amber_rosetta_methods
temp repo for rosetta-amber project
Science Score: 31.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
-
○DOI references
-
○Academic publication links
-
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (0.7%) to scientific vocabulary
Last synced: 10 months ago
·
JSON representation
·
Repository
temp repo for rosetta-amber project
Basic Info
- Host: GitHub
- Owner: hainm
- License: lgpl-3.0
- Language: Python
- Default Branch: master
- Size: 2.28 MB
Statistics
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
- Releases: 0
Created about 10 years ago
· Last pushed almost 10 years ago
Metadata Files
Readme
License
Citation
README.md
@arubenstein, @kmb413
This is my temporary repo for AMBER methods
Owner
- Name: Hai Nguyen
- Login: hainm
- Kind: user
- Location: New York
- Company: Schrodinger
- Website: http://hainm.github.io/
- Repositories: 246
- Profile: https://github.com/hainm
Technical Lead and Principal Scientist at Schrödinger.
Citation (citations.bib)
# ff14SBonlysc (and 14SB)
@Article{Maier15a,
author = {Maier, J.A. and Martinez, C. and Kasavajhala, K. and Wickstrom, L.
and Hauser, K.E. and Simmerling, C.},
title = {{ff14SB: Improving the Accuracy of Protein Side Chain and Backbone
Parameters from ff99SB}},
journal = {J. Chem. Theory Comput.},
volume = {11},
pages = {3696-3713},
year = {2015}
}
# GBNeck2
@Article{Nguyen2013,
author = {Nguyen, Hai and Roe, Daniel R. and Simmerling,
Carlos},
title = {{Improved Generalized Born Solvent Model Parameters
for Protein Simulations}},
journal = {J. Chem. Theory Comput.},
year = 2013,
volume = 9,
pages = {2020--2034},
}
# MMPBSA.py
@Article{Miller12,
author = {Miller, Bill R. and McGee, T. Dwight and Swails,
Jason M. and Homeyer, Nadine and Gohlke, Holger and
Roitberg, Adrian E.},
title = {{MMPBSA.py: An Efficient Program for End-State Free
Energy Calculations}},
journal = {J. Chem. Theory Comput.},
year = 2012,
volume = 8,
pages = {3314--3321}
}
# original MMPBSA method
@article{kollman2000calculating,
title={Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models},
author={Kollman, Peter A and Massova, Irina and Reyes, Carolina and Kuhn, Bernd and Huo, Shuanghong and Chong, Lillian and Lee, Matthew and Lee, Taisung and Duan, Yong and Wang, Wei and Donini, Oreola and Cieplak, Piotr and Srinivasan, Jaysharee and Case, David A. and Cheatham, Thomas E.},
journal={Accounts of chemical research},
volume={33},
number={12},
pages={889--897},
year={2000},
publisher={ACS Publications}
}
# AmberTools16
# Not a bib file
# D.A. Case, R.M. Betz, W. Botello-Smith, D.S. Cerutti, T.E. Cheatham, III, T.A. Darden, R.E. Duke, T.J. Giese, H. Gohlke, A.W. Goetz, N. Homeyer, S. Izadi, P. Janowski, J. Kaus, A. Kovalenko, T.S. Lee, S. LeGrand, P. Li, C. Lin, T. Luchko, R. Luo, B. Madej, D. Mermelstein, K.M. Merz, G. Monard, H. Nguyen, H.T. Nguyen, I. Omelyan, A. Onufriev, D.R. Roe, A. Roitberg, C. Sagui, C.L. Simmerling, J. Swails, R.C. Walker, J. Wang, R.M. Wolf, X. Wu, L. Xiao, D.M. York and P.A. Kollman (2016), AMBER 2016, University of California, San Francisco.
GitHub Events
Total
Last Year
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 0
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0