Learning, Observing and Outputting Protein Patterns (LOOPP)

LOOPP is a public domain package for protein recognition and design of folding potentials. Versions 1.0 and 2.0  were written when I was working with Ron Elber at the Cornell's Computer Science Dept. and Ron contributed in many ways into the development of these early versions. LOOPP 2.0 includes standard and novel sequence to structure (threading), sequence to sequence and structure to structure alignment algorithms and potentials. LOOPP can also be used to develop new folding potentials. To download the source code of LOOPP 2.0(00) follow the links included below or go to the LOOPP web page at the Cornell Theory Center.



NEW VERSION (to be released when time permits):


Check out the following textbook (chapter on protein structure and folding includes Loopp): Gibson and Muse, A Primer of Genome Science, Sinauer 2002.

About our (collaboration with group of Prof. Tanksley of Cornell University) Science paper and predicted similarity between tomato fruit size gene and human oncogene Ras: Cornell Chronicle, ScienceDaily.

Loopp predictions during CASP4/CAFASP2 (PowerPoint file).

Loopp was inlcuded in the paper summarizing the CAFASP2 experiment.

The original "Loopp" paper:  Proteins Struct. Fun. Gen. 45: 241-261 (2001).

Author: Jarek Meller