Free proteins 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

Python Macromolecular Library (mmLib) is a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language.

Python Macromolecular Library is accessed via a layered, object-oriented application programming interface, and provides a range of useful software components for parsing mmCIF, and PDB files, a library of atomic elements and monomers, an object-oriented data structure describing biological macromolecules, and an OpenGL molecular viewer.

The mmLib data model is designed to provide easy access to the various levels of detail needed to implement high-level application programs for macromolecular crystallography, NMR, modeling, and visualization.

This includes specialized classes for proteins, DNA, amino acids, and nucleic acids. Also included is a extensive monomer library, element library, and specialized classes for performing unit cell calculations combined with a full space group library.

Aero AIO: Folding@Home is a plugin for Aero AIO to monitor your Folding@Home client. It comes with a simple configuration dialog to set the update interval and client path.

It was inspired by navyrains folding-karamba theme.

Folding@Home is a distributed computing project to understand protein folding, misfolding and related diseases (http://folding.stanford.edu).

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

nmr-relax is designed for the study of the dynamics of proteins or other macromolecules though the analysis of NMR relaxation data. Its primary purpose is for the Lipari and Szabo model-free analysis of the R1 and R2 relaxation rates together with the steady state heteronuclear NOE. The program also supports relaxation curve fitting for the calculation of the R1 and R2 rates and their errors, the calculation of the NOE and its error, and reduced spectral density mapping.

Flexibility

The aim of relax is to provide a seamless and extremely flexible environment able to accept input in any format produced by other NMR software, able to faultlessly create input files, control, and read output from various programs including Modelfree and Dasha, output results in many formats, and visualise the data by controlling programs such as Grace, OpenDX, and MOLMOL.

All data analysis tools from optimisation to model selection to Monte Carlo simulations are inbuilt into relax. Therefore the use of additional programs is optional.

The power of Python

The flexibility of relax arises from the choice of either relaxs scripting capabilities or its Python prompt interface. Extremely complex scripts can be created from simple building blocks to fully automate data analysis. A number of sample scripts have been provided to help understand script construction. In addition, any of Pythons powerful features or functions can be incorporated as the script is executed as an arbitrary Python source file within relaxs environment.

CLC Free Workbench creates a software environment enabling users to make basic bioinformatics analyses and smooth data management, combined with excellent graphical viewing and output options.
Main features:
- GenBank searching and viewing (linear and circular views)
- Multiple alignment of DNA, RNA and proteins (2 alignment algorithms)
- Open reading frame determination
- Translation from DNA to proteins (all genetic translation tables)
- Reports with residue composition, molecular weight and iso electric point (for proteins)
- Neighbor-joining and UPGMA phylogenies
- Restriction site analysis and viewing
- Other reporting facilities
- Import/export to a number of data formats
- Launch of external files
- Detailed History Log

Optimization Algorithm Toolkit is a workbench and toolkit for developing, evaluating, and playing with classical and state-of-the-art optimization algorithms on standard benchmark problem domains; including reference algorithm implementations, graphing, visualizations and much more. The project was developed initially by Jason Brownlee as a part of his Ph.D. program.
The goal of this project is to deliver obscure-and-prevalent, old-and-new optimization algorithms from research literature to both research scientists and algorithm practitioners alike. Algorithms include biologically inspired approaches such as evolutionary algorithms (genetic algorithms), swarm algorithms (ants and particle swarm), and immune system algorithms.
Also included are more conventional approaches such as approaches inspired by physics including simulated annealing and extremal optimization. Problem domains include numerical function optimization, traveling salesman problems, and protein folding all with many standard benchmark instances taken from research literature.
A user-friendly graphical interface is provided to rapidly evaluate and compare algorithm and problem configurations, visualize algorithm behavior, and graph algorithm performance over time. A robust, modular, and extensible framework underlies the platform to facilitate the easy addition and modification of algorithms, addition of new problem domains and problem instances as well as facilitate more advanced algorithm experimentation.
The algorithm implementations are extensible and easily support modification and applicaition to varied problem domains. Please report any bugs, feature requests or include your own algorithms by accessing the services on the project home website. This is an open source project (released under the GPL) so the source code is available. The project was compiled with Java 1.5 (update 9).
Enhancements:
- This release includes many framework and graphical interface fixes, as well as a few new algorithms to play with.