NUCPLOT 1.1.4 – Generate Schematic Diagrams of Protein-nucleic Acid Interactions

NUCPLOT 1.1.4

:: DESCRIPTION

NUCPLOT is a program that automatically generates schematic 2D representations of protein-nucleic acid interactions. The input is a standard PDB file and the output is a colour or black-and-white PostScript file which gives a simple, at-a-glance representation of the hydrogen bonds and hydrophobic contacts between proteins and nucleic acids.

::DEVELOPER

Roman Laskowski

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

NUCPLOT

:: MORE INFORMATION

Citation:

Luscombe N M, Laskowski R A, Thornton J M. (1997).
NUCPLOT: a program to generate schematic diagams of protein-DNA interactions.
Nucleic Acids Research, 25, 4940-4945.

Dangle 0.63 – Read PDB File & Generate Geometric Measurement Table

Dangle 0.63

:: DESCRIPTION

Dangle an updated and more general version of our program Dang in that it reads coordinates from a Protein DataBank (PDB) coordinate file for either protein or nucleic acid and generates geometric measurements for each residue. It is different from Dang in that Dangle: is Java-based, includes the capability of reporting deviations from ideal geometry as well as measurement values, and has a very flexible input syntax for specified the measurements desired. Dangle output is given as colon-delimited values, one line per residue. It is designed for facile use in scripts, and is the usual source of input for Suitename, either to generate the data for MolProbity’s multi-criterion table or in individual command-line use.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

Java

:: DOWNLOAD

Dangle

:: MORE INFORMATION

Dangle is free software available under the terms of its own BSD-style license.

Dang 1.8 – Read PDB File & Generate Geometric Measurement Table

Dang 1.8

:: DESCRIPTION

Dang reads coordinates from a Protein DataBank (PDB) molecular structure file and generates a table of several useful geometric measurements for each residue or base. In its most basic form, it writes out dihedral angles (phi, psi, chi) hence the name. The output is formated for easy parsing by awk, grep, sort and other UNIX utilities.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

Linux/Mac OsX/SGI-irix/Sun-SPARC

:: DOWNLOAD

Dang

:: MORE INFORMATION

Dang is free software available under the terms of its own BSD-style license.