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CORRECTION

Protein Science 11: 2714–2726 (2002)

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

A bug was discovered in our original program that generated the DFIRE potential of mean force. As a result, some results were changed. The number of atomic pairs for 1011 proteins is 57 millions at the distance shell of 14 Å–15 Å. The radius of each reference sphere is 1.225R_g. The value of is now 1.61. The constant prefactor is now 0.0157. We also set the potential for zero occurrences to 2 kcal/mole, same as that in RAPDF and atomic KBP for comparison. The change of these values does not change the accuracy of the DFIRE potential, nor the conclusion of the paper. For multiple decoy sets, the number of correctly identified proteins continues to be 27 out of 32 decoy sets. The average Z-score of the 32 sets increases further from 4.27 to 4.52. The accuracy of loop prediction among 11 loop decoys is unchanged. The average correlation coefficient between the scores and the rmsd values for the 4state–reduced set is reduced (improved) slightly from 0.63 to 0.61 whereas the average correlation coefficient for the loop decoys is unchanged. The correlation coefficient between theoretically predicted and experimentally measured change in stability due to mutation is unchanged whereas rmsd is reduced slightly from 1.52 kcal/mole to 1.49 kcal/mole. Full detailed corrections on figures and tables can be found in the supplemental material (at www.proteinscience.org and at http://theory.med.buffalo.edu).

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This Article Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Zhou, H. Articles by Zhou, Y. Search for Related Content PubMed Articles by Zhou, H. Articles by Zhou, Y. Social Bookmarking                   What's this?