AMMP is a modern full-featured molecular mechanics, dynamics and modeling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers. In addition to standard features, like numerically stable molecular dynamics, fast multipole method for including all atoms in the calculation of long range potentials and robust structural optimizers, it has a flexible choice of potentials and a simple yet powerful ability to manipulate molecules and analyze individual energy terms.
(commercial) AMPAC is a fully-featured semiempirical quantum mechanical program. It also includes a graphical user interface (GUI) that builds molecules and offers full visualization of results.
Chime shows molecular structure in three dimensions. Its
images look like RasMol's because Chime is derived, in part, from RasMol. Chime differs from RasMol in that Chime sits directly on a web page.
E-Cell is a software package for cellular and biochemical modeling and simulation. E-CELL attempts to provide a framework not only for analyzing metabolism, but also for higher-order cellular phenomena such as gene regulation networks, DNA replication, and other occurrences in the cell cycle.
EDFbrowser is a multi-platform viewer for EEG, EMG, and ECG storage files. It supports the EDF, EDF+, BDF, and Nihon Kohden file formats. It supports montages, annotations, precise measurements by using crosshairs, and a zoom function by drawing a rectangle with the mouse. It shows signals from different files at the same time. It includes a built-in EDF/EDF+/BDF to ASCII converter, a built-in Nihon Kohden to EDF+ converter (including annotations), and a built-in EDF/EDF+/BDF compatibility checker. It is available for Linux and Windows.
GenomePixelizer 2D plotter (or genoPix2D) generates images (actually interactive canvases) of genomic similarity dot plots, in which each "dot" indicates similarity between a pair of genes. Diagonal runs of dots generally indicate collinearity in the genomic regions being compared. The program can compare large (chromosome-scale or even eukaryotic genome-scale) genomic regions, and can produce PostScript output of the dot plots.
Grany-3 is a full-featured cellular automaton simulator, made in C++ with Gtk--, flex++/bison++, doxygen and gettext, useful to granular media physicists.
MidasPlus is an advanced molecular modeling system developed by the Computer Graphics Laboratory (CGL) at the University of California, San Francisco. The system is used daily in university-level research programs in order to display and manipulate macromolecules such as proteins and nucleic acids.
Pathomx is an interactive tool for the analysis and visualisation of metabolic data. Built on the MetaCyc database it allows rapid exploration of complex datasets through configurable and extensible plugin.
Protein Explorer enables you to view and explore the three-dimensional (3D) structure of any macromolecule.
Sequence Alignment and Modeling System: a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis. The model states can be viewed as representing the sequence of columns in a multiple sequence alignment, with provisions for arbitrary position-dependent insertions and deletions in each sequence
seaview is a graphical multiple sequence alignment editor. SeaView is able to read various alignment formats (MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows ones to manually edit the alignment, and also to run DOT-PLOT or CLUSTAL programs to locally improve the alignment.
Seg3D is a volume editing and processing tool that combines a flexible manual segmentation interface with powerful higher-dimensional image processing and segmentation algorithms from the Insight Toolkit. DICOM, VFF, META, NRRD, and many other volume formats are supported. Users can explore and label image volumes using configurable, orthogonal slice view windows and 3D volume rendering.
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. It is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies. Read more
Volumevis is simple viewer for displaying 3D voxel datasets such as medical images from CT and MR using volume rendering. Supported 3D raster image formats are RVF, RAW, and 2D slices of any format, including Dicom. In addition, surface models (3DS and VRML) can be loaded. Volumevis is written in a highly modular structure, so that components can easily be added or reused.
Washington University BLAST (WU BLAST) is a powerful software package for gene and protein identification, using sensitive, selective and rapid similarity searches of protein and nucleotide sequence databases.
Zeobuilder is a user-friendly GUI toolkit for the construction of advanced molecular models. It is extensible via a plugin framework and contains several advanced tools for building, aligning, manipulating, and analyzing molecular structures. It describes a molecular model with a hierarchical data-structure of reference frames. This facilitates operations on models at different levels of detail.