https://github.com/choderalab/ensembler
Automated omics-scale protein modeling and simulation setup.
Science Score: 13.0%
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Low similarity (14.7%) to scientific vocabulary
Keywords
Repository
Automated omics-scale protein modeling and simulation setup.
Basic Info
- Host: GitHub
- Owner: choderalab
- License: gpl-2.0
- Language: Python
- Default Branch: master
- Homepage: http://ensembler.readthedocs.io/
- Size: 30.7 MB
Statistics
- Stars: 52
- Watchers: 22
- Forks: 21
- Open Issues: 41
- Releases: 0
Topics
Metadata Files
README.md
Ensembler
Software pipeline for automating omics-scale protein modeling and simulation setup.
Online documentation
- Go to the official online documentation.
- Read a preprint of the paper on bioRxiv.
- See the example dataset from modeling all human tyrosine kinases.
Authors
- Daniel L. Parton | daniel.parton@choderalab.org
- John D. Chodera | john.chodera@choderalab.org
- Patrick B. Grinaway | patrick.grinaway@choderalab.org
Overview of pipeline
- Retrieve protein target sequences and template structures.
- Build models by mapping each target sequence onto every available template structure, using Modeller.
- Filter out non-unique models (based on a RMSD cutoff).
- Refine models with implicit solvent molecular dynamics simulation.
- Refine models with explicit solvent molecular dynamics simulation.
- (optional) Package and/or compress the final models, ready for transfer or for set-up on other platforms such as Folding@Home.
Installation
First go to the Modeller website and get a license key (registration required; free for academic non-profit institutions).
Save the key as an environment variable:
bash
export KEY_MODELLER=XXX
Then, using conda (installs all dependencies except the optional dependency Rosetta):
bash
conda config --add channels omnia
conda config --add channels salilab
conda install ensembler
From source:
bash
git clone https://github.com/choderalab/ensembler.git
cd ensembler
python setup.py install
Dependencies
- OpenMM - https://simtk.org/home/openmm
- Modeller - http://salilab.org/modeller/
- mdtraj - http://mdtraj.org/
- MSMBuilder - http://msmbuilder.org/
- PDBFixer - https://github.com/pandegroup/pdbfixer
- BioPython
- NumPy
- lxml
- PyYAML
- docopt
- mock
- Optional:
- Rosetta (optional, for template loop reconstruction) - https://www.rosettacommons.org/software
- MPI4Py (allows many Ensembler functions to be run in parallel using MPI)
- Pandas (required for certain analysis functions)
- subprocess32 (if using Python 2)
- PyMOL (optional, for model alignment/visualization) - http://www.pymol.org/
Recommended approach is to install using conda (https://store.continuum.io/cshop/anaconda/). This will install all dependencies except for the optional dependency Rosetta, which must be installed separately by the user.
Owner
- Name: Chodera lab // Memorial Sloan Kettering Cancer Center
- Login: choderalab
- Kind: organization
- Email: john.chodera@choderalab.org
- Location: Memorial Sloan-Kettering Cancer Center, Manhattan, NY
- Website: http://choderalab.org
- Repositories: 269
- Profile: https://github.com/choderalab
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