GDFuzz3D

GDFuzz3D is a software tool that predicts protein 3D structures from predicted contact maps using a new multi-step protocol. The method is based on a novel distance function acting on a fuzzy residue proximity graph that predicts a 2D distance map from a 2D predicted contact map. The application of a Multi-Dimensional Scaling algorithm transforms that predicted 2D distance map into a coarse 3D model, which is further refined by typical modeling programs into an all-atom representation. GDFuzz3D generates more accurate 3D models than the state-of-the-art method for 3D structure reconstruction from 2D maps, with an average improvement of 4.87 Å in terms of RMSD. The tool is freely available as a server and standalone version.

Topic

Molecular modelling;Proteins;Protein structure analysis

Detail

  • Operation: Protein structure prediction

  • Software interface: Web user interface

  • Language: Mathematica

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: European Research Council, the European Social Fund through Subcarpathian Doctoral Stipend Fund, the Polish National Science Center, the ‘Ideas for Poland’ fellowship from the Foundation for Polish Science, EU structural funds.

  • Input: -

  • Output: -

  • Contact: michalp@genesilico.pl;lukasz.kozlowski.lpk@gmail.com

  • Collection: -

  • Maturity: -

Publications

  • GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function.
  • Pietal MJ, et al. GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function. GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function. 2015; 31:3499-505. doi: 10.1093/bioinformatics/btv390
  • https://doi.org/10.1093/bioinformatics/btv390
  • PMID: 26130575
  • PMC: -

Download and documentation

    Currently not available or not maintained.

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