PseAA server

Instead of using the conventional 20-D amino acid composition to represent the sample of a protein, Prof. Kuo-Chen Chou proposed the pseudo amino acid (PseAA) composition in order for inluding the sequence-order information. Based on the concept of Chou's pseudo amino acid composition, the server PseAA was designed in a flexible way, allowing users to generate various kinds of pseudo amino acid composition for a given protein sequence by selecting different parameters and their combinations. For further information, please see the publications or contact @ Hong-Bin (1) What's the hydrophobicity, hydrophilicity, mass ,pK1(alpha-COOH), pK2(NH3) and pI(at 25oC) values values used by PseAA? Amino acid Hydrophobicity a Hydrophilicity b Mass c pK1(a-CO2H) d pK2(NH3) d pI(at 25oC) d A 0.62 -0.5 15.0 2.35 9.87 6.11 C 0.29 -1.0 47.0 1.71 10.78 5.02 D -0.90 3.0 59.0 1.88 9.60 2.98 E -0.74 3.0 73.0 2.19 9.67 3.08 F 1.19 -2.5 91.0 2.58 9.24 5.91 G 0.48 0.0 1.0 2.34 9.60 6.06 H -0.40 -0.5 82.0 1.78 8.97 7.64 I 1.38 -1.8 57.0 2.32 9.76 6.04 K -1.50 3.0 73.0 2.20 8.90 9.47 L 1.06 -1.8 57.0 2.36 9.60 6.04 M 0.64 -1.3 75.0 2.28 9.21 5.74 N -0.78 0.2 58.0 2.18 9.09 10.76 P 0.12 0.0 42.0 1.99 10.60 6.30 Q -0.85 0.2 72.0 2.17 9.13 5.65 R -2.53 3.0 101.0 2.18 9.09 10.76 S -0.18 0.3 31.0 2.21 9.15 5.68 T -0.05 -0.4 45.0 2.15 9.12 5.60 V 1.08 -1.5 43.0 2.29 9.74 6.02 W 0.81 -3.4 130.0 2.38 9.39 5.88 Y 0.26 -2.3 107.0 2.20 9.11 5.63 a  The hydrophobicity values are from JACS, 1962, 84: 4240-4246. (C. Tanford). b  The hydrophilicity values are from PNAS, 1981, 78:3824-3828 (T.P.Hopp & K.R.Woods). c  The side-chain mass for each of the 20 amino acids. d  CRC Handbook of Chemistry and Physics, 66th ed., CRC Press, Boca Raton, Florida (1985).     R.M.C. Dawson, D.C. Elliott, W.H. Elliott, K.M. Jones, Data for Biochemical Research 3rd ed., Clarendon Press Oxford (1986). (2) What's the difference of "Type 1" PseAA composition, "Type 2" PseAA composition, and "Dipeptide" PseAA composition"?       The above three kinds of PseAA compositons are supported by PseAA currently,one is called Type 1 PseAA composition, which is also called parallel-correlation type and generates (20+)-D vector for each protein sequence; Type 2 is also called the series-correlation type and generates (20+i*)-D vector, where i is the number of attributes selected; dipeptide PseAA composition generates 420-D discrete numbers to represent a protein sequence.       For detailed information, please click Type 1, Type 2, and dipeptide respectively or please refer the publications and contact @ Hong-Bin (3) What's the normalization weight?       The weight factor is designed for the users to put weight to the addional PseAA components with respect to the conventional AA components. The users are allowed to select the weight factor from 0.05 to 0.70. For detailed information, please click weight. (4) What's the factor?       The counted rank (or tier) of the correlation along a protein sequence is usually represented by . In Type 1 PseAA composition, the user will obtain(20+)-D vector for each sequence; in Type 2 PseAA composition, (20+i*)-D vector is generated, (where i is the number of amino acid attributes selected). It's also important to note that should not exceed the length of the sequence. If the user choose =0, then the output will be the conventional 20-D amino aicd compositon for both cases. For detailed information, please click lambda. (5) What's the input format?       The user must input the protein sequences in FASTA(example) format. Currently, PseAA accepts maximum 50 protein sequences for each submission.