NDB | Tools & Software

Tools | Software

RNA Viewer View RNA 2-dimensional structure using the RNAView program.
2D structure is fully annotated according to Leontis and Westhof (2001) RNA, 7, 499-512.

View base pairs, RNA patterns according to LW annotation.

Generate fully annotated secondary structure with tertiary interactions. (Yang et al., (2003) Nucleic Acids Research, 31:3450-3460)

Base Pair Viewer View RNA Base pairs using the BPView program

For linux/unix system users, Java Plug-in or RASMOL / CHIME is required

For PC windows system users, Java Plug-in or CHIME is required

DNA-binding Predictions for Protein Structures

HTHQuery Predicts whether a given three-dimensional protein structure contains a DNA-binding Helix-Turn-Helix (HTH) structural motif. (Ferrer-Costa, C., Shanahan, H. P., Jones, S. & Thornton, J. M. (2005).Bioinformatics 21, 3679-3680.)

predictdnahth Predicts whether a given three-dimensional protein structure contains a DNA-binding Helix-Turn-Helix (HTH) structural motif. (McLaughlin WA, Berman HM. Statistical models for discerning protein structures containing the DNA-binding helix-turn-helix motif. J Mol Biol. 2003 Jun 27;330(1):43-55.)

Protein-DNA interaction tutorial A walkthrough of PDNA-pred and predictdnahth.

QPROF (Query of PROtein Features) A web utility for secondary structural similarity search of protein three-dimensional structure.

Pop-up windows must be enabled for qprof.rutgers.edu. Click here for browser-specific instructions.

Software | Tools

RNAView Program Quickly generate display of RNA/DNA secondary structures with tertiary interactions

RNAMLview Program Display and/or edit RNAView 2-dimensional diagrams

3DNA A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures (Xiang-Jun Lu and Wilma K. Olson (2003) Nucleic Acids Research, 31: 5108-5121)

Freehelix98 as described in "DNA bending: the prevalence of kinkiness and the virtues of normality" Richard E. Dickerson (1998) Nucleic Acids Research, 26, 1906-1926.

hel_param (Unix Compressed Archive (.tar.Z)) The nucleic acid helical analysis program by Marla Babcock as described in J. Biomol. Struct. and Dyn. 11 (1993), 597-628.

sfcheck SFCheck (A.A. Vaguine, J. Richelle, and S.J. Wodak, 1999, Acta Cryst. D, 55, 191-205).

FR3D Finding local and composite recurrent structural motifs in RNA 3D structures

WebFR3D Search RNA-containing 3D structures for fragments according to geometry or pairwise interactions