Important

We are very sorry that the old link for RNABPDB was not functional for some time. Now, you can find the database again at our new addresses:

• https://rnabpdb.dbioin.in/

or

• http://pdbi.nii.ac.in/~rnabpdb/rnabpdb/

RNAHelix server is available at :

• https://rnabpdb.dbioin.in/Tools/RNAHelix

or

• http://pdbi.nii.ac.in/~rnabpdb/Tools/RNAHelix/

Base Pair and Base Pair Step Parameters

Bhattacharyya, D., Halder, S., Basu, S. et al. RNAHelix: computational modeling of nucleic acid structures with Watson–Crick and non-canonical base pairs. J Comput Aided Mol Des 31, 219–235 (2017).

Base Pair Stacking

Pingali, P.K., Halder, S., Mukherjee, D. et al. Analysis of stacking overlap in nucleic acid structures: algorithm and application. J Comput Aided Mol Des 28, 851–867 (2014).

RNABPDB

RNA Base Pair Databae raw flat files for version 1 and version 2 is stored as tab seperated format. Please follow references above for parameter description.

Pdb Information tab is representing : pdbid_BasePair_Pairing Edge_1st residue number according to bpfind_2nd residue number according to bpfind_1st residue number according to PDB_1st Chain id according to bpfind_2nd residue number according to PDB_2nd Chain id according to bpfind

*Basepair.tsv

Buckle	Open	Propeller	Stagger	Shear	Stretch	C1'-C1'_Distance	Evalue	Proximity	Pdb Information
-29.12	15.47	-22.86	-0.80	2.32	2.68	0.63	12.52	9.68	6ys3_AA_wwC_2919_2993_2817_b_2891_b

*BasepairStep.tsv

Tilt	Roll	Twist	Shift	Slide	Rise	Cup	Overlap	Alpha11	Beta11	Gamma11	Chi11	Eta11	Theta11	Phase11	Eps12	Zeta12	Chi12	Phase12	C1c111	Alpha21	Beta21	Gamma21	Chi21	Eta21	Theta21	Phase21	Eps22	Zeta22	Chi22	Phase22	C1c121	Pdb Information
2.65	12.52	34.84	1.29	-2.84	3.03	-8.41	37.18	-57.20	142.70	59.60	-159.90	153.80	-118.00	11.80	-141.80	-72.90	-177.20	14.50	5.89	-60.90	171.50	52.10	-159.40	165.10	-175.80	16.40	-145.80	-68.20	-170.10	12.00	6.15	6zm6_AA_wwC_256_308_1926_A_1978_A