TopPred II is an improved software tool for predicting the topologies of integral membrane proteins, specifically those with α-helical structures. It is an enhanced version of the freeware TOP-PRED, written in Symantec THINK Pascal to run on Macintosh computers. The program constructs a hydrophobicity profile to identify transmembrane segments and predicts topologies using different criteria for eukaryotic and prokaryotic proteins. For prokaryotes, the number of positively charged residues at inter-transmembrane segments is counted, while for eukaryotes, additional criteria include net charge differences and amino acid composition. TopPred II ranks structures based on the bias of positively charged residues, with the correct structure having the largest charge bias. The software has been shown to predict the topologies of 95% of tested prokaryotic proteins and 83% of tested eukaryotic proteins. It is freely available via FTP from the EMBL server or on floppy disks.TopPred II is an improved software tool for predicting the topologies of integral membrane proteins, specifically those with α-helical structures. It is an enhanced version of the freeware TOP-PRED, written in Symantec THINK Pascal to run on Macintosh computers. The program constructs a hydrophobicity profile to identify transmembrane segments and predicts topologies using different criteria for eukaryotic and prokaryotic proteins. For prokaryotes, the number of positively charged residues at inter-transmembrane segments is counted, while for eukaryotes, additional criteria include net charge differences and amino acid composition. TopPred II ranks structures based on the bias of positively charged residues, with the correct structure having the largest charge bias. The software has been shown to predict the topologies of 95% of tested prokaryotic proteins and 83% of tested eukaryotic proteins. It is freely available via FTP from the EMBL server or on floppy disks.