issues
search
choderalab
/
ensembler
Automated omics-scale protein modeling and simulation setup.
http://ensembler.readthedocs.io/
GNU General Public License v2.0
52
stars
21
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Allow optional user-specified substitution matrix names
#45
jchodera
closed
9 years ago
1
Added simple test for `refine_explicit_md`
#44
danielparton
closed
9 years ago
1
Expose additional arguments to simtk.openmm.app.createSystem() in explicit solvent refinement API
#43
jchodera
closed
9 years ago
3
Is there a way in gather_templates to use an input file for query, like a pre-made list of PDBs?
#42
sonyahanson
opened
9 years ago
1
1.0.4 release
#41
danielparton
closed
9 years ago
0
Allow user to specify one or more forcefield (ffxml) files during implicit and explicit solvent steps
#40
jchodera
opened
9 years ago
0
Giving users flexibility in specifying residue numbering
#39
jchodera
opened
9 years ago
2
Ability to fix protonation states of specific residues
#38
danielparton
closed
9 years ago
3
Add ability to make models that have same hydrogens as final trajectories.
#37
sonyahanson
opened
9 years ago
1
Some test failures on `osx`
#36
jchodera
closed
9 years ago
3
Add an option to specify (or "pin") the protonation states / variants of specified residues
#35
jchodera
opened
9 years ago
8
Fixing travis / conda 1.0.3 release via some direct commits
#34
jchodera
opened
9 years ago
3
Selecting protonation states?
#33
jchodera
opened
9 years ago
0
Version 1.0.3 release
#32
danielparton
closed
9 years ago
1
Package ensembler models for FAH using renumbered residues
#31
jchodera
opened
9 years ago
2
Packaging Ensembler models for FAH
#30
jchodera
opened
9 years ago
0
Version 1.0.3 release
#29
danielparton
closed
9 years ago
0
Modified build to install Modeller via conda
#28
danielparton
closed
9 years ago
0
Update to use modeller conda package
#27
jchodera
opened
9 years ago
2
Trying to get Travis to work properly with PRs
#26
danielparton
closed
9 years ago
0
Updated README to add link to bioRxiv manuscript and Dryad database.
#25
jchodera
closed
9 years ago
5
Add option to specify number of waters we should end up with
#24
jchodera
opened
9 years ago
0
Include a kinase family tree figure in paper, with TKs highlighted?
#23
jchodera
opened
9 years ago
1
Disulfide bonds
#22
danielparton
opened
9 years ago
1
Model residue variants are not consistent for target FAK2_HUMAN_D0
#21
danielparton
closed
9 years ago
8
Conditional imports in nosetests?
#20
kyleabeauchamp
opened
9 years ago
0
py3k support
#19
kyleabeauchamp
opened
9 years ago
2
Default pH for refinement stages is currently 8 - change to 7?
#18
danielparton
opened
9 years ago
4
Add travis continuous integration?
#17
jchodera
closed
9 years ago
3
Added prominent link to readthedocs in README.md
#16
jchodera
closed
9 years ago
1
Added functionality for selecting templates by sequence identity cutoff
#15
danielparton
closed
9 years ago
0
Omnia binstar
#14
jchodera
closed
9 years ago
2
Rosetta loopmodel gets stuck on some models
#13
danielparton
closed
9 years ago
11
SIFTS file format has changed
#12
danielparton
closed
9 years ago
3
Write test runner script
#11
danielparton
closed
9 years ago
2
Investigate alternative loop modeling schemes
#10
jchodera
closed
9 years ago
1
Create aggregated multi model PDB files
#9
jchodera
closed
9 years ago
1
Timings for various stages?
#8
jchodera
closed
9 years ago
5
New name?
#7
jchodera
closed
9 years ago
28
Rewriting Spark-MSMSeeder
#6
pgrinaway
closed
9 years ago
1
Default Collision Frequency
#5
kyleabeauchamp
closed
9 years ago
23
Major refactoring
#4
danielparton
closed
10 years ago
1
Write good driver script
#3
pgrinaway
closed
9 years ago
1
Serialization problems
#2
pgrinaway
closed
9 years ago
2
Take a closer look at pH and protonation state selection
#1
danielparton
opened
10 years ago
2
Previous