Methodology article
Full cyclic coordinate descent: solving the protein loop closure problem in Cα space
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* Corresponding author: Thomas Hamelryck thamelry@binf.ku.dk
Bioinformatics center, Institute of Molecular Biology and Physiology, University of Copenhagen, Universitetsparken 15, Building 10, DK-2100 Copenhagen, Denmark
BMC Bioinformatics 2005, 6:159 doi:10.1186/1471-2105-6-159
Published: 28 June 2005Additional files
Additional File 1:
The file FCCD.py contains an implementation of the FCCD algorithm. The program was implemented in the interpreted, object oriented language Python http://www.python.org webcite. The Numeric Python package http://numeric.scipy.org/ webcite, a Python module that implements many advanced mathematical operations efficiently in C and FORTRAN, provided implementations of singular value decomposition and various matrix operations. In addition, the Biopython toolkit, a set of Bioinformatics modules implemented in Python, was used to represent atomic coordinates as vector objects [25]. The core of the FCCD implementation comprises only 50 lines of Python code. Numeric Python and Biopython (version 1.4b) are needed to execute the sample code.
Format: PY Size: 3KB Download file
