Systematic Approaches for Functional Annotation of LncRNAs



ISSNLncFA Tools/Dabases developed in this projects are

PDB-2-PB[1] is a curated online Protein Block (PB) sequence database. Here, we encoded and provide the PB sequences for all the protein structures available in PDB using de Brevern, encoding procedure. From our PDB-2-PB, users can extract the PB sequences along with their corresponding information as follows; (i) amino acid sequence, (ii) chain length, (iii) sequence start and end positions, (iv) resolution (only for X-ray solved entries), (v) experimental method used, and (vi) dihedral angles ( and ), which we used to assign PB letters.

Click here to access PDB-2-PB.

[1] Suresh V, Zhou X and Parthasarathy S (2015) PDB-2-PBv.2.0: an updated database for Protein Block sequences. Submitted. Database. 2015



RPI-Pred[2] is a RNA-protein interaction prediction server based on Support Vector Machine (SVM). The RPI-Pred uses primary sequence and predicted structural fragments information of given protein and RNA. The RPI-Pred perform interaction prediction for two different cases; (1) Single RNA with multiple protein entries and (2) Multiple RNA entries with single protein. Usage of RPI-Pred is user friendly, users are requested to submit "one or multiple RNA sequence in fasta format" and upload "one or multiple, predicted protein block information in single file". The final outcome of RPI-Pred shows, whether given RNAs and proteins can possibly interact or not.

Click here to access
RPI-Pred.

[2]  Suresh V, Liu L, Adjeroh D, Zhou X: RPI-Pred: Predicting ncRNA-protein interaction using sequence and structural information. Accepted in Nucleic Acid Research. 2015



RPI-Bind-Pred under development ..

LncFA under development ..


Please, send your comments, suggestions to: svenkat@wakehalth.edu