivier Elemento; ICB Conference Room - Y.1301
Apr 9th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Emre Aksay; ICB Conference Room - Y.1301
May 14th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Jonathan D. Victor; ICB Conference Room - Y.1301
Jun 11th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Harel Weinstein; ICB Conference Room - Y.1301
Jul 9th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Duane Hassane; ICB Conference Room - Y.1301