Structural Bioinformatics Resource Materials
developed at SINP
NUPARM: A Software for analysis of nucleic acid structure mainly through different base pair parameters. A web-server version of the same is also available at through IISc. The methods have been described in various publications, the most recent ones are S. Mukherjee, M. Bansal and D. Bhattacharyya (2006) J. Comput. Aided Mol. Des.20,629-645; P. Pingali, S. Halder, D. Mukherjee, et al. (2014) J. Comput. Aided Mol. Des. 28: 851-867. We strongly recommend users to run BPFIND prior to running NUPARM especially for RNA structures containing loop, junction, helix, etc.
RNAHelix: A Software for generation of structures of base pairs of nucleic acid double helices using base pair and base pair step parameters. The base pairs can be Watson-Crick type or even non-canonical type. Developed at SINP and IISc by D. Bhattacharyya, S. Halder, S. Basu, D. Mukherjee, P. Kumar, M. Bansal (2017) J. Comp. Aided Mol. Des. 31: 219-235 (RNAHelix paper)
Sarama: A software suite to plot the distribution of interior residues of a globular protein chain in the Complementarity Plot (S. Basu, D. Bhattacharyya and R. Banerjee, J. Bioinfo. Intelli. Control 3, 1–6, 2014)
BPFIND: A Software for detection and analysis of Hydrogen Bonded Base Pairs in a nucleic acid structure. The program looks for at least two hydrogen bonds between two nucleotide bases. This can also detect possible protonated base pairs (Das, J, Mukherjee, S, Mitra A and Bhattacharyya, D, J.Biomol.Struct.Dynam. 24, 149-161.
RNAbase-pair: Analysis of all kinds of base pairs (canonical G:C, A:U or G:U as well as all possible non-canonical ones) in available RNA crystal structures (Das J, Mukherjee S, Mitra A and Bhattacharyya D 2006, J. Biomol. Struct. Dynam. 24, 149-161). More detail informations can be found at RNABP COGEST database (S. Bhattacharyya et al. (2015) Database (Oxford) (DOI:10.1093/database/bav011).
pyrHBfind: A Software (Linux executable) for analysis of Hydrogen Bonding between protein and DNA in a protein-DNA complex structure, considering Amino Group Pyramidalization (Majumdar, S, Mukherjee, S and Bhattacharyya, D, J. Phys. Chem B 2005, 109, 10484-10492).
HD-RNAS: A Database of RNA crystal structures classified according to function and source of the molecules (S. Ray, S. Halder, S. Kaypee and D. Bhattacharyya (2012) Frontiers in Genetics, 3,59).
PolDNAMelt: A Server for calculations of melting thermodynamics of a Contiguous ds-DNA in solution (with absolute base pairing complimentarity) spliting it into sizes of preferred window and overlap by the user (S. Basu and D. Bhattacharyya, J. Bioinfo. Intelli Control 2, 316–320, 2013).
DetectMode: Normal Mode Analysis toolkit for detection of major modes of vibrations in calculated normal mode by GAMESS-US package. The details of the method can be found at Sen, K, Basu, S and Bhattacharyya, D, Int J. Quant. Chem. 106 (2006) 106, 913-927.
NonPlanarPeptides Analysis of non-planar peptides in extremely high resolution structures in Protein Data Bank (Dasgupta, A, Majumdar, R and Bhattacharyya, D (2004) Ind. J. Biochem. Biophys.41, 233-240).
Nucleic Acid Model Building: Coordinates of DNA/RNA of different structural forms can be generated using published cylindrical coordinates based on X-ray fiber or crystal data.
Last update May 25, 2016; maintained by Dhananjay Bhattacharyya