Sequence annotation visualization software tools | Protein structure data analysis

Generates high-quality publication-ready molecular graphics images and animations. PyMOL is a molecular graphics system targeted at medium to large biomolecules like proteins. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. It includes visualization of molecules, molecular trajectories and surfaces of crystallography data or orbitals, molecular builder and sculptor, internal raytracer and movie generator.

Visualizes static and dynamic features of macromolecular structures. CCP4mg offers a platform that allows users to generate both images and movies. It includes multiple features such as: (i) an automatic generation of multiple drawing styles; (ii) graphics utilities; (iii) the possibility to handle electron density maps or (iv) to create presentations. It also can be used for superposing and analyzing structures.

A program for the macromolecular structure visualization. CueMol's aims are to visualize and create the publication-quality images of the macromolecular structures with user-friendly interfaces. Supported files are molecular coordinates, electron density, MSMS surface data, and APBS electrostatic potential map.

Calculates covariance scores for constrained regions of background conservation. McBASC can be utilized as a covarying or highly conserved filter. This software gives an equally high score to conserved or covarying alignments and allows, without a reduction in score, substitution of conserved pairs of residues for covarying ones.

A freeware graphical user interface that offers preprocessing and postprocessing adapted (to date) to nine computational chemistry software packages. Gabedit includes tools for editing, displaying, analyzing, converting, and animating molecular systems. It can generate a Povray file for geometry, surfaces, contours, and color-coded planes. This tool is developed to facilitate the production of results from quantum chemistry methods through various computational chemistry software (CCS) and to provide a thorough analysis of these results.