Protein SUMO modification is an important post-translational modification and the optimization of prediction methods remains a challenge. Here, by using Support Vector Machines algorithm (SVM), a novel computational method was developed for SUMO modification site prediction based on Sequential Forward Selection (SFS) of hundreds of amino acid properties, which are collected by Amino Acid Index database (http://www.genome.jp/aaindex). Our method also compares with the 0/1 system, in which the 20 amino acids are represented by 20-dimensional vectors (A = 00000000000000000001, C = 00000000000000000010 and so on). The overall accuracy of leave-one-out cross-validation for our method reaches 89.18%, which is higher than 0/1 system. It indicated that the SUMO modification prediction process is highly related to the amino acid property and this approach here provide a helpful toot for further investigation of the SUMO modification and identification of sumoylation sites in proteins. The software is available at http://www.biosino.org/sumo. (c) 2007 Elsevier Inc. All rights reserved.