PDF《BMC Bioinformatics》

s original URL. BMC Bioinformatics 2004,

5 http://www.biomedcentral.com/1471-2105/5/51 Page

2 of

5 (page number not for citation purposes) output of solvent accessibility from solvent accessibility data in different file formats such as DSSP and other pro- grams. Further, the output obtained from the real-value prediction can also be used to display the ASA. Postscript graphics produced by our program have been converted to acrobat PDF and PNG formats using Latex2HTML tools [11]. Implementation This so-called ASAView algorithm involves carrying out the following steps: 1. Calculation of the solvent accessibility of each amino acid residue: If the complete three-dimensional structures are known, ASA values may be calculated using programs such as ACCESS [12], DSSP [13], ASC [14], NACCESS [15] and GETAREA [16]. The ASA values can also be obtained directly from the DSSP database, if the corresponding PDB code is known. GETAREA gives the ASA online and executable files are available for other programs. We have used DSSP for calculating ASA for all proteins contained in the February

2003 release of PDB. However, one can use the computer program to get these plots for any pro- tein, which is freely available from the corresponding author. If ASA values are taken from a prediction, a real- value prediction of ASA is necessary, as category predic- tions (e.g., classification as buried or exposed) cannot be plotted. Further, the ASA values obtained from the real- value prediction algorithm [8] can also be used as the ASA inputs for ASAView. 2. Representation of each amino acid residue by a filled circle: Equivalent radii are calculated from the ASA values obtained in step 1;

consequently, the size of each circle representing a residue is proportional to its relative sol- vent accessibility. If the available ASA values are not in rel- ative scale (as is mostly the case), the absolute ASA values are changed to relative values using appropriate scaling factors [2], thus normalizing the view for relative exposed surfaces rather than absolute area. For the scaling the ASA of the extended states of Ala-X-Ala for every residue X are used (assuming that the absolute values include side chain and backbone surface area). These values are (in ?2) 110.2 (Ala), 144.1 (Asp),140.4 (Cys), 174.7 (Glu), 200.7 (Phe), 78.7 (Gly), 181.9 (His), 185.0 (Ile), 205.7 (Lys), 183.1 (Leu), 200.1 (Met),146.4 (Asn), 141.9 (Pro), 178.6 (Gln), 229.0 (Arg), 117.2 (Ser), 138.7 (Thr), 153.7 (Val), 240.5 (Trp), and 213.7 (Tyr) respectively. 3. Color-coding is assigned to the residues: In the online version, gray, red, blue and green are used to represent hydrophobic, negatively charged, positively charged and polar neutral residues, respectively. Cystein residues are shown in yellow color due to its unique properties. 4. A residue number, a residue name, and an equivalent radius now identify each residue. These residues are then sorted in the order of their equivalent radii, calculated in step (2). 5. A two-dimensional spiral plot in postscript language is then generated through appropriate placement of the cir- cles representing amino acid residues. The residue with the smallest relative ASA is placed at the origin of the spi- ral, and residues with larger ASAs are successively placed on the spiral, whose radius is properly scaled. 6. The size of the spiral plot is forced to remain within one page and hence a protein with large number of residues will have a smaller size of circles for the same ASA. For the actual value of ASA, bar plots (see next point) or the tex- tual data can be used as a reference. 7. Bar plots are also generated for the protein by retaining the order of residues as they occur in the original input file. This will show the ASA of residues for a protein sequence, similar to hydrophobicity plot [17,18]. ASAView software also provides several additional fea- tures for better visualization: 1. Input file formats: To generate images, ASAView can make use of ASA inputs in four different formats: (a) DSSP: Files from DSSP, the most popular database of secondary structure and solvent accessibility, may be directly input into ASAView in the form of PDB code. (b) RVP: Real-value prediction obtained from RVP-Net may also be directly input into ASAView [8]. (c) Percentages: Solvent accessibility values obtained by any other methods (ASC, GETAREA, ACCESS, Naccess) may be used for plots, provided they are written in a two column format in which the first column contains a list of residues (single letter codes), and the second column con- tains the corresponding solvent accessibility values as per- centages. This will help to compare the ASA from different methods, visually. (d) Relative ASA: Relative ASAs normalized to a value of