※ User Guide:
Frequently Asked Questions:
1 . Q: How to read the FSL-Kla results?
A: Here we use the human protein RAF-1 as the example. After clicking "Submit", the prediction results of lactylation sites with medium threshold are shown as follows:
<1>. The table of the FSL-Kla results
ID: The name/id of the protein sequence that you input to predict.
Position: The position of the site which is predicted to be lactylated.
Peptide: The predicted phosphopeptide with 10 amino acids upstream and 10 amino acids downstream around the modified residue.
Score: The value calculated by FSL-Kla to evaluate the potential of binding.
Cutoff: The cutoff value under the threshold. Different threshold means different precision, sensitivity and specificity.
Source: Whether the interactions is validated by experiment, "Exp." means YES, while "Pred." means NO.
2. Q: Is FSL-Kla accurate?
A: Yes, but not all. Systematically predicting lactylation sites is an extremely hard task. If the training data is more enough, the prediction is more satisfying and accurate. But for lactylation sites, the training data set are constrained which made the performance lower. However, in comparison, FSL-Kla achieved a higher accuracy than other existing tools.
3 . Q: How to choose the cut-off values and the thresholds?
A: Firstly, we calculated the theoretically maximal false positive rate (FPR) for each cluster. The three thresholds of FSL-Kla were decided based on calculated FPRs in which the high, medium and low thresholds were selected with FPRs of 4%, 9% and 15%. in substrates.
4 . Q: What's the meaning of False Positive Rate (FPR)?
A: To estimate the false positive rate (FPR) of prediction, we randomly retrieved 10,000 PSP(10, 10) peptides from eukaryotic proteomes to construct a near-negative data set. However, precise calculation of FPR is unavailable due to lack of a "gold-standard" negative data set. The process was repeated twenty times and the average FPR was calculated by FSL-Kla as the theoretically maximal FPR.
5 . Q: I have a few questions which are not listed above, how can I contact the authors of FSL-Kla?
A: Please contact the major author: Dr. Yaping Guo for details.