bytedance/protenix issues and pull requests

#54 - Muti-device Running

Issue - State: open - Opened by Lin-zeng 5 days ago - 1 comment

#53 - Posebuster v2 evaluation issue

Issue - State: open - Opened by kanghw0325 8 days ago - 3 comments

#52 - WeChat group for Chinese users

Issue - State: open - Opened by zhangyuxuann 9 days ago - 1 comment

#51 - Evaluation issue

Issue - State: open - Opened by Luchixiang 11 days ago - 1 comment

#50 - CIF structure file format error

Issue - State: open - Opened by yx0516 11 days ago - 3 comments

#49 - MSA error

Issue - State: closed - Opened by shienliu 13 days ago - 5 comments

#48 - GLA ptm

Issue - State: closed - Opened by exenks 13 days ago

#47 - covalent bond issue

Issue - State: closed - Opened by kanghw0325 15 days ago - 6 comments

#46 - Paper citation

Issue - State: closed - Opened by zhaisilong 16 days ago - 5 comments

#45 - Protein ubiquitination

Issue - State: closed - Opened by jonleebiochem 17 days ago - 2 comments

#44 - Multithread

Issue - State: open - Opened by Rayca0 23 days ago - 1 comment

#43 - Issue with inference_demo.sh: NoneType Error During MET Parsing in CCD CIF File

Issue - State: open - Opened by Oaklight 25 days ago - 10 comments

#42 - How to Fine-Tune with PDBs Outside the Preprocessed Dataset?

Issue - State: open - Opened by rcossio 27 days ago - 3 comments

#41 - How to run "protenix predict -- input examples/example.json"?

Issue - State: closed - Opened by Rayca0 28 days ago - 1 comment

#40 - OOM error in training process

Issue - State: open - Opened by camel2000 about 1 month ago - 2 comments

#39 - Use Colab_search-generated a3m file as input for Protenix

Issue - State: closed - Opened by kjogr12 about 1 month ago - 5 comments

#38 - Exception: Given checkpoint path not exist [/af3-dev/release_model/model_v0.2.0.pt]

Issue - State: closed - Opened by chen10089 about 1 month ago - 1 comment

#37 - Discord link has expired

Issue - State: closed - Opened by sokrypton about 1 month ago - 3 comments

#36 - Sync on 1210

Pull Request - State: closed - Opened by heidongxianhua about 1 month ago - 1 comment

#35 - Error when only predicting ligand

Issue - State: closed - Opened by v-shaoningli about 1 month ago - 2 comments

#34 - Include seed in final name

Pull Request - State: closed - Opened by hypnopump about 2 months ago - 2 comments

#33 - Issue with stereochemistry

Issue - State: open - Opened by karlyy123 about 2 months ago - 2 comments

#33 - Issue with stereochemistry

Issue - State: open - Opened by karlyy123 about 2 months ago

#32 - CCD code of N-glycan modifications

Issue - State: closed - Opened by JelleMVir about 2 months ago - 2 comments

#31 - How to do the atom permutation for ligand prediciton?

Issue - State: closed - Opened by fuxuliu about 2 months ago - 4 comments

#30 - Question about the MSA datasets

Issue - State: closed - Opened by dohyeonscottkim about 2 months ago - 2 comments

#29 - train error

Issue - State: closed - Opened by lfs119 2 months ago - 2 comments
Labels: bug

#28 - Issues with cuda cusparse and cuda_runtime.api

Issue - State: closed - Opened by celalp 2 months ago - 1 comment
Labels: question

#27 - need help to decrease allocated memory

Issue - State: closed - Opened by nimrod-bio 2 months ago - 3 comments
Labels: question

#26 - About template module

Issue - State: open - Opened by wensm77 2 months ago - 1 comment
Labels: question

#26 - About template module

Issue - State: open - Opened by wensm77 2 months ago - 1 comment

#25 - Questions about model_v1.pt vs models trained using train_demo.sh, and low performance on antibody-antigen complex

Issue - State: closed - Opened by RJWANGbioinfo 2 months ago - 4 comments
Labels: question

#25 - Questions about model_v1.pt vs models trained using train_demo.sh, and low performance on antibody-antigen complex

Issue - State: open - Opened by RJWANGbioinfo 2 months ago - 3 comments
Labels: question

#24 - Licensing Question

Issue - State: closed - Opened by jaketanderson 2 months ago - 2 comments

#24 - Licensing Question

Issue - State: closed - Opened by jaketanderson 2 months ago - 2 comments

#23 - Using AF3 weights with Protenix

Issue - State: open - Opened by abhinavb22 2 months ago - 1 comment
Labels: question

#23 - Using AF3 weights with Protenix

Issue - State: closed - Opened by abhinavb22 2 months ago - 1 comment
Labels: question

#22 - remove layernorm chunk code which will make train/inference slow down

Pull Request - State: closed - Opened by yangyanpinghpc 2 months ago - 2 comments

#22 - remove layernorm chunk code which will make train/inference slow down

Pull Request - State: closed - Opened by yangyanpinghpc 2 months ago - 2 comments

#21 - Mismatched args in finetune_demo.h

Issue - State: closed - Opened by Stamcini 2 months ago - 1 comment

#21 - Mismatched args in finetune_demo.h

Issue - State: closed - Opened by Stamcini 2 months ago - 1 comment

#20 - unify letter cases of keys used in frontend

Pull Request - State: closed - Opened by Kqiii 2 months ago - 1 comment

#20 - unify letter cases of keys used in frontend

Pull Request - State: closed - Opened by Kqiii 2 months ago - 1 comment

#19 - Compatibility issues with string types in input JSON

Pull Request - State: closed - Opened by cloverzizi 2 months ago - 1 comment

#19 - Compatibility issues with string types in input JSON

Pull Request - State: closed - Opened by cloverzizi 2 months ago - 1 comment

#18 - JSON CHECK

Issue - State: closed - Opened by kanghw0325 2 months ago - 2 comments

#18 - JSON CHECK

Issue - State: closed - Opened by kanghw0325 2 months ago - 2 comments

#17 - Fixed cmd to test docker GPU

Pull Request - State: closed - Opened by jaketanderson 2 months ago - 1 comment

#17 - Fixed cmd to test docker GPU

Pull Request - State: closed - Opened by jaketanderson 2 months ago - 1 comment

#16 - Docker test command not working

Issue - State: closed - Opened by jaketanderson 2 months ago - 2 comments
Labels: bug, documentation

#16 - Docker test command not working

Issue - State: closed - Opened by jaketanderson 2 months ago - 2 comments
Labels: bug, documentation

#15 - Fix: layer_norm.py unnecessary writes

Pull Request - State: closed - Opened by alexzhang13 2 months ago - 1 comment

#15 - Fix: layer_norm.py unnecessary writes

Pull Request - State: closed - Opened by alexzhang13 2 months ago - 1 comment

#14 - update readme

Pull Request - State: closed - Opened by zhangyuxuann 2 months ago - 1 comment

#14 - update readme

Pull Request - State: closed - Opened by zhangyuxuann 2 months ago - 1 comment

#13 - How to make mmcif_bioassembly.pkl.gz data

Issue - State: open - Opened by fuxuliu 2 months ago - 1 comment
Labels: question

#13 - How to make mmcif_bioassembly.pkl.gz data

Issue - State: open - Opened by fuxuliu 2 months ago - 1 comment
Labels: question

#12 - Update layer_norm.py

Pull Request - State: closed - Opened by alexzhang13 2 months ago - 3 comments

#12 - Update layer_norm.py

Pull Request - State: closed - Opened by alexzhang13 2 months ago - 3 comments

#11 - About reproducing PoseBusters performance

Issue - State: closed - Opened by fuxuliu 2 months ago - 3 comments

#11 - About reproducing PoseBusters performance

Issue - State: closed - Opened by fuxuliu 2 months ago - 3 comments

#10 - Missing key(s) in state_dict:

Issue - State: closed - Opened by QUEST2179 2 months ago - 6 comments
Labels: question

#10 - Missing key(s) in state_dict:

Issue - State: open - Opened by QUEST2179 2 months ago - 6 comments
Labels: question

#9 - How is masking implemented for padded structures?

Issue - State: closed - Opened by ardagoreci 2 months ago - 2 comments
Labels: question

#9 - How is masking implemented for padded structures?

Issue - State: closed - Opened by ardagoreci 2 months ago - 2 comments
Labels: question

#8 - Confirm the AF3 typo

Issue - State: open - Opened by v-shaoningli 2 months ago - 1 comment
Labels: documentation

#8 - Confirm the AF3 typo

Issue - State: closed - Opened by v-shaoningli 2 months ago - 1 comment
Labels: documentation

#7 - How to get seq_to_pdb_index.json when fine-tuning

Issue - State: closed - Opened by bestz123 2 months ago - 6 comments
Labels: question

#7 - How to get seq_to_pdb_index.json when fine-tuning

Issue - State: open - Opened by bestz123 2 months ago - 5 comments
Labels: question

#6 - About Protenix: Protein + X

Issue - State: closed - Opened by jiaweiguan 2 months ago - 4 comments
Labels: question

#6 - About Protenix: Protein + X

Issue - State: closed - Opened by jiaweiguan 2 months ago - 4 comments
Labels: question

#5 - Request for conda environment

Issue - State: closed - Opened by jinungsong 2 months ago - 6 comments
Labels: enhancement

#5 - Request for conda environment

Issue - State: open - Opened by jinungsong 2 months ago - 6 comments
Labels: enhancement

#4 - High ipTM, low pLDDT

Issue - State: closed - Opened by stianale 2 months ago - 2 comments
Labels: enhancement

#3 - AssertionError: The provided precomputed MSA path of entities ['1'] does not exists: None

Issue - State: closed - Opened by SuperTiefeng 2 months ago - 3 comments

#2 - RuntimeError: DataLoader worker (pid 572) is killed by signal: Bus error. It is possible that dataloader's workers are out of shared memory. Please try to raise your shared memory limit.

Issue - State: closed - Opened by yipy0005 2 months ago - 5 comments
Labels: documentation

#1 - Having issues running "bash inference_demo.sh"

Issue - State: closed - Opened by yipy0005 2 months ago - 2 comments

GitHub / bytedance/protenix issues and pull requests