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BPFIND & NUPARM Server



Provide pdbid:

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Modify specific BPFIND options
Click here to change the default parameters set for BPFIND run [Default]InfoJeffrey[2] categorizes H bonds with donor-acceptor distances of 2.2-2.5 Å as “strong, mostly covalent”,
2.5-3.2 Å as “moderate, mostly electrostatic”,
3.2-4.0 Å as “weak, electrostatic”
hydrogen bond distance cutoff:
pseudo angle cutoff:
E-value cutoff:
select desired chain identifier in PDB File(all):
Structure solved using NMR
include HETATM entries in PDB
avoid identification of base pairs stabilized by C-H...O/N H-bonds
avoid identification of base pairs involvingsugar O2' atoms
avoid base pairing between residue no. i and i+1
avoid printing base pairing information w.r.t.the second strand.
This is suitable for simple oligonucleotides
Modify specific NUPARM options
Click here to change the default parameters set for NUPARM run [Default]InfoJeffrey[2] categorizes H bonds with donor-acceptor distances of 2.2-2.5 Å as “strong, mostly covalent”,
2.5-3.2 Å as “moderate, mostly electrostatic”,
3.2-4.0 Å as “weak, electrostatic”
Calculate single stranded parameters:
The supplied file is not in pdb format:
Do not use default cross-product method:
Use C1' - C1' as Y-axis:
Do not use C6-C8 midpoint as BP center
Required Single stranded parameters
Calculate P-P distance
Calculate Torsion angle
Calculate Stacking Overlap values
Show Axis for base and base pair

The server would identify base pairs from the chosen file by using BPFIND software (1). This hypothesis driven algorithm looks for at least two hydrogen bonds between the bases.

The Intra base pair and Inter base pair parameters along with several other parameters would be calculated using base pairing edge specific axis system using NUPARM (2, 3, 4).

References:
1. Non-Canonical Base Pairs and Higher Order Structures in Nucleic Acids: Crystal Structure Database Analysis. J. Das, S. Mukherjee, A. Mitra, D. Bhattacharyya (2006) J. Biomol. Struct. Dynam. 24: 149-161.

2. NUPARM and NUCGEN: Software for Analysis and Generation of Sequence Dependent Nucleic Acid Structures. M. Bansal, D. Bhattacharyya, B. Ravi. (1995) CABIOS 11: 281-287.

3. Conformational Specificity of Non-canonical Base Pairs and Higher Order Structures in Nucleic Acids: Crystal Structure Database Analysis. S. Mukherjee, M. Bansal, D. Bhattacharyya (2006) J. Comp. Aided Mol. Des. 20: 629-645.

4. Analysis of stacking overlap in nucleic acid structures: algorithm and application. P. K. Pingali, S. Halder, D. Mukherjee, S. Basu, R. Banerjee, D. Choudhury,D. Bhattacharyya (2014) J. Comp. Aided Mol. Des. 28: 851-867.



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