Sequence annotation visualization software tools | Protein structure data analysis

A publicly available web resource that streamlines and simplifies the process of gleaning insight from protein structures. In contrast to most molecular graphics tools, the user interface of Aquaria is organized primarily by protein sequence, not structure. A user starts by specifying a protein of interest by name and organism, by identifier or by URL; Aquaria then generates a concise visual summary of all related PDB structures, using a precalculated all-against-all comparison of Swiss-Prot and PDB sequences (updated monthly). Aquaria is designed for biologists; its user interface creates clear and useful default views that show only the most relevant structural information tightly integrated with sequence, features and text that provide biological context.

Provides a platform for visualize biomolecular structures. Autodesk Molecule Viewer is a web application allowing the preparation, exploration, editing and sharing of 3D models. Users can import structures through a Protein data Bank (PDB) ID, generate structural representations, annotate in space, and create customized gallery. Besides, the program includes a virtual reality mode authorizing the use of a virtual reality (VR) headset.

A web server for mapping protein sequence annotations onto a protein structure and visualizing them simultaneously with the structure. ProSAT+ incorporates many of the features of the preceding ProSAT and ProSAT2 tools but also provides new options for the visualization and sharing of protein annotations. Data are extracted from the UniProt KnowledgeBase, the RCSB PDB and the PDBe SIFTS resource, and visualization is performed using JSmol. User-defined sequence annotations can be added directly to the URL, thus enabling visualization and easy data sharing.

Displays discrete motifs. 3MATRIX offers a 3D structural context for conserved amino acids aiming to link sequence motifs and existing structural data. It provides different manner to select and visualize sequence motif atoms, and furnishes links to data related to query motifs. This tool can determine the degree of conservation and the chemical environments of conserved amino acids.

Represents a web-based protein structure visualization tool. Web3DMol provides interactive 3D presentation of protein structures. It permits users to create graphical results easily. To reveal the correspondence between the linear sequence and 3D structure, this tool illustrates as a plot, the primary and secondary structures of the visualized proteins. By using the fragment segmentation, several parts of a molecule can be presented as different modes.

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.

Assists users in the visualization of sequence-related annotations over available experimental or predicted structures. MolArt is a JavaScript tool and library that delivers an integrated environment with sequence and structure visualization capabilities and uses public APIs providing sequence-structure mapping. The package includes all its dependencies bundled into a single JavaScript file making it easy to embed into any web site.

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.

Analyzes interactively geometric preferences of noncovalent interactions around user-defined substructures on any user-selected data. NAOMInova is an application that allows the analysis of potential interaction partners of custom-defined chemical substructures. This method can support interactive analyses even if large data sets are used. It can also be applied in very heterogeneous scenarios.

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.

Provides a framework to support electron density maps and their interpretations. Molstack is a cloud-based tool that allows the visualization and analysis of multiple sets of coordinate and electron density data in stacks in dual, synchronized side-by-side windows for easy comparison. It organizes the sharing and dissemination of these structural models along with their experimental evidence as an interactive session.

A package to view and display 3D ICM graphical slides and animations interactively inside Microsoft PowerPoint and web browsers such as Internet Explorer, Safari and Mozilla Firefox. Inside a single file users can save and display many different data types such as sequences, alignments, plots, tables, protein and DNA/RNA structures. Each data element can be linked to one another and annotated, and then shared via the web, MS Office tools or in the free ICM-Browser.

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.