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13.6 Loop Modeling
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Background

Building an accurate model of a loop is very tough. However with small loops ICM has been very succesful. ICM was used to design two new 7 residue loops and in both cases the designs were successful. Moreover, the predicted conformations turned out to be exactly right (accuracy of 0.5A RMSD) after the crystallographic structures of the designed proteins were determined in Rik Wierenga's lab (Thanki et al Protein Eng. 1997 10, 159-167). In 2010, scientists at MolSoft developed a a new physics-based internal coordinate mechanices force field (Arnautova et al Proteins. 2010, 79:477) and was tested on loop structures. The new force-field contains new parametization for the dielectric constant, an improved hydrogen bond determination method, and implementation of novel backbone atom torsional potentials which include bond anlges of the carbon (alpha) atoms into the internal variable set. Loop modeling using the new force-field can be accessed by clicking on the tab labeled High Precision Sampling in Batch in the MolMechanics/Sample Loop window.

Interative fast loop sampling:

To sample the conformation of a loop using new ICM force-field in batch mode Arnautova et al Proteins. 2010, 79:477:


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