Long loop prediction using the protein local optimization program.

@article{citeulike:819615, abstract = {We have developed an improved sampling algorithm and energy model for protein loop prediction, the combination of which has yielded the first methodology capable of achieving good results for the prediction of loop backbone conformations of 11 residue length or greater. Applied to our newly constructed test suite of 104 loops ranging from 11 to 13 residues, our method obtains average/median global backbone root-mean-square deviations (RMSDs) to the native structure (superimposing the body of the protein, not the loop itself) of 1.00/0.62 A for 11 residue loops, 1.15/0.60 A for 12 residue loops, and 1.25/0.76 A for 13 residue loops. Sampling errors are virtually eliminated, while energy errors leading to large backbone RMSDs are very infrequent compared to any previously reported efforts, including our own previous study. We attribute this success to both an improved sampling algorithm and, more critically, the inclusion of a hydrophobic term, which appears to approximately fix a major flaw in SGB solvation model that we have been employing. A discussion of these results in the context of the general question of the accuracy of continuum solvation models is presented. Proteins 2006. (c) 2006 Wiley-Liss, Inc.}, address = {Department of Chemistry, Columbia University, New York, New York.}, author = {Zhu, Kai and Pincus, David L L. and Zhao, Suwen and Friesner, Richard A A. }, citeulike-article-id = {819615}, doi = {http://dx.doi.org/10.1002/prot.21040}, issn = {1097-0134}, journal = {Proteins}, keywords = {ab\_initio, loop\_prediction, protein}, month = {August}, posted-at = {2006-08-28 09:32:33}, priority = {3}, title = {Long loop prediction using the protein local optimization program.}, url = {http://dx.doi.org/10.1002/prot.21040}, year = {2006} }

TY - JOUR ID - citeulike:819615 L3 - citeulike-article-id:819615 TI - Long loop prediction using the protein local optimization program. JF - Proteins AD - Department of Chemistry, Columbia University, New York, New York. SN - 1097-0134 N2 - We have developed an improved sampling algorithm and energy model for protein loop prediction, the combination of which has yielded the first methodology capable of achieving good results for the prediction of loop backbone conformations of 11 residue length or greater. Applied to our newly constructed test suite of 104 loops ranging from 11 to 13 residues, our method obtains average/median global backbone root-mean-square deviations (RMSDs) to the native structure (superimposing the body of the protein, not the loop itself) of 1.00/0.62 A for 11 residue loops, 1.15/0.60 A for 12 residue loops, and 1.25/0.76 A for 13 residue loops. Sampling errors are virtually eliminated, while energy errors leading to large backbone RMSDs are very infrequent compared to any previously reported efforts, including our own previous study. We attribute this success to both an improved sampling algorithm and, more critically, the inclusion of a hydrophobic term, which appears to approximately fix a major flaw in SGB solvation model that we have been employing. A discussion of these results in the context of the general question of the accuracy of continuum solvation models is presented. Proteins 2006. (c) 2006 Wiley-Liss, Inc. KW - ab_initio KW - loop_prediction KW - protein AU - Zhu, Kai AU - Pincus, David L AU - Zhao, Suwen AU - Friesner, Richard A PY - 2006/08/22/ UR - http://dx.doi.org/10.1002/prot.21040 ER -