BioJava-ModFinder

BioJava-ModFinder effectively identifies over 400 types of protein modifications found in 3D structures stored in the Protein Data Bank. It categorizes these modifications into modified residues, attachment modifications, and cross-links. This package includes a systematic method that allows users to identify these modifications and adds protein modification annotations to the sequence diagram and structure display, all with the help of the RCSB PDB web application.

Topic

Protein structure analysis;Protein structural motifs and surfaces;Protein modifications

Detail

  • Operation: Protein modelling (mutation)

  • Software interface: Graphical user interface

  • Language: Java

  • License: GNU Lesser General Public License v2.1

  • Cost: Free

  • Version name: -

  • Credit: Google Summer of Code 2010 program, National Institutes of Health, National Science Foundation, National Institute of General Medical Sciences (NIGMS), Office of Science, Department of Energy (DOE), National Library of Medicine (NLM), National Cancer Institute (NCI), National Institute of Neurological Disorders and Stroke (NINDS), the National Institute of Diabetes & Digestive & Kidney Diseases (NIDDK).

  • Input: -

  • Output: -

  • Contact: Peter W Rose pwrose@ucsd.edu

  • Collection: -

  • Maturity: -

Publications

  • BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank.
  • Gao J, et al. BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank. BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank. 2017; 33:2047-2049. doi: 10.1093/bioinformatics/btx101
  • https://doi.org/10.1093/bioinformatics/btx101
  • PMID: 28334105
  • PMC: PMC5870676

Download and documentation

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