1. Q: How to use CSS-Palm 2.0 web service?

A: Please visit the latest version of CSS-Palm 2.0 at http://bioinformatics.lcd-ustc.org/css_palm/prediction.php. An JAVA applet will be shown within ten seconds. So, please wait a little while for using the program. For Windows and Unix/Linux users, please use the keyboard shortcuts "Ctrl+C & Ctrl+V" to copy and paste your FASTA format sequences into TEXT form for prediction. And for Mac users, please use the keyboard shortcuts "Command+C & Command+V". Then please click on the "Submit" button to run the program. The prediction results will be shown in the Prediction form. Again, please use the "Crtl+A & Ctrl+C & Ctrl+V" or "Command+A & Command+C & Command+V" to select, copy and paste the results into a new file, e.g., an Excel file, for further manipulation.

A: We have tested CSS-Palm 2.0 on several internet browsers, including Internet Explorer 6.0, Netscape Browser 8.1.3 and Firefox 2 under Windows XP Operating System (OS), Mozilla Firefox 1.5 of Fedora Core 6 OS (Linux), and Safari 3.0 of Apple Mac OS X 10.4 (Tiger) and 10.5 (Leopard). For Windows and Linux systems, a latest version of Java Runtime Environment (JRE) package (JAVA 1.4.2 or later versions) of Sun Microsystems should be pre-installed for using the CSS-Palm 2.0 program. Please download and install the proper JRE package on your computer from "Java(TM) SE Runtime Environment 6 Update 3" page or our website. However, for Mac OS, the CSS-Palm 2.0 could be used directly without any additional packages. Finally, if you can still not view the program properly, please send use an email and tell me the OS information on your computer. We will resolve the problem ASAP.

3. Q: Is CSS-Palm 2.0 much better than CSS-Palm 1.0 and NBA-Palm 1.0?

A: Yes! Firstly, an updated CSS algorithm (Clustering and Scoring Strategy), also called as GPS algorithm (Group-based Phosphorylation Scoring) was used for CSS-Palm 2.0. The prediction performance was greatly improved against our previous tools. Also, in CSS-Palm 1.0 and NBA-Palm 1.0, it will be a heavy burden if too many sequences are submitted. Usually, CSS-Palm 1.0 and NBA-Palm 1.0 only permit less than 50 sequences per time. However, CSS-Palm 2.0 will use the local CPU for computation. Thus, an up to 1,000 proteins (average length ~1000aa) could be input. Finally, the speed of CSS-Palm 2.0 was greatly improved. Even in our laptop (IBM ThinkPad R51, 1.60GHz, 768MB), it only cost <3 minutes to predict palmitoylation sites for 1,000 protein sequences (average length ~1,000aa).

4. Q: I have 20,000 proteins for prediction, what should I do?

A: For a large-scale prediction, we recommend two approaches for you. You can input the sequences for 20 times, with 1,000 proteins per time. Also, please download a stand-alone software of CSS-Palm 2.0 linked as below. In the stand-alone versions, the limitation of sequences number is removed. You can use "Batch Predictor" in the local software for a large-scale prediction.

5. Q: I have a few questions which are not listed above, how can I contact the authors of CSS-Palm 2.0?

A: Please contact the two major authors: Dr. Yu Xue and Dr. Jian Ren for details.

Comparisons of CSS-Palm 2.0 with CSS-Palm 1.0 and NBA-Palm 1.0

We searched the scientific literature from PubMed with keywords of "palmitoylation" or "palmitoylated", and manually collected 340 experimentally verified palmitoylation sites in 145 proteins which were published before Oct. 8th, 2007. After redundant clearing, we arbitrarily took 263 palmitoylation sites from 109 proteins published before Nov, 2006 as the training data set. And the remaining 53 sites in 26 proteins were not included in training as an additional data set for performance evaluation (New data set). Previously, the CSS-Palm 1.0 was constructed with 210 palmitoylation in 83 proteins. We regard this data set as the Old data set. We compared CSS-Palm 2.0 to CSS-Palm 1.0 and NBA-Palm 1.0, with both the old data set and the new data set. The default thresholds were chosen for CSS-Palm 1.0 and NBA-Palm 1.0. Then we fixed the Sn of CSS-Palm 2.0 to be similar with the other two predictors and compare the Sp values.