Amino Acid Alignment

A Mass Spectrometer B and Y ion labeling software for proteomics researchers. Peptide sequences can be read from a library and b and y ions will be calculated and sequence can be manipulated by the user (chem. mod. or amino acid mod.)

Gabedit is a Graphical User Interface to Gamess-US, Gaussian, Molcas, Molpro, MPQC and Q-Chem computational chemistry packages.Gabedit includes graphical facilities for generating keywords and options, molecule specifications and their input sections for even the most advanced calculation...

The sixth MATLAB Programming Contest, Protein, will run from November 6-13, 2002.This contest concerns a very simplified two-dimensional version of the protein folding problem. Given the amino acid sequence of a simplified protein, your job is to determine a final "optimally folded"...


Platforms: Matlab

Some of the logic from this program was provided from PDBRead.m by Sachin Nikumbh. The version I made is a trimmed down version of it that only outputs the data from one atom type (protein by default), and formats it as convenient cell variables. For smaller PDB files, the time difference between...


Platforms: Matlab

This contest concerns a very simplified two-dimensional version of the protein folding problem. Given the amino acid sequence of a simplified protein, your job is to determine a final "optimally folded" configuration. Each potential arrangement of the protein sequence is associated with an energy...


Platforms: Matlab

This application is an interactive simulation of gene expression that allows the user to: Explore a sample gene: Explore the correspondence between DNA, pre-mRNA, mature mRNA, and protein Map the functional elements of a gene. Create mutations in a gene and explore their effects. Design...


Platforms: Mac

Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid...


Platforms: Mac

Clusterfunc is a simple and fast method for Clustering functionally divergent genes by Functional Category. Changes in protein structure and function are reflected at the level of amino acid sequence. This principle suggests that functional divergence - changes in protein function, for instance...


Platforms: Mac

What is snpEff? It's a variant effect predictor tool, it predicts the effect of genetic variations (SNPs, insertions, deletions and MNPs). Release Candidate 1 Take a look at all the new features added Database download command, e.g. "java -jar snpEff.jar download GRCH37.64" RefSeq annotations...


Platforms: Mac

nebseq is a Python module for basic biological sequence manipulations. Import as usual >>> import nebseq Reverse complements The only note here is that revcomp does not check the input sequence to see if it looks like DNA or RNA. >>> nebseq.revcomp('ACGT') 'ACGT' >>>...


Platforms: *nix

The program "Satellite Antenna Alignment" is used to calculate the angles necessary for installing satellite dishes. The main difference from similar software is the possibility to calculate the position for all satellites at once. Thus, you get a clear picture about what satellites can be...


Platforms: Windows, Windows 8, Windows 7

Bio::Graphics::Glyph::alignment is the "alignment" glyph. SYNOPSIS See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >. This is identical to the "graded_segments" glyph, and is used for drawing features that consist of discontinuous segments. The color intensity of each segment is...


Platforms: *nix

Domino on Acid project is a weird colorful solitaire variant of dominoes that visualizes natural deduction. Superficially, Dominoes on Acid is a solitaire variant of Dominoes with weird colorful tiles (and this view is enough to play the game). But on a deeper level it is a GUI for natural...


Platforms: *nix

Acid EA Simply attach Acid EA to any chart to close all open positions Good for Professional Trader/Money Manager Managed Forex Accounts for clients with Meta Trader Broker. Your account traded by professionals. Bitter EA is a useful Expert Advisor for active trader who needs a precise...


Platforms: Windows, Other

This collection of functions is used to clean the alignment of m-code. It arranges all programming constructs in an easily readable manner.


Platforms: Matlab

This is a GUI tool for the alignment of Simulink blocks.


Platforms: Matlab

This extension allows for use of two other alignment methods which are otherwise not distributed with the CLC Workbench.


Platforms: Mac

Alignment API is a development tool that allows various ontology matchers to share the same format and interface for accessing matching results. Using ontologies is the privileged way to achieve interoperability among heterogeneous systems within the Semantic web. However, as the ontologies...


Platforms: *nix

Acid Dreams is a Windows screen saver which displays colorful moving patterns fairly quickly on most computers. The screen saver is very customizable, allowing for nearly endless possible combinations of different effects and colors. The small file size makes it an easy download. Its nostalgic...


Platforms: Windows

CurTiPot pH & Acid-Base Titration Curves. A powerful all-in-one freeware for pH calculation, experimental data analysis and simulation of titration curves of acids, bases, salts and buffers (from simple solutions to complex mixtures), with interpolation, smoothing and nonlinear regression....


Platforms: Windows