PMID: 9194158Apr 1, 1997Paper

Assessment of pseudo-energy potentials by the best-five test: a new use of the three-dimensional profiles of proteins

Protein Engineering
M Ota, K Nishikawa

Abstract

We propose a new assessment, called the best-five test, for the pseudo-energy potential empirically derived from the protein structural database. The object of the test is the three-dimensional (3D) profiles of proteins, which are directly connected to the pseudo-energy potentials. In the 3D profile, the fitness of each amino acid type is ranked at each residue site of a protein. A site whose native residue type is ranked within the best-five out of 20 amino acids is regarded as satisfactory and the ratio of the satisfactory sites over all the sites of all the proteins examined is indicative of the efficiency of the pseudo-energy potential employed. We applied the test to our potential function consisting of four terms; side-chain packing, hydration, backbone hydrogen-bonding and local conformation, by setting various kinds of definitions for each term. Through this test, the validity of the minus average operation is confirmed, where the energy level of potential functions is adjusted by referring to the random-environmental state of the proteins. Especially in the side-chain packing function, the success ratio increases from about 30 to 50% with this operation. Failure without the operation is ascribed to bulky hydrophobic re...Continue Reading

Citations

May 18, 2000·Biochemical and Biophysical Research Communications·K Igarashi, K Kashiwagi
Nov 14, 1997·FEBS Letters·M OtaK Nishikawa
Jun 8, 2002·Journal of Molecular Biology·Lieh Yoon LowBen Luisi
Aug 7, 2002·Current Opinion in Structural Biology·William P Russ, Rama Ranganathan
Oct 6, 2000·Journal of Molecular Graphics & Modelling·K Ogata, H Umeyama
Dec 10, 1999·The Biochemical Journal·K Igarashi, K Kashiwagi
Jul 17, 1999·European Journal of Biochemistry·Y ItoT Kohsaka
May 25, 1999·Protein Science : a Publication of the Protein Society·M Ota, K Nishikawa
Oct 15, 2011·Proteins·Andriy KryshtafovychAnna Tramontano
Nov 18, 2005·Journal of Molecular Biology·Yasuhiro IsogaiMotonori Ota
Dec 3, 2014·Computational Biology and Chemistry·Márcio DornLuis C Lamb
Oct 16, 1999·FEBS Letters·N NaganoK Nishikawa

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