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biasmv/pv #192

Display problem of structure of alphafold2

Hi, @biasmv When I visualize my structure of alphafold2 as cartoon, it shows like a tube as follows: ![ALPHA](https://user-images.githubusercontent.com/24219321/187941264-14306964-fb80-418e-affc-a85b…

lh12565 updated 2 years ago
6
sokrypton/ColabFold #497

Question: Issue with automated model ranking in mmseqs noteb…

Yesterdays protein modeling gave the following log output with regard to the ranking of the five generated models: `2023-09-22 18:52:35,633 alphafold2_ptm_model_1_seed_000 recycle=0 pLDDT=88.1 pTM=…

MWNautilus updated 1 year ago
3
bayer-science-for-a-better-life/prettymol #1

[SCENE] Antibody contact prediction

Braindump WIP **Goals** - Unexplored: how modern DL workflows can predict HCDR3 conformations? - How meaningful is an MSA for an antibody (vs the importance of MSA in standard protein conformat…

sdvillal updated 3 years ago
6
nf-core/proteinfold #121

Database uniref30_2202_db does not exist while running colab…

### Description of the bug The python code search.py cannot find uniref30_2202_db even though I already specified the path. Maybe I lost something important? Thanks a lot in advance. ERROR ~ Err…

nash73b91203005 updated 4 months ago
4
google-deepmind/dm-haiku #528

Ask for help using alphafold2_advanced.py ; haiku error

Hello: I have a protein receptor sequence file r.fasta, two protein ligand sequence files a.fasta and b.fasta and two peptide chains pep1 and prp2 selected from b.fasta. I wish to compare the strengt…

Zero-Sun updated 2 years ago
1
google-deepmind/alphafold #653

run_docker.py failure caused by module not found error

When I run the run_docker.py with the following command, python3 docker/run_docker.py \ --fasta_paths=/data/xiaoai/alphafold2_software/alphafold-main/T1082.fasta \ --max_template_date=2020-05-1…

ailiqiangCSU updated 1 year ago
1
lhatsk/AlphaLink #13

problem with model loading

Hi AlphaLink developers! I am trying to use AlphaLink. I've downloaded the model via your dropbox link and unpacked it with gunzip. So I start the prediction like this: ``` python predict_with_c…

SimpleNumber updated 1 year ago
12
lucidrains/alphafold2 #101

__init__() got an unexpected keyword argument 'structure_mod…

When I run ``` import torch from alphafold2_pytorch import Alphafold2 model = Alphafold2( dim = 256, depth = 2, heads = 8, dim_head = 64, predict_coords = True, st…

ifromeast updated 2 years ago
4
evolutionaryscale/esm #63

Cannot reproduce results on CAMEO (194 targets) and CASP14 (…

Hi Team, Thank you for the excellent work on ESM3. I am currently comparing the performance of ESM3 on the CAMEO and CASP14 datasets with ESMFold and AlphaFold2. The CAMEO dataset I am using is …

zhujianwei31415 updated 1 month ago
13
google-deepmind/alphafold #1021

Endless "[Perf]: MatMul reference implementation being execu…

Hello, One of my systems, running Ubuntu 22.04, updated docker to version 27.3.1 (build ce12230)... after which running AlphaFold2 produces a neverending series of messages like the following once …

lucajovine updated 3 weeks ago
3

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695 results for alphafold2

695 results
for alphafold2