Boitechnology

ASARA, Yet Another Scientific Artificial Reality Application, is a molecular visualisation, modelling, and dynamics program that can be used for a series of scientific applications as is expressed by the large number of scientific articles mentioning this software. The free version of YASARA (YASARA-View) is well suited for bioinformatics education. A series of freely available bioinformatics courses exist that use this software.

Students working on an educational task using YASARA.

See the CMBI education pages for a series of examples.
Krieger E, Koraimann G, Vriend G (May 2002). “Increasing the precision of comparative models with YASARA NOVA—a self-parameterizing force field”. Proteins 47 (3): 393–402. doi:10.1002/prot.10104. PMID 11948792.
Modelling:
Krieger E, Vriend G (Feb 2002). “Models@Home: distributed computing in bioinformatics using a screensaver based approach”. Bioinformatics 18 (2): 315–8. PMID 11847079.
Dynamics:
Krieger E, Darden T, Nabuurs SB, Finkelstein A, Vriend G (Dec 2004). “Making optimal use of empirical energy functions: force-field parameterization in crystal space”. Proteins 57 (4): 678–83. doi:10.1002/prot.20251. PMID 15390263

WHAT IF is a computer program used in a wide variety of in silico macromolecular structure research fields such as:
Homology models of protein tertiary structures as well as quaternary structures,
Validation of protein structures, noticeably those deposited in the PDB
Correction of protein structures
Visualisation of macromolecules and their interaction partners (lipids, drugs, ions, water).
Interactive manipulation of macromolecules

The software was initiated in 1987 at the University of Groningen. Most of its development took place in the period 1989-2000 at the EMBL in Heidelberg. Lately the software is being maintained at the CMBI in Nijmegen. It is available for in-house use, or as free servers. Its best known use has been the detection of many millions (often small, but sometimes catastrophic) errors in PDB files.

VMD has been developed by the Theoretical and Computational Biophysics group at the University of Illinois and the Beckman Institute. The original version, called VRChem, was developed in 1992 by M. Krogh, W. Humphrey, and R. Kufrin. The initial version of VMD was written by Andrew Dalke, Jeff Ulrich, and William Humphrey and was released in 1995. The earliest versions of VMD were developed for Silicon Graphics workstations and could also run in the CAVE. After the original VMD developers moved on to other careers, Sergei Izrailev took over maintaining the program until 1998. In 1998, John Stone became the main VMD developer, porting VMD to many other Unix operating systems and completing the first full-featured OpenGL version. The first version of VMD for the Microsoft Windows platform was released in 1999. In 2001, Justin Gullingsrud, and Paul Grayson, and John Stone added support for haptic feedback devices and developed an interface between VMD and NAMD for performing interactive molecular dynamics simulations. In subsequent developments, Jordi Cohen, Gullingsrud, and John Stone entirely rewrote the graphical user interfaces, added built-in support for display and processing of volumetric data, and the first use of OpenGL Shading Language.

Visual molecular dynamics (VMD) is a molecular modelling and visualization computer program. VMD is primarily developed as a tool for viewing and analyzing the results of molecular dynamics simulations, but it also includes tools for working with volumetric data, sequence data, and arbitrary graphics objects. Molecular scenes can be exported to external rendering tools such as POV-Ray, Renderman, Tachyon, VRML, and many others. Users can run their own Tcl and Python scripts within VMD as it includes embedded Tcl and Python interpreters. VMD is available free of charge, and includes source code, but it’s under a non-free license.

ViewMol3D is a 3D OpenGL viewer for molecular structures from the output of quantum chemistry calculations.

many sequence alignment formats read, edited, written
Newick tree format read
automatic, mismatch-tolerant association of structures with alignment sequences
sequence-structure crosstalk: highlighting in one highlights the other
multiple methods for calculating conservation and displaying values on associated structures
structure superposition using the associated sequence alignment
in the absence of a pre-existing alignment, structure superposition using both residue type and secondary structure information
generation of structure-based sequence alignments from superpositions of two or more proteins

many formats of volume data maps (electron density, electrostatic potential, others) read, several written
interactive threshold adjustment, multiple isosurfaces (mesh or solid), transparent renderings
fitting of atomic coordinates to maps and maps to maps
density maps can be created from atomic coordinates
markers can be placed in maps and connected with smooth paths
display of single data planes, optionally as topographic maps
volume data time series playback and morphing
many tools for segmenting and editing maps
Gaussian smoothing, Fourier transform
surface area and surface-enclosed volume measurements

images can be saved at arbitrarily high resolution
adjustable background color, lighting, depth-cueing, silhouette edges
stick, ball-and-stick, sphere, ribbon, and surface displays
nonmolecular geometric objects
labeling with arbitrary text and symbols, color keys
isosurfaces and transparent renderings of volume data (see below)
different structures can be clipped differently and at any angle
optional raytracing with bundled POV-Ray
scene export to X3D and other formats
simple graphical interface for creating movies interactively
alternatively, movie content and recording can be scripted
movie recording is integrated with morphing and MD trajectory playback

automatic atom type identification
hydrogen addition and partial charge assignment
high-quality hydrogen bond, contact, and clash detection
distance and angle measurements, rotatable bonds
amino acid rotamer libraries (backbone-dependent and -independent)
molecular dynamics trajectory playback (many formats)
clustering of conformational ensembles
morphing between conformations of a protein or even different proteins
display of attributes (B-factor, hydrophobicity, etc.) with colors, radii, “worms”
easy creation of new attributes with simple text file inputs
rich set of commands, powerful specification syntax
many formats read, PDB and Mol2 written
web fetch from Protein Data Bank, PQS (predicted quaternary structure), CASTp (protein pocket measurements), EDS (density maps), ModBase (comparative models), Pub3D (small molecule structures), others

UCSF Chimera (or simply Chimera) is an 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 movies can be created. Chimera includes complete documentation and can be downloaded free of charge for noncommercial use.

Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics (RBVI) at the University of California, San Francisco. Development is funded by the NIH National Center for Research Resources (grant P41-RR01081).