Prediction of protein cellular attributes using pseudo‐amino acid composition

Abstract The cellular attributes of a protein, such as which compartment of a cell it belongs to and how it is associated with the lipid bilayer of an organelle, are closely correlated with its biological functions. The success of human genome project and the rapid increase in the number of protein sequences entering into data bank have stimulated a challenging frontier: How to develop a fast and accurate method to predict the cellular attributes of a protein based on its amino acid sequence? The existing algorithms for predicting these attributes were all based on the amino acid composition in which no sequence order effect was taken into account. To improve the prediction quality, it is necessary to incorporate such an effect. However, the number of possible patterns for protein sequences is extremely large, which has posed a formidable difficulty for realizing this goal. To deal with such a difficulty, the pseudo‐amino acid composition is introduced. It is a combination of a set of discrete sequence correlation factors and the 20 components of the conventional amino acid composition. A remarkable improvement in prediction quality has been observed by using the pseudo‐amino acid composition. The success rates of prediction thus obtained are so far the highest for the same classification schemes and same data sets. It has not escaped from our notice that the concept of pseudo‐amino acid composition as well as its mathematical framework and biochemical implication may also have a notable impact on improving the prediction quality of other protein features. Proteins 2001;43:246–255. © 2001 Wiley‐Liss, Inc.