Structural Bioinformatics Resource Materials

developed at SINP

  pyrHBfind: A Software (RedHat 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).

  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.

  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 one is S. Mukherjee, M. Bansal and D. Bhattacharyya, J. Comput.Aided Mol.Des.20,629-645.

  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).

HD-RNAS: A Database of RNA crystal structures classified according to function and source of the molecules (S. Ray, S. Halder and D. Bhattacharyya).

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 & overlap by the user (S. Basu and D. Bhattacharyya).

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 June 23, 2009; maintained by Dhananjay Bhattacharyya