Molecular graphics

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use.

MolViewer is a program for visualizing and modifying small molecules under NeXTStep. It is capable of constructing peptides from scratch (given a sequence). It has many display options and can be used to rotate bonds, dihedrals, etc. It will even do some simple energy minimization.

Background: To understand protein function, it is important to study protein- protein interaction networks. These networks can be represented in network diagrams called protein interaction maps that can lead to better understanding by visualization. We address the problem of drawing of protein interactions in Kohn's Molecular Interaction Map (MIM) notation. Even though there are some existing tools for graphical visualization of protein interactions in general, there is no tool that can draw protein interactions with MIM notation with full support. Results: MIMTool was developed for drawing protein interaction maps in Kohn's MIM notation. MIMTool was developed using the Qt toolkit libraries and introduces several unique features such as full interactivity, object dragging, ability to export files in MIMML, SBML and line drawing with automatic bending and crossover minimization, which are not available in other diagram editors. MIMTool also has a unique orthogonal edge drawing method that is both easy and more flexible than other orthogonal drawing methods present in other interaction drawing tools. Conclusions: MIMTool facilitates faster drawing, updating and exchanging of MIMs. Among its several features, it also includes a semi-automatic drawing algorithm that makes use of shortest path algorithm for constructing lines with small number of bends and crossings. MIMTool contributes a much needed software tool that was missing and will facilitate wider adoption of Kohn's MIM notation.

SketchBio aims to provide a rapid-to-use and easy-to-learn 3D modeling tool for biologists to enable effective interactive 3D “what if” scenario exploration for the exploration of subcellular structures.

It includes three novel features: crystal by example, pose-mode physics, and spring-based layout that accelerate operations common in the formation of molecular models. 

MDMap is a system designed to summarize long-running molecular dynamics (MD) simulations. MDMap is an automated system to visualize MD simulations as state-transition diagrams, and can replace the current tedious manual layouts of biomolecular folding landscapes with an automated tool. The layout of the representative states and the corresponding transitions among them is presented to the user as a visual synopsis of the long-running MD simulation. 

We propose an optimization of the Contour-Buildup algorithm for the Solvent Excluded Surface (SES) to remedy this issue. An optimized subdivision of calculation tasks of the original algorithm allows for full utilization of massive parallel processing hardware. Our approach is especially well suited for modern graphics hardware employing the CUDA programming language. As we do not rely on any pre-computations our method is intrinsically applicable to time-dependent data with arbitrarily long trajectories. We are able to visualize the SES for molecules with up to ten thousand atoms interactively on standard consumer graphics cards.

ZigCell3D is a virtual 3D whiteboard approach to chemical reaction modelling. It aims to provide a realtime interactive environment, where complex biophysics research is turned into a creative and game-like 3D environment. The complete system entails modelling, simulation and visualisation as part of a unified framework.

The core visualisation is based on a multi-core parallel C/C++ ray tracing engine, that builds a complete 3D iso-surface model of the cell, its organelles and molecules down to the atomic level using PDB files. The simulator itself is based on coarse-grained Brownian motion of the individual molecules, which is visualised in detail in a tightly coupled manner. Using a virtual fluorescence microscope the virtual simulation environment can be benchmarked against real life experimental data.