Computational protocol: A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs

Similar protocols

Protocol publication

[…] Li lab and Xiaoyong Pan provided RNAProSite and xypan prediction results respectively, with default parameter. aaRNA was used by inputting the structure file with default parameters. RNABindR and RNABindRPlus were predicted with default parameters, while removing 95% sequence identity in RNABindRPlus. KYG was predicted with command line using “method_type = 8” option. RBscore_SVM was based on the training set of R246. DBS-PSSM, DBS-Pred, RBRIdent, PPRInt, PRBR, DNABind, RBRDetector and ProteDNA were used with default parameter. The DISPLAR program was provided by Sanbo Qin and was run with default parameters. BindN and BindN+ were used by default parameters, while suffix “_RNA” and “_DNA” are RNA mode and DNA mode respectively. PRNA and Predict_RBP were trained on PRNA_R205 and BindN_R107 respectively, without cross-validation and applied with default parameters. DNABINDPROT was predicted with option “Fast 1” and DR_bind1 was predicted in the RNA mode. N-terminal and C-terminal residues not predicted by PRBR are taken as non-binding sites and assigned 0 as prediction score. For binary predictions of DNABINDPROT, DISPLAR, DBS-Pred and DBS-PSSM, positive sites are assigned a prediction score of 1, while negatives are assigned 0. […]

Pipeline specifications