Showing 93 open source projects for "protein"

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  • 1
    GESPA

    GESPA

    Accurately predicts disease association of single nucleotide mutations

    GESPA (GEnomic Single nucleotide Polymorphism Analyzer) is a bioinformatics tool for classifying Nonsynonymous Single Nucleotide Polymorphisms (nsSNPs). GESPA predicts if a nsSNP is pathogenic using reports from literature and various algorithms to assess conservation in orthologous and paralogous protein alignments. Using reports from literature, GESPA is also able to predict the phenotype of a nsSNP with high accuracy. The software can be used clinically to determine if observed nsSNPs...
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  • 2

    nextprot2rdf

    Convert NeXtprot protein data to the rdf format

    This project aims in providing open source tools to convert NeXtprot protein data (see http://www.nextprot.org) to RDF. It is meant as afeasibility study in the context of the IM project OpenPHACTS ( http://www.openphacts.org )
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  • 3
    Toolkit to examine the topology of a phylogenetic tree, place amino acid substitutions on specific branches, polarize them and compare amino acid sequences of homologous proteins to answer a wide range of questions about protein evolution.
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  • 4
    Java class libraries for structural biology development: includes protein format conversion tool, printf-based text formatting, Pred2ary secondary structure prediction, neural net library, Hooke-Jeeves global optimizer, and misc. math & statistics.
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  • 5

    HRDAG

    Framework for Hierarchical Graph Decomposition

    This is a framework used to decompose hierarchical graphs, i.e.,graphs which were created from or contain a hierarchy of modules. Each module is reused several times in the hierarchy. This may be useful to reverse-engineer human constructs like electronic equipment, manufactured machines, or bureaucratic hierarchies; but also to decompose natural constructs like gene-relation or protein-relation nets.
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  • 6
    CIG-P

    CIG-P

    CIG-P is a simple yet flexible data visualization tool

    .../1471-2105/15/344/ Previously known as PIVOT (Protein Interaction Visualization and Observation Tool)
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  • 7

    IQuant

    A pipeline for quantitative proteomics based upon isobaric tags

    IQuant is an automated pipeline for quantitative proteomics based upon isobaric tags. It integrates post-processing tool of protein identification and advanced statistical algorithms to process the MS/MS signals generated from the peptides labeled by isobaric tags for quantification. IQuant can run from a graphical user interface (GUI) as well as a command-line interface and work with both Windows and Linux system. This website contains the IQuant software, an example data labeled by iTRAQ...
    Downloads: 1 This Week
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  • 8
    FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.
    Downloads: 1 This Week
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  • 9
    SecStAnT

    SecStAnT

    Secondary Structure Analysis Tool for data selection and statistics

    SecStAnT is a tool for the automatic creation of data-sets of structures from Protein Data Bank (PDB) with user-defined structural composition, and for the calculation of their internal variables distributions. SecStAnT is able to 1. Select from PDB data sets of structures based on user specified secondary structures (defined based on internal PDB classification or on DSSP) and/or sequence motives. 2. Build Data-sets at different levels of resolution (all atoms, only backbone, only Cα...
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  • 10

    MatrixMaker

    Custom substitution matrix creator

    Create custom substitution matrices for BLAST protein search. Easy to use GUI based application.
    Downloads: 1 This Week
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  • 11
    Tools for mass spectrometry, especially for protein mass spectrometry and proteomics: Quantification tools, converters for Applied Biosystems (Q Star and Q Trap), calculation of in-silico fragmentation spectra, converter for Mascot result files
    Downloads: 0 This Week
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  • 12

    SLiMScape

    A Protein Short Linear Motif Analysis Plugin for Cytoscape

    SLiMScape adds Short linear motif discovery tools to Cytoscape, transforming it into a SLiM discovery platform. A tutorial is available at the following URL: http://bioware.ucd.ie/slimscape/
    Downloads: 0 This Week
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  • 13
    PIVOT

    PIVOT

    PIVOT is a simple yet flexible visualization data tool

    PIVOT is a simple yet flexible visualization tool based on Circos (Krzywinski et al., 2009), which offers a fast and aesthetical visualization of data and information. The Protein Interaction Visualization and Observation Tool (PIVOT) was developed specifically for the visualization of protein interaction. It is difficult to spot the proteins that have an interaction when given a large list of proteins but with PIVOT, it is easy to identify the them at a glance. PIVOT displays an image showing...
    Downloads: 1 This Week
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  • 14
    GEPETTO - Gene Prioritization in Java

    GEPETTO - Gene Prioritization in Java

    GEPETTO (GEne Prioritization ExTended TOol)

    GEPETTO (GEne PrioriTization ExTended TOol) is an original open-source framework, distributed under the LGPL license, for gene selection and prioritization on a desktop computer that ensures confidentiality of personal data. It takes advantage of the data integration capabilities in the SM2PH-Central Framework(KD4v,MSV3d,BIRD,..), combined with in-house developed gene prioritization methods. It currently incorporates six prioritization modules, based on gene sequence, protein-protein...
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  • 15

    Autmated Peptide Screening

    Screening peptides for MHC and/or MHC-T cell receptor affinity

    ... in. A detailed method for determining the peptide ligand for any sequenced and modeled T cell receptor will be published and link added at some point. These scripts are written quickly in a couple weeks to meet a task and could be re-written more eloquently. I may or may not work on this project again, the goal would be to introduce amino acids into any protein in openCL to allow automated design on GPU's.Limits-The standard PDB codes used slightly modified, proline not at angles, peptide shld be linear,
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  • 16

    MDL2SBML

    Convert MCell input files into SBML

    MCell is a Monte-Carlo simulator for spatial stochastic modelling of protein interactions. It requires a specific input file format called Model Description Language (MDL). MDL2SBML is a converter that translates MDL into the more widely recognised Systems Biology Markup Language (SBML) in order to facilitate model sharing and analysis with a wider range of tools. MDL2SBML translates molecule definitions, reactions and variables from MDL to SBML. MCell concepts that have (as of yet...
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  • 17

    Exact Subgraph Matching Algorithm

    Exact Subgraph Matching Algorithm for Dependency Graphs

    The subgraph matching problem (subgraph isomorphism) is NP-complete. We designed a simple exact subgraph matching (ESM) algorithm for dependency graphs using a backtracking approach. The total worst-case algorithm complexity is O(n^2 * k^n) where n is the number of vertices and k is the vertex degree. We have demonstrated the successful usage of our algorithm in three biomedical relation and event extraction applications: BioNLP 2011 shared tasks on event extraction, Protein-Residue...
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  • 18
    GenLab abbreviation of Genetics Laboratory .It is a user-friendly bioinformatics tool to support your bioinformatics lab work. GenLab creates a software user-friendly environment, which makes users to make a large number of protein, DNA, and RNA sequence analysis and excellent graphical viewing. It also provides powerful environment for simulations of Protein 3D molecular models. GenLab typically provides: •User-friendly graphical tools used for finding and working with relevant regions...
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  • 19
    This Java software implements Profile Hidden Markov Models (PHMMs) for protein classification for the WEKA workbench. Standard PHMMs and newly introduced binary PHMMs are used. In addition the software allows propositionalisation of PHMMs.
    Downloads: 0 This Week
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  • 20
    ProteinTracker

    ProteinTracker

    Protein Reagent Tracking and Request

    A web based application to track protein related reagents including DNA constructs, cell lines, supes, and purified proteins. Supports creating, tracking, and prioritizing requests for transfections and DNA. Includes search and PDF reports.
    Downloads: 0 This Week
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  • 21
    IMPACT

    IMPACT

    Integrated Multiprogram Platform for Analyses in ConTest

    Graphical User Interface for a software used to assess adaptive evolution in protein-coding genes. Makes use of several known bioinformatics software. IMPACT is free software, targeted to the scientific community. Maldonado E, Dutheil JY, da Fonseca RR, Vasconcelos V, Antunes A (2011) IMPACT: Integrated Multiprogram Platform for Analyses in ConTest. Journal of Heredity, 102 (3): 366-369. doi: https://doi.org/10.1093/jhered/esr003
    Downloads: 0 This Week
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  • 22
    JPS Java Protein Surface
    From a pdb file, the java program calculates the van der Walls surface of the protein in the file.
    Downloads: 0 This Week
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  • 23
    Software environment for manipulation of DNA and protein sequences in a phylogenetic context.
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  • 24
    JNutrition is a Nutrition Manager. Create meal plans and meals and let it calculate the total amount of calories, carbs, protein and fat of them.
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  • 25
    Protein Data Bank transformed into an SQL database with a very powerful search engine and a rich web interface. The engine combines chemical, sequence and 3D structure searches. The interface provides statistics, sequence and 3D structure alignments.
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