Ecosyste.ms: Issues

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GitHub / nrbennet/dl_binder_design issues and pull requests

#45 - Examples and Envs

Pull Request - State: closed - Opened by nrbennet about 1 year ago

#45 - Examples and Envs

Pull Request - State: closed - Opened by nrbennet about 1 year ago

#44 - Add Preetham's fix for addFIXEDlabels.py

Pull Request - State: closed - Opened by nrbennet about 1 year ago

#44 - Add Preetham's fix for addFIXEDlabels.py

Pull Request - State: closed - Opened by nrbennet about 1 year ago

#42 - runlist no output

Issue - State: closed - Opened by jelka71 about 1 year ago - 1 comment

#42 - runlist no output

Issue - State: closed - Opened by jelka71 about 1 year ago - 1 comment

#41 - af2_complex_error

Issue - State: closed - Opened by pedrovaliente79 over 1 year ago - 2 comments

#41 - af2_complex_error

Issue - State: closed - Opened by pedrovaliente79 over 1 year ago - 2 comments

#40 - af2_complex running error

Issue - State: closed - Opened by pedrovaliente79 over 1 year ago - 1 comment

#40 - af2_complex running error

Issue - State: closed - Opened by pedrovaliente79 over 1 year ago - 1 comment

#39 - Conda environment setup does not work

Issue - State: closed - Opened by brystingjosephine over 1 year ago - 1 comment

#39 - Conda environment setup does not work

Issue - State: closed - Opened by brystingjosephine over 1 year ago - 1 comment

#36 - for symmetric multimers

Issue - State: closed - Opened by jongseo-park over 1 year ago - 1 comment

#36 - for symmetric multimers

Issue - State: closed - Opened by jongseo-park over 1 year ago - 1 comment

#35 - Add force_monomer option to predict.py

Pull Request - State: closed - Opened by nrbennet over 1 year ago

#35 - Add force_monomer option to predict.py

Pull Request - State: closed - Opened by nrbennet over 1 year ago

#34 - Force monomer

Pull Request - State: closed - Opened by nrbennet over 1 year ago

#34 - Force monomer

Pull Request - State: closed - Opened by nrbennet over 1 year ago

#33 - GPU error: Segmentation fault (core dumped)

Issue - State: closed - Opened by ning-2022 over 1 year ago - 3 comments

#33 - GPU error: Segmentation fault (core dumped)

Issue - State: closed - Opened by ning-2022 over 1 year ago - 3 comments

#32 - Deep Learning Binder Results

Issue - State: open - Opened by okanders over 1 year ago - 2 comments

#32 - Deep Learning Binder Results

Issue - State: open - Opened by okanders over 1 year ago - 2 comments

#31 - tensorflow 2.12.1 requires jax>=0.3.15

Issue - State: closed - Opened by frankligy over 1 year ago - 2 comments

#31 - tensorflow 2.12.1 requires jax>=0.3.15

Issue - State: closed - Opened by frankligy over 1 year ago - 2 comments

#30 - More than two chains?

Issue - State: open - Opened by okanders over 1 year ago - 2 comments

#30 - More than two chains?

Issue - State: open - Opened by okanders over 1 year ago - 2 comments

#29 - Jupyter notebook available?

Issue - State: closed - Opened by slives-lab over 1 year ago - 1 comment

#29 - Jupyter notebook available?

Issue - State: closed - Opened by slives-lab over 1 year ago - 1 comment

#28 - Adapting initial guess without Rosetta

Issue - State: closed - Opened by okanders over 1 year ago - 1 comment

#28 - Adapting initial guess without Rosetta

Issue - State: closed - Opened by okanders over 1 year ago - 1 comment

#27 - How to set seqs_per_struct >=2 when relax_cycles =1 ?

Issue - State: closed - Opened by Samuel-gwb over 1 year ago - 3 comments

#27 - How to set seqs_per_struct >=2 when relax_cycles =1 ?

Issue - State: closed - Opened by Samuel-gwb over 1 year ago - 3 comments

#26 - Major Refactor

Pull Request - State: closed - Opened by nrbennet over 1 year ago

#26 - Major Refactor

Pull Request - State: closed - Opened by nrbennet over 1 year ago

#25 - Question about AlphaFold initial guess

Issue - State: open - Opened by sangzhe over 1 year ago - 1 comment

#25 - Question about AlphaFold initial guess

Issue - State: open - Opened by sangzhe over 1 year ago - 1 comment

#24 - Why can't GPU be used for inference?

Issue - State: closed - Opened by aw10279 over 1 year ago - 1 comment

#24 - Why can't GPU be used for inference?

Issue - State: closed - Opened by aw10279 over 1 year ago - 1 comment

#23 - Fixed Issue with ProteinMPNN-FR Tag Numbering

Pull Request - State: closed - Opened by nrbennet over 1 year ago

#23 - Fixed Issue with ProteinMPNN-FR Tag Numbering

Pull Request - State: closed - Opened by nrbennet over 1 year ago

#22 - interfaceAF2predict.py

Issue - State: open - Opened by yebinase over 1 year ago - 1 comment

#22 - interfaceAF2predict.py

Issue - State: open - Opened by yebinase over 1 year ago - 1 comment

#21 - Possible relax protocol issue

Issue - State: open - Opened by data2code over 1 year ago

#21 - Possible relax protocol issue

Issue - State: open - Opened by data2code over 1 year ago

#20 - pyjd2 in silentfrompdb

Issue - State: closed - Opened by youngh81 over 1 year ago - 3 comments

#20 - pyjd2 in silentfrompdb

Issue - State: closed - Opened by youngh81 over 1 year ago - 3 comments

#19 - IndexError in dl_interface_design.py

Issue - State: open - Opened by hklz over 1 year ago

#19 - IndexError in dl_interface_design.py

Issue - State: open - Opened by hklz over 1 year ago

#17 - Fix to bug in fixed res argument

Pull Request - State: closed - Opened by nrbennet over 1 year ago

#16 - Running without silent tools?

Issue - State: closed - Opened by jvenderley-lilly over 1 year ago - 1 comment

#15 - Fixing residues of binder chain in ProteinMPNN

Issue - State: closed - Opened by alllirik over 1 year ago - 1 comment

#14 - Several Bug Fixes

Pull Request - State: closed - Opened by nrbennet over 1 year ago

#13 - issue with silentfrompdbs

Issue - State: closed - Opened by JA-Hull over 1 year ago - 1 comment

#12 - Some questions about pdb_interfaceAF2predict.py

Issue - State: open - Opened by LDAIprotein over 1 year ago - 2 comments

#10 - Add multi seq MPNN script

Pull Request - State: closed - Opened by nrbennet over 1 year ago

#9 - Add writing of per-residue plddt to af2 scripts

Pull Request - State: closed - Opened by nrbennet over 1 year ago

#8 - Column concatenation in .pdb file when residue index > 999

Pull Request - State: closed - Opened by alllirik over 1 year ago - 2 comments

#7 - Issue with silent file index

Issue - State: closed - Opened by arikat over 1 year ago - 2 comments

#6 - Error when using silent tools

Issue - State: closed - Opened by Samuel-gwb over 1 year ago

#5 - Change some functions in AF2 to allow for use with newer versions of JAX

Pull Request - State: closed - Opened by nrbennet over 1 year ago

#4 - Running with alternate AF2 models

Issue - State: closed - Opened by swanss over 1 year ago - 2 comments

#3 - -checkpoint_path

Issue - State: closed - Opened by gha2012 over 1 year ago - 6 comments

#2 - For dl_interface_design.py

Issue - State: closed - Opened by Lyang556 over 1 year ago - 1 comment

#1 - for interfaceAF2predict.py

Issue - State: closed - Opened by jongseo-park over 1 year ago - 2 comments