Download JAR files tagged by protein with all dependencies

strucmotif-search from group org.rcsb (version 0.19.8)

Real-time search for structural motifs in protein structures

Group: org.rcsb Artifact: strucmotif-search
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Artifact strucmotif-search
Group org.rcsb
Version 0.19.8
Last update 14. March 2024
Organization RCSB PDB
URL https://github.com/rcsb/strucmotif-search
License MIT License
Dependencies amount 0
Dependencies No dependencies
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biojava-protein-disorder from group org.biojava (version 7.1.1)

This module is for predicting disordered regions in protein sequences

Group: org.biojava Artifact: biojava-protein-disorder
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3 downloads

Artifact biojava-protein-disorder
Group org.biojava
Version 7.1.1
Last update 06. March 2024
Organization not specified
URL Not specified
License GNU LGPL v2
Dependencies amount 7
Dependencies biojava-core, slf4j-api, log4j-slf4j-impl, log4j-api, log4j-core, jakarta.xml.bind-api, jaxb-runtime,
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biozernike from group org.rcsb (version 1.0.0-alpha11)

Protein structure descriptors and alignment based on 3D Zernike moments.

Group: org.rcsb Artifact: biozernike
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Artifact biozernike
Group org.rcsb
Version 1.0.0-alpha11
Last update 02. February 2023
Organization not specified
URL http://shape.rcsb.org
License MIT License
Dependencies amount 7
Dependencies vecmath, j3d-core, slf4j-api, log4j-slf4j-impl, log4j-api, log4j-core, commons-math3,
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UniMod from group se.lth.immun (version 1.3.3)

Java implementation of the UniMod database of protein modifications. Extends se.lth.immun.Proteins.

Group: se.lth.immun Artifact: UniMod
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2 downloads

Artifact UniMod
Group se.lth.immun
Version 1.3.3
Last update 19. May 2016
Organization not specified
URL https://github.com/fickludd/proteomicore
License The Apache License, Version 2.0
Dependencies amount 1
Dependencies Proteins,
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jmztab from group io.github.bigbio.external (version 3.0.13)

JmzTab is a Java-based library to read mzTab files containing peptide/protein quantitative data

Group: io.github.bigbio.external Artifact: jmztab
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Artifact jmztab
Group io.github.bigbio.external
Version 3.0.13
Last update 17. August 2021
Organization not specified
URL https://github.com/bigbio/jmztab
License Apache 2.0
Dependencies amount 8
Dependencies junit, lombok, slf4j-api, jcl-over-slf4j, pride-utilities, px-submission-core, jmzidentml, commons-cli,
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interproscan from group uk.ac.ebi.interpro.scan (version 5.36-75.0)

InterProScan is the software package that allows sequences (protein and nucleic) to be scanned against InterPro's signatures.

Group: uk.ac.ebi.interpro.scan Artifact: interproscan
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Artifact interproscan
Group uk.ac.ebi.interpro.scan
Version 5.36-75.0
Last update 15. July 2019
Organization European Bioinformatics Institute
URL http://www.ebi.ac.uk/interpro/
License The Apache Software License, Version 2.0
Dependencies amount 10
Dependencies log4j, slf4j-log4j12, commons-logging, spring-jdbc, spring-context, spring-core, spring-orm, spring-test, commons-io, joda-time,
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pia from group io.github.bigbio.external (version 1.3.23)

Protein inference toolbox that contains algorithms to merge results from search engines in mass spectrometry and proteomics. It provides functionalities to compute FDR at different levels including PSM, peptide and Protein levels.

Group: io.github.bigbio.external Artifact: pia
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Artifact pia
Group io.github.bigbio.external
Version 1.3.23
Last update 02. December 2021
Organization Medizinisches Proteom-Center, Medical Bioinformatics
URL https://github.com/mpc-bioinformatics/pia
License BSD license
Dependencies amount 25
Dependencies lombok, picocli, commons-lang3, commons-collections4, jmzidentml, jaxb-api, jaxb-impl, jaxb-core, pride-mod, jmztab, px-submission-core, gson, pride-jaxb, fastutil, xxindex, mascotdatfile, xtandem-parser, biojava-ontology, BaseLib, CvtBaseLib, PDLibrary, sqlite4java, sqlite-jdbc, ehcache, utilities,
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phmm4weka from group nz.ac.waikato.cms.weka (version 1.1.3)

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.

Group: nz.ac.waikato.cms.weka Artifact: phmm4weka
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3 downloads

Artifact phmm4weka
Group nz.ac.waikato.cms.weka
Version 1.1.3
Last update 27. April 2012
Organization University of Waikato, Hamilton, NZ
URL http://weka.sourceforge.net/doc.packages/WekaExcel
License GNU General Public License 3
Dependencies amount 1
Dependencies weka-dev,
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jcore-bionlpgold-pred-gene-merge-ae from group de.julielab (version 2.6.0)

Given the gold BioNLP ST gene mentions and other gene mentions - possibly from gene recognizer - merges the two different sources of genes. For simplicity, this component employs two different types to represent genes. The BioNLP ST reader uses the de.julielab.jcore.types.Gene type. The other genes should be realized with de.julielab.jcore.types.Protein annotations.

Group: de.julielab Artifact: jcore-bionlpgold-pred-gene-merge-ae
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Artifact jcore-bionlpgold-pred-gene-merge-ae
Group de.julielab
Version 2.6.0
Last update 25. November 2022
Organization JULIE Lab Jena, Germany
URL https://github.com/JULIELab/jcore-base/tree/master/jcore-bionlpgold-pred-gene-merge-ae
License BSD 2-Clause
Dependencies amount 5
Dependencies jcore-utilities, slf4j-api, jcore-types, jcore-descriptor-creator, junit-jupiter-engine,
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xTracker from group org.bessantlab (version 2.0.1)

X-Tracker is a PSI-standards-compliant software framework for supporting mass spectrometry-based protein quantitation. Through an abstraction of the main steps involved in quantitation, X-Tracker should technically be able to support quantitation by means of all the current protocols, both at MS1 and/or MS2 level, and provide a flexible, platform-independent quantitation environment.

Group: org.bessantlab Artifact: xTracker
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Artifact xTracker
Group org.bessantlab
Version 2.0.1
Last update 09. March 2016
Organization not specified
URL http://x-Tracker.info
License The Apache License, Version 2.0
Dependencies amount 8
Dependencies xstream, jxl, xpp3, jmztab, Jama, jmzidentml, jmzquantml, jmzml,
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