google-deepmind/alphafold issues and pull requests

#1028 - Updated requirements.txt

Pull Request - State: open - Opened by vignesh1507 about 1 month ago - 2 comments

#1027 - Hopefully that helps.

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

#1026 - Installation without docker

Issue - State: open - Opened by fglaser about 1 month ago

#1024 - Remove $ROOT_DIR from the argument of gunzip command

Pull Request - State: open - Opened by kojiwell about 1 month ago - 1 comment

#1023 - lost some output files

Issue - State: open - Opened by xjhzjucas about 1 month ago

#1021 - Endless "[Perf]: MatMul reference implementation being executed generated" messages and dramatic inference slowdown upon updating to docker 27.3.1

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

#1018 - Could we track how long one AlphaFold program run?

Issue - State: open - Opened by WenWu-Bio about 2 months ago - 1 comment

#958 - Running AlphaFold on models larger than AMD GPU available memory

Issue - State: open - Opened by dipietrantonio 4 months ago - 1 comment

#914 - Fatal Python error: Segmentation fault

Issue - State: open - Opened by ghost 8 months ago - 1 comment

#885 - ImportError: cannot import name 'SCOPData' from 'Bio.Data'

Issue - State: open - Opened by lx19930 10 months ago - 7 comments

#104 - docker build

Issue - State: closed - Opened by jianhaoc over 3 years ago - 5 comments
Labels: setup

#103 - Alphafold raises an error when it is predicting protein structure

Issue - State: closed - Opened by psp3dcg over 3 years ago - 2 comments

#102 - How to use？

Issue - State: closed - Opened by genomicsgroup over 3 years ago - 6 comments

#101 - ERROR: Could not find a version that satisfies the requirement numpy==1.19.5 (from versions: none)

Issue - State: closed - Opened by Rusfell over 3 years ago - 3 comments
Labels: error report, docker, setup

#100 - Unable to download pdb_mmcif database due to some recurring error.

Issue - State: closed - Opened by Comp-era over 3 years ago - 2 comments

#99 - /opt/conda/lib/python3.7/site-packages/absl/flags Issue while runnning alphafold

Issue - State: closed - Opened by Comp-era over 3 years ago - 2 comments

#98 - python3 docker/run_docker.py error: requests.exceptions.HTTPError: 400 Client Error

Issue - State: closed - Opened by mglgc over 3 years ago - 12 comments
Labels: error report, docker, setup

#97 - RuntimeError: HHblits failed

Issue - State: closed - Opened by huangjk1103 over 3 years ago - 20 comments
Labels: error report

#96 - Added singularity file and README

Pull Request - State: closed - Opened by davidhemp over 3 years ago - 5 comments
Labels: cla: yes

#95 - max connections (25) reached -- try again later

Issue - State: closed - Opened by mabingqi1 over 3 years ago

#94 - Download speed of database pdb_mmcif is very slow, about 80 KB/s

Issue - State: closed - Opened by liuboeo over 3 years ago - 2 comments

#93 - How to predict homo-oligomer's and hetero-oligomer's structure?

Issue - State: closed - Opened by RodenLuo over 3 years ago - 7 comments

#92 - How to visualize the result?

Issue - State: closed - Opened by RodenLuo over 3 years ago - 12 comments

#91 - Run prediction jobs in background

Issue - State: closed - Opened by siwei-deng over 3 years ago - 1 comment

#90 - Switch setup.py to Tensorflow CPU-only.

Pull Request - State: closed - Opened by chrisroat over 3 years ago - 1 comment
Labels: cla: yes

#89 - 400 Client Error: Bad Request for url: http+docker://localhost/v1.41/containers/create

Issue - State: closed - Opened by siwei-deng over 3 years ago - 3 comments

#88 - tensorflow-cpu

Issue - State: closed - Opened by akhoroshev over 3 years ago - 1 comment

#87 - run_docker.py: Run as non-root user by default, allow setting the user via flag

Pull Request - State: closed - Opened by akors over 3 years ago - 3 comments
Labels: cla: yes

#86 - meet problem in path -p openmm.patch

Issue - State: closed - Opened by Luanxins over 3 years ago - 3 comments

#85 - out of memory w/ colab notebook

Issue - State: closed - Opened by ttianchen over 3 years ago - 4 comments
Labels: error report, colab

#84 - Building wheel for dm-tree (setup.py) ... error

Issue - State: closed - Opened by ZQiangdeng over 3 years ago - 3 comments

#83 - tensorflow issue

Issue - State: closed - Opened by ajian-he over 3 years ago - 3 comments

#82 - high RAM usage w reduced_dbs

Issue - State: closed - Opened by biohegedus over 3 years ago - 3 comments
Labels: error report, third-party tool

#81 - /usr/local/nvidia not found

Issue - State: closed - Opened by cyclicdiamp over 3 years ago - 1 comment

#80 - how to compile alphafold with multiple CPUs

Issue - State: closed - Opened by ZengTao-hub over 3 years ago - 7 comments

#79 - Confusing wording/procedure in the Colab notebook

Issue - State: closed - Opened by josephrocca over 3 years ago - 1 comment
Labels: feature request, colab

#78 - ModuleNotFoundError: No module named 'py3Dmol'

Issue - State: closed - Opened by Leon-HXL over 3 years ago - 3 comments

#77 - Supplement/source code discrepancy in TriangleMultiplicationIncoming

Issue - State: closed - Opened by gahdritz over 3 years ago - 3 comments

#76 - Add flags: download_dir, docker_image_name, output_dir

Pull Request - State: closed - Opened by chrisroat over 3 years ago - 1 comment
Labels: cla: yes

#75 - Flag for output directory, write to current working directory by default

Pull Request - State: closed - Opened by akors over 3 years ago - 3 comments
Labels: cla: yes

#74 - [Question] Speed up prediction speed on GPUs with large memory?

Issue - State: closed - Opened by ashrafgt over 3 years ago - 2 comments

#73 - RuntimeError: HHblits failed

Issue - State: closed - Opened by LuGarfield over 3 years ago - 14 comments
Labels: error report, third-party tool

#72 - CUDA / Tensorflow version mismatch in Dockerfile

Issue - State: closed - Opened by chrisroat over 3 years ago - 9 comments

#71 - Getting "ValueError: Cannot create a tensor proto whose content is larger than 2GB." for smaller sequences

Issue - State: closed - Opened by DavidB256 over 3 years ago - 26 comments
Labels: error report

#70 - issue on docker build

Issue - State: closed - Opened by ajian-he over 3 years ago - 2 comments

#69 - Look for data file relative to current module

Pull Request - State: closed - Opened by rjgildea over 3 years ago - 2 comments
Labels: cla: yes

#68 - have the version of mgnify in run_docker.py match what is in download…

Pull Request - State: closed - Opened by joemin over 3 years ago - 1 comment
Labels: cla: yes

#67 - 100% GPU-memory and 0% GPU-Util when building model

Issue - State: closed - Opened by sunnybirds over 3 years ago - 2 comments

#66 - Why the alphafold use only one gpu , even though my system has two gpus.

Issue - State: closed - Opened by jongseo-park over 3 years ago - 3 comments

#65 - Reason behind 'msa_channel': 256 and 'seq_channel': 384 in config.py?

Issue - State: closed - Opened by xinformatics over 3 years ago - 1 comment

#64 - 'Directory not empty' during Docker build

Issue - State: closed - Opened by RJ3 over 3 years ago - 1 comment

#63 - how to continue predicting without repeating msas

Issue - State: closed - Opened by GuShaocheng over 3 years ago - 2 comments

#62 - 400 Client Error

Issue - State: closed - Opened by lukaszsobala over 3 years ago - 3 comments

#61 - predicted TM-score (pTM) and predicted aligned errors

Issue - State: closed - Opened by baoxingsong over 3 years ago - 2 comments

#60 - Running on CUDA 10.X

Issue - State: closed - Opened by skyungyong over 3 years ago - 1 comment

#57 - Is there any way to turn off the relaxation option without modifications ?

Issue - State: closed - Opened by jongseo-park over 3 years ago - 1 comment

#56 - Session crashed after using all available RAM (AlphaFold Colab)

Issue - State: closed - Opened by Pankaj-99 over 3 years ago - 1 comment

#55 - Failure on Nvidia devices with compute capability 8.6

Issue - State: closed - Opened by miesav over 3 years ago - 9 comments
Labels: error report, docker, cuda

#54 - ValueError: Could not find Jackhmmer database /mnt/mgnify_database_path/mgy_clusters_2018_08.fa

Issue - State: closed - Opened by hradhakrishnan over 3 years ago - 5 comments

#53 - GDT Score

Issue - State: closed - Opened by Planet-KIM over 3 years ago - 1 comment

#52 - absl FATAL flags parsing error

Issue - State: closed - Opened by SeaTalk over 3 years ago - 2 comments
Labels: error report

#51 - GPU supported

Issue - State: closed - Opened by q1134269149 over 3 years ago - 4 comments

#50 - Is there a way to get per-residue embeddings from the model?

Issue - State: closed - Opened by aghanbar over 3 years ago - 2 comments

#49 - About RuntimeError of hhsearch

Issue - State: closed - Opened by Maikuraky over 3 years ago - 10 comments

#48 - Alphafold protein domain compartmentalization

Issue - State: closed - Opened by jnielsen20 over 3 years ago - 1 comment

#47 - ModuleNotFoundError

Issue - State: closed - Opened by cdaversin over 3 years ago - 6 comments

#46 - OpenMM patch fails in docker build (python version discrepancy)

Issue - State: closed - Opened by mokca over 3 years ago - 1 comment

#45 - ModuleNotFoundError

Issue - State: closed - Opened by rubindg over 3 years ago - 6 comments

#44 - [WIP] Adjust Dockerfile

Pull Request - State: closed - Opened by calufa over 3 years ago - 1 comment

#43 - ValueError: Cannot create a tensor proto whose content is larger than 2GB.

Issue - State: closed - Opened by SSchott over 3 years ago - 4 comments

#42 - how to get databases without aria2?

Issue - State: closed - Opened by ctmckee over 3 years ago - 5 comments

#41 - Fix typo in small BFD name

Pull Request - State: closed - Opened by amorehead over 3 years ago - 3 comments

#40 - Error downloading PDB mmCIF

Issue - State: closed - Opened by shlomita over 3 years ago - 12 comments

#39 - Failed to build docker on Step 16/19 - patch issue

Issue - State: closed - Opened by durrantmm over 3 years ago - 3 comments

#38 - About distogram format

Issue - State: closed - Opened by FilomenoSanchez over 3 years ago - 2 comments

#37 - full_dbs setting requires no creative commons license only Apache?

Issue - State: closed - Opened by effectsToCause over 3 years ago - 2 comments
Labels: licensing

#36 - Update base image to cuda 11.2-cudnn8-runtime

Pull Request - State: closed - Opened by chrisroat over 3 years ago - 6 comments

#35 - Donload data "uniclust30" problem

Issue - State: closed - Opened by NITROGENousFish over 3 years ago - 2 comments

#34 - Rerunning models using existing MSAs

Issue - State: closed - Opened by InfProbSciX over 3 years ago

#33 - CUDA error out of memory

Issue - State: closed - Opened by vhu43 over 3 years ago - 12 comments
Labels: error report

#32 - "stereo_chemical_props.txt" missing for model relaxation

Issue - State: closed - Opened by jhpanda over 3 years ago - 4 comments

#31 - How many GPUs has Alphafold used for training?

Issue - State: closed - Opened by xiongzhp over 3 years ago - 2 comments

#30 - Distribution over multiple GPUs

Issue - State: closed - Opened by georgkempf over 3 years ago - 12 comments

#29 - Releasing the AlphaFold package on pypi

Issue - State: closed - Opened by ashrafgt over 3 years ago - 6 comments

#28 - Install libcudnn8 and libcusolver-11 in Docker

Pull Request - State: closed - Opened by YoshitakaMo over 3 years ago - 14 comments

#27 - Fix typos discovered by codespell

Pull Request - State: closed - Opened by cclauss over 3 years ago - 1 comment

#26 - Docker image missing cuda libs

Issue - State: closed - Opened by chrisroat over 3 years ago - 6 comments

#25 - running via docker: cannot initialize backend TPU

Issue - State: closed - Opened by chrisroat over 3 years ago - 2 comments

#24 - Non docker setup

Issue - State: closed - Opened by sanjaysrikakulam over 3 years ago - 15 comments
Labels: setup

#23 - Fix highlighting in BibTeX entry in README

Pull Request - State: closed - Opened by bryant1410 over 3 years ago - 1 comment

#20 - jax and jaxlib versions

Issue - State: closed - Opened by huhlim over 3 years ago - 6 comments

#19 - uniclust30 bottleneck

Issue - State: closed - Opened by chrisroat over 3 years ago - 2 comments

#18 - Operation system?

Issue - State: closed - Opened by Wenzhe-Ma over 3 years ago - 1 comment

#17 - Using a subset of genetic databases

Issue - State: closed - Opened by InfProbSciX over 3 years ago

#16 - MGnify download unreachable

Issue - State: closed - Opened by prolatium over 3 years ago - 2 comments

#15 - Protein Embedding with last activation layers?

Issue - State: closed - Opened by victormaricato over 3 years ago - 9 comments

#14 - Commercial license: how to obtain one.

Issue - State: closed - Opened by javierbq over 3 years ago - 6 comments
Labels: licensing

GitHub / google-deepmind/alphafold issues and pull requests