Free protein structure software for linux

pokertimer project is just a very little script for poker-turnaments.

Just execute the file. (You may want to configure the file to fit your desired blind-structure).

NOC 3.01 is a program to visualize and analyze protein structure, for crystallographic modeling and mapping, for Gromacs/Amber MD trajectories viewing and analysis. NOC is an open source project and is distributed with precompiled binaries for MS Windows, MacOSX, Linux/Unix.

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.)

Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. Jmol is cross-platform, running on Linux/Unix, Mac OS X, and Windows systems.
- The JmolApplet is a web browser applet that can be integrated into web pages.
- The Jmol application is a standalone Java application that runs on the desktop.
- The JmolViewer is a development tool kit that can be integrated into other Java applications.
Main features:
- Free, open-source software licensed under the GNU Lesser General Public License
- Applet, Application, and Systems Integration Component
- Cross-platform
- Supports all major web browsers
- High-performance 3D rendering with no hardware requirements
- File formats
- Animations
- Vibrations
- basic unit-cell support
- schematic shapes for secondary structures
- measurements
- RasMol/Chime scripting language support
- JavaScript support library
- Exports to .jpg, .pdf, and PovRay
Jmol v10 is a complete rearchitecture and rewrite of Jmol, undertaken in the Spring of 2003, with the specific goal of developing Jmol into a replacement for the Chime Plug-in.
Jmol v10 retains most of the features and functionality of the previous Jmol releases while offering significant enhancments in the following areas:
- true 3D graphics engine that requires no special hardware
- 24 bit color with accurate lighting and shading
- substantially higher rendering performance
- handles large macromolecules with excellent performance
- protein/nucleic acid secondary structure graphics
- RasMol/Chime script compatibility
Enhancements:
- bug fix: isosurface color -- not operating for some isosurface types
- bug fix: isosurface "xxxx.cube" -- not assigning proper default colors
- bug fix: gamess reader MO fix
- bug fix: state save of STRUCTURE misplaced

mcl-algorithm is a scalable cluster algorithm for graphs based on stochastic flow.
The flow process employed by the algorithm is mathematically sound and intrinsically tied to cluster structure in graphs, which is revealed as the imprint left by the process.
The threaded implementation has handled graphs of up to one million nodes within hours, and is widely used in the field of protein family analysis. It comes with a wide range of sibling utilities for handling and analyzing graphs, matrices, and clusterings.
The MCL algorithm simulates flow using (alternating) two simple algebraic operations on matrices. Its formulation is simple and elegant. There are no high-level procedural instructions for assembling, joining, or splitting of groups - cluster structure is bootstrapped via a flow process that is inherently affected by any cluster structure present.
The first operation used by MCL is expansion, which coincides with normal matrix multiplication. Expansion models the spreading out of flow, it becoming more homogeneous. The second is inflation, which is mathematically speaking a Hadamard power followed by a diagonal scaling. Inflation models the contraction of flow, it becoming thicker in regions of higher current and thinner in regions of lower current. The MCL process causes flow to spread out within natural clusters and evaporate inbetween different clusters.
- By varying parameters, clusterings on different scales of granularity can be found. The number of clusters can not and need not be specified in advance, but the algorithm can be adapted to different contexts.
- The issue how many clusters? is not dealt with in an arbitrary manner, but rather by strong internal logic. Cluster structure leaves its marks on the flow process simulated by the algorithm, and the flow parameters control the granularity of the cluster imprint.
- The limit of the MCL process (the process simulated by the algorithm) is in general extremely sparse, and the iterands are sparse in a weighted sense. This gives the means to scale the algorithm drastically, leading to a worst-case complexity of order Nk^2, where N is the number of nodes of the input graph, and where k is a threshold for the number of resources allocated per node.
- The rate of convergence of the MCL process, and projection of the iterands afterwards onto the resulting clustering, give hooks for unsupervised parameter adjustment.
- The iterands of the MCL process have structural properties which allow a cluster interpretation, and which generalize the mapping of MCL limits onto clusterings. The mathematics associated with the MCL process shows that there is an intrinsic relationship between the MCL process and cluster structure in graphs. This is very valuable given the many heuristic approaches in cluster analysis.
Enhancements:
- Numerous cleanups in much of the code.
- Improvements in caching intermediate results.

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

Folding@Gnome project is an applet is a GUI that keeps track of the background protein folding progress done by Folding@Home

The Folding@Gnome applet is merely a GUI in which you can adjust your Folding@Home settings and view the folding progress. Folding@Home is a background process that uses spare CPU cycles to calculate the folding of proteins. For more info, please visit Stanfords Folding@Home homepage.

Bio::Tools::Run::PiseApplication::consensus is a Perl module.

Bioperl class for:

CONSENSUS Identification of consensus patterns in unaligned DNA and protein sequences (Hertz, Stormo)

References:

G.Z. Hertz and G.D. Stormo. Identification of consensus patterns in unaligned DNA and protein sequences: a large-deviation statistical basis for penalizing gaps. In: Proceedings of the Third International Conference on Bioinformatics and Genome Research (H.A. Lim, and C.R. Cantor, editors). World Scientific Publishing Co., Ltd. Singapore, 1995. pages 201--216.

Parameters:

(see also:
http://bioweb.pasteur.fr/seqanal/interfaces/consensus.html
for available values):


consensus (Excl)
Program to run

sequence (Sequence)
Sequences file (-f)
pipe: seqsfile

width (Integer)
Width of pattern (consensus only) (-L)

out (String)

consensus_matrix (String)

complement (Excl)
Complement of nucleic acid sequences (-c)

ascii_alphabet (InFile)
Alphabet and normalization information (if not DNA) (-a)

prior (Switch)
Use the designated prior probabilities of the letters to override the observed frequencies (-d)

dna (Switch)
Alphabet and normalization information for DNA

protein (Switch)
Alphabet and normalization information for protein

queue (Integer)
Maximum number of matrices to save between cycles of the program -- ie: queue size (-q)

standard_deviation (Float)
Number of standard deviations to lower the information content at each position before identifying information peaks (mandatory for wconsensus) (-s)

progeny (Excl)
Save the top progeny matrices (-pr1)

linearly (Switch)
Seed with the first sequence and proceed linearly through the list (-l)

max_cycle_nb (Integer)
Maximum repeat of the matrix building cycle (-n or -N)

max_cycle (Excl)
How many words per matrix for each sequence to contribute (-n or -N)

distance (Integer)
Minimum distance between the starting points of words within the same matrix pattern (-m)

terminate (Integer)
Terminate the program this number of cycles after the current most significant alignment is identified (-t)

terminal_gap (Excl)
Permit terminal gaps (-pg) (wconsensus only)

top_matrices (Integer)
Number of top matrices to print (-pt)

final_matrices (Integer)
Number of final matrices to print (-pf)