A method for determining overall protein fold from NMR distance restraints |
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Authors: | Jeffrey C Hoch Alan S Stern |
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Institution: | (1) The Rowland Institute for Science, 100 Cambridge Parkway, 02142 Cambridge, MA, USA |
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Abstract: | Summary We describe a simple method for determining the overall fold of a polypeptide chain from NOE-derived distance restraints. The method uses a reduced representation consisting of two particles per residue, and a force field containing pseudo-bond and pseudo-angle terms, an electrostatic term, but no van der Waals or hard shell repulsive terms. The method is fast and robust, requiring relatively few distance restraints to approximate the correct fold, and the correct mirror image is readily determined. The method is easily implemented using commercially available molecular modeling software. |
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Keywords: | Protein fold Distance restraint Molecular dynamics Distance geometry Reduced representation Structure determination |
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