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Identification of ligand binding pathways by a multi-objective genetic algorithm
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README.rst

GPathFinder

https://readthedocs.org/projects/gpathfinder/badge/?version=latest https://img.shields.io/github/license/insilichem/gpathfinder.svg?color=orange

https://img.shields.io/static/v1.svg?label=platform&message=linux%20|%20macOS&color=lightgrey

GPathFinder is an extension built over GaudiMM core to allow the identification of ligand binding pathways at atomistic level.

GPathFinder logo

Features

Different options for generate pathways

  • Unbinding routes from a known binding site
  • Binding routes to a known binding site
  • Channel analysis (given starting and final points)

Flexibility for the ligand

  • Dihedral angles

Different levels of flexibility for the receptor

  • Side-chain flexibility using rotamer libraries
  • Global movements by Normal Mode Analysis sampling

Different options for evalute and optimize the solutions

  • Steric clashes
  • Vina scoring function
  • Smoothness of the ligand movements

NEW!

Version 1.0.1 25th July 2019

  • New summary.csv file in the output with score data of all the solutions.
  • New format for the .pdb files of the output that can be imported as a MD movie in UCSF Chimera.
  • New trajectory.pdb file in the output. For each solution, shows the trajectory of the ligand, taking its center as a reference.
  • Command to lauch the program is now gpath run instead of gaudi run to ensure compatibility with GaudiMM.
  • Similarity between solutions is calculated now at each generation, to avoid some cases where repeated or very similar solutions appeared, especially when using only clashes evaluation.

Documentation and support

Documentation source is available in docs/ subdirectory, and also compiled as HTML at this webpage.

If you need help with GPathFinder, please use the issues page of our GitHub repo. You can drop me a message at joseemilio.sanchez@uab.cat too.

Developer friendly

If the provided genes and objectives are not enough, you can always code your own ones. Check out the developer docs!

License

GPathFinder and GaudiMM are licensed under the Apache License, Version 2.0. Check the details in the LICENSE file.

History of versions

  • v1.0.1: 25th July 2019

New summary.csv file in the output with score data of all the solutions.

New format for the .pdb files of the output that can be imported as a MD movie in UCSF Chimera.

New trajectory.pdb file in the output. For each solution, shows the trajectory of the ligand, taking its center as a reference.

Command to lauch the program is now gpath run instead of gaudi run to ensure compatibility with GaudiMM.

Bug fix: similarity between solutions is calculated now at each generation, to avoid some cases where repeated or very similar solutions appeared, especially when using only clashes evaluation.

  • v1.0.0: Release version. Used in the benchmark and cases study of the article.

OS Compatibility

GPathFinder is compatible with Linux and macOS.

If you find some dificulties when installing it in a concrete distribution, please use the issues page to report them.

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