https://github.com/unixjunkie/seed
mirror of https://gitlab.com/CaflischLab/SEED.git
https://github.com/unixjunkie/seed
Last synced: 10 months ago
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mirror of https://gitlab.com/CaflischLab/SEED.git
- Host: GitHub
- URL: https://github.com/unixjunkie/seed
- Owner: UnixJunkie
- License: gpl-3.0
- Created: 2020-08-26T03:03:28.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2020-08-26T03:04:16.000Z (over 5 years ago)
- Last Synced: 2025-01-31T09:31:14.398Z (11 months ago)
- Language: C++
- Size: 18.6 MB
- Stars: 2
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# SEED (Solvation Energy for Exhaustive Docking) version 4.0.0
SEED is a program for fragment docking with force-field based evaluation of binding energy.
The new SEED documentation is now online at: [https://caflischlab-seed.readthedocs.io/en/latest/](https://caflischlab-seed.readthedocs.io/en/latest/)!
For details about the energy models implemented in SEED please refer to the original publications and to the pdf user manual (seed_4.0.0_doc.pdf).
### Installation ###
cd to directory src and make SEED with the following command (you may have to modify the Makefile.local):
```sh
make seed
```
The binary is compiled into the bin directory.
### Run SEED ###
Run SEED with the following command:
```sh
./seed_4 seed.inp >& log
```
You can find an example seed.inp and seed.par, along with the results of simple study cases,
in the test_cases folder.
### Citations ###
Review of the applications of SEED in the period 1999-2018, includes a discussion on its strenghts/weaknesses in light of our experience:
* J.-R. Marchand, and A. Caflisch. In silico fragment-based drug design with SEED.
European Journal of Medicinal Chemistry, 156:907-917, 2018.
Original paper describing SEED:
* N. Majeux, M. Scarsi, J. Apostolakis, C. Ehrhardt, and A. Caflisch. Exhaustive docking of
molecular fragments on protein binding sites with electrostatic solvation.
Proteins: Structure, Function and Genetics, 37:88-105, 1999.
The description of the fast energy evaluation is in the second SEED paper:
* N. Majeux, M. Scarsi, and A. Caflisch. Efficient electrostatic solvation model for protein-
fragment docking.
Proteins: Structure, Function and Genetics, 42:256-268, 2001.