Free protein software for linux

PROMPT is a system for retrieval, analysis, mapping and comparison of protein sets. It allows easy mapping of different types of sequence identifiers, automatic data retrieval and integration, many analysis and comparison algorithms, and a full-featured GUI application.

Exhaustive statistical tests are conducted automatically in appropriate cases, but can be performed manually. All analysis results can be viewed or visualized and exported in various formats.

All methods can be used in your own Java code or with beanshell scripting in your own scripts, a pipeline, or grid systems.

Raster3D is a powerful set of tools for generating high quality raster images of proteins or other molecules.
The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing.
It uses an efficient software Z-buffer algorithm that is independent of any graphics hardware.
Main features:
- Raster3D uses a fast Z-buffer algorithm to produce high quality pixel images featuring one shadowing light source, additional non-shadowing light sources, specular highlighting, transparency, and Phong shaded surfaces. Output is in the form of a pixel image with 24 bits of color information per pixel plus one matte channel.
- Raster3D does not depend on graphics hardware. The rendering program currently supports output to files in AVS, JPEG, TIFF, PNG and SGI libimage format. To actually view or manipulate the images produced, you must also have installed an image viewing package (e.g. John Cristys ImageMagick or the SGI libimage utilities). The Raster3D rendering program can be integrated with ImageMagick to expand the flexibility of output formats and interactive use.
- Ancillary programs are provided for the generation of object descriptions based on atomic coordinates stored in PDB format. Although Raster3D is not intended as a general purpose ray-tracing package, nothing in the rendering process is specific to molecular graphics. Some of the algorithms used have been chosen for speed rather than generality, however. They work well for molecular graphics images, but possibly would produce odd results if used for very different types of image.
- Raster3D currently supports rendering six object types: spheres, triangles, planes, smooth-ended cylinders, round-ended cylinders, and quadric surfaces. It also supports the definition of material properties (transparency, bounding planes, color, reflectivity) that apply to groups of objects within the rendered scene.
Enhancements:
- changed the default output format to PNG for all programs

ToBiX is a Morphix-based Linux live CD containing a range of specialist applications for bioinformatics. With this distrubution you just boot from the CD and you have a fully functional LINUX OS distribution with open source applications.
Besides using some RAM, ToBiX doesnt touch the host computer and is ideal for presentations, workshops or other learning or scientific activity on bioinformatics and computational biology.
ToBiX comprises some of the most useful and powerful bioinformatics tools such as:
- Blast 2.0 - Basic Local Alignment Search Tool for rapid searching of nucleotide and protein databases;
- Copasi - software application for simulation and analysis of biochemical networks;
- mpiBLAST - MPI based parallel implementation of NCBI BLAST;
- SimWiz - collection of Java tools for visualization of data resulting from different kinds of biochemical simulation processes;
- Cellware - tool to model whole cell biochemical reactions;
- Gromacs - molecular dynamics simulation package;
- SBML-Editor - tool for the quick creation and edition of SBML files;
- Stocks 2 - software for simulation of biochemical processes using Maximal Time Step Method

StrBio is a set of Java classes and libraries useful for development of software for computational structural biology research.

They are licenced under the LGPL.

he strbio.org classes are the basis for several published research projects, including the Pred2ary secondary structure prediction program and the ASTRAL database of protein domain sequences.

The most interesting structural biology applications included are:

Pred2ary protein secondary structure prediction
JThread protein fold prediction
ConvertProtein for interconversion of protein file formats (FASTA, PDB, MSF, ALN, CASP, DSSP, HSSP, YAPF)
Filters to exchange data with commonly used molecular biology applications (e.g., BLAST, MinArea, MODELLER)
MakeRAF tool to create the Rapid Access Format sequence maps for the ASTRAL database.

Other more general-purpose functionality that is included:

Neural network library, including Scaled Conjugate Gradient or Steepest Descent optimization
Hooke and Jeeves derivative-free global optimization algorithm
Misc mathematical objects and algorithms (vectors, matrices, etc)
Efficient string formatting using Printf-based syntax (printf, atoi, atof, etc.)

SigInt project is a command-line software tool that can be used to find and rank mammalian proteins/genes that specifically and significantly interact with a list of proteins/genes in context of a background mammalian signalome and interactome networks.

The inputs to the program are: (a) a seed list of human Entrez Gene gene symbols, (b) a background networks in SIG format, and (c) a name for the output file (web-page file name with the htm extension). SigInt outputs a sorted list of genes/proteins that interacts with components from the seed list. These components are sorted by a z-score that measures the specificity of these intermediate components to interact with the genes/proteins from the seed list.

SigInt can be run on Linux, Mac and Windows operating systems and it requires a background network text file in SIG format.

Usage:

Extract the archive
chmod +x sigint_lnx.exe
./sigint_lnx.exe

QuteMol is an open source, interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilities through OpenGL shaders to offers an array of innovative visual effects.
QuteMol visualization techniques are aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins.
Main features:
- Real Time Ambient Occlusion
- Depth Aware Silhouette Enhancement
- Ball and Sticks, Space-Fill and Liquorice visualization modes
- High resolution antialiased snapshots for creating publication quality renderings
- Interactive rendering of large molecules and protein (100k atoms)
- Standard PDB input
QuteMol was developed by Marco Tarini and Paolo Cignoni of the Visual Computing Lab at ISTI - CNR.
Enhancements:
- Major stable release.
New Features:
- Color per chain selectable. (rather then per atom). Random color schemas can be cycled.
- Export of GIF animation Is is now possible to export GIF animations featuring the current model under inspections (useful for websites)
Minor Features:
- Progress bar shown during any long processing task (which can be cancelled)!
- Various minor speed improvements
- Save snapshot dialog to change the resolution of the fly
Bugfixes:
- Link to Qutemol webpage fixed (now using wxWidgets v. 8.0)
- Fixed a bug that prevented some 2-letter atoms to be correctly understood
- Fixed the clipping plane bug (large molecules where shown as if cut in half)
- Various minor fixes

Plasmidb project is a interface to a simple MySQL database, which itself contains information about projects in molecular biology.
The focus is the data pertaining to bacterial plasmids, but also the protein sequences which are being worked on for a particular project, DNA sequences of target genes.
The database is designed to be extensible, so after learning about how the interface works, a user could add data types in SQL tables and write an interface to be able to edit it easily.
Main features:
- Standard cloning or expression plasmids (e.g. their antibiotic selection markers, any RNA polymerase promoters).
- Database sequences you may be currently working on (their accession numbers, sequences, coding sequences).
- Products you may wish to express or purify from them. e.g. His-tagged protein or RNA run-off transcripts etc.
- Primers you have ordered.
- Restriction enzymes.
- DNA sequencing data.
- Protein prep yields and data about purity.
Despite this being a work-in-progress, I have found the database to be very useful.
The database contains user and session information, so only upon logging-in, can one view and edit the database information.
Enhancements:
- User interface improvements, CSS restyle and many framework improvements are included in this release.
- PDF maps can now be added easily to the list of standard plasmids.
- Many Invitrogen and Novagen plasmids are included in the standard database.
- This is the last major release before migrating to Ruby on Rails.

This program places the required number of sodium ions around a system of electric charges, e.g., the atoms of a biological macromolecule (protein, DNA, protein/DNA complex).

The ions are placed in the nodes of a cubic grid, in which the electrostatic energy achieves the smallest values. The energy is re-computed after placement of each ion. A simple Coulombic formula is used for the energy:

Energy(R) = Sum(i_atoms,ions) Q_i / |R-R_i|

All the constants are dropped out from this formula, resulting in some weird energy units; that doesnt matter for the purpose of energy comparison. To speed the program up, the atoms of the macromolecule are re-located to the grid nodes, closest to their original locations.

The resulting error is believed to be minor, compared to that resulting from the one-by-one ions placement, or from using the simplified energy function. The coordinates of the placed ions are printed out in the PDB format for further usage.

It is recommended that the placed ions are equilibrated in a separate Monte Carlo or Molecular Dynamics simulation. Trivial modifications to the program should allow the placement of any combination of multivalent ions of different charges.