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1 TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

1 1999

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The ECEPP package for conformational analysis of polypeptides

Ripoll D. R., Liwo A., Czaplewski C.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

1999

Vol. 3, No 3

313-331

We present here the ECEPPAK (developed in the laboratory of prof. H.A. Scheraga, Cornell University) and ANALYZE packages for the conformational search of polypeptides that is based on the ECEPP/3 force field. The functions of the program include energy calculation and minimization and global conformational search using the Electrostatically Driven Monte Carlo (EDMC) method. The search can be constrained using experimental information e.g., the distance constraints from NMR measurements. The sister program, ANALYZE, allows the user to classify the conformations by means of cluster analysis and fit the statistical weights of the conformations to best fit the experimental observables. The package is extensively parallelized, which allows the user to carry out the conformational search even of comparatively large polypeptides in real time.