Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / baker-laboratory/RoseTTAFold-All-Atom issues and pull requests

#101 - Covalently Modified Protein Notation

Issue - State: closed - Opened by jaydebertoch 10 months ago

#98 - heterodimer config file

Issue - State: open - Opened by velocirraptor23 10 months ago - 1 comment

#97 - Add link to RFAA paper for convenience.

Pull Request - State: closed - Opened by AlexanderMath 10 months ago

#96 - The predicted protein-small molecule structure exhibits numerous clashes

Issue - State: open - Opened by gky2023 10 months ago - 1 comment

#95 - [issue] just following covalent modification tutorial

Issue - State: open - Opened by kimdn 10 months ago - 1 comment

#94 - error while testing the examples

Issue - State: open - Opened by Anupam-5 10 months ago - 1 comment

#93 - The output PDB file contains errors in sulfur residues and HIS residues

Issue - State: open - Opened by ygzn12138 10 months ago - 3 comments

#92 - Error -- failed: Connection timed out when downloading

Issue - State: closed - Opened by Thomas8081 10 months ago - 4 comments

#91 - rf2aa not found

Issue - State: closed - Opened by velocirraptor23 10 months ago - 3 comments

#90 - Is There a way to disable MSA or Templates

Issue - State: open - Opened by Jkerrison 10 months ago

#89 - Docker for RoseTTAFold-All-Atom?

Issue - State: open - Opened by arvindsemwal20 10 months ago

#88 - protein small molecule binding prediction algorithm

Issue - State: open - Opened by simonkim1347 10 months ago - 1 comment

#87 - Getting multiple designs

Issue - State: open - Opened by jmProteins2024 10 months ago

#86 - mmff94 force field fails for inorganic ligands

Issue - State: open - Opened by jayunruh 10 months ago - 1 comment

#85 - Update make_msa.sh

Pull Request - State: closed - Opened by NiklasTR 10 months ago

#84 - Chilarity of Covalently Modified Proteins

Issue - State: open - Opened by gilep 10 months ago

#83 - RoseTTAFold ValueError: No valid inputs were provided

Issue - State: closed - Opened by jmProteins2024 10 months ago - 1 comment

#82 - Question about xyz_prev

Issue - State: open - Opened by constantin-schneider 10 months ago

#81 - Why is the predicted DNA disconnected?

Issue - State: open - Opened by ygzn12138 10 months ago

#80 - Can protein_sm job use pdb as protein input?

Issue - State: open - Opened by sevengo8378 11 months ago

#79 - Out of Memory error when using RFAA

Issue - State: open - Opened by AaranWang 11 months ago - 1 comment

#78 - rf2aa as a Python module

Pull Request - State: closed - Opened by YaoYinYing 11 months ago

#75 - ValueError: No valid inputs were provided

Issue - State: open - Opened by merryxiang 11 months ago - 2 comments

#74 - Activate RFAA

Issue - State: open - Opened by jmProteins2024 11 months ago - 5 comments

#72 - psipred buffer overflow detected

Issue - State: open - Opened by cdienem 11 months ago - 3 comments

#71 - pdb100_2021Mar03.tar.gz download problem

Issue - State: open - Opened by iungyu-snu 11 months ago - 2 comments

#70 - pae_inter is NaN

Issue - State: closed - Opened by Leo-T-Zang 11 months ago - 5 comments

#69 - Multiple PDB structures prediction for protein-protein complex

Issue - State: open - Opened by mtahe 11 months ago - 1 comment

#68 - Solving Environment failed

Issue - State: open - Opened by EulusMaximus 11 months ago - 4 comments

#67 - Problems with the model output results

Issue - State: open - Opened by mh8859 11 months ago

#66 - Uniref Mirror

Issue - State: open - Opened by smilenaderi 11 months ago - 1 comment

#65 - How can I specify Output files path?

Issue - State: closed - Opened by Leo-T-Zang 11 months ago - 1 comment

#63 - CUDA Out of Memory Error Predicting Protein with 1200 Amino Acids

Issue - State: open - Opened by RichenLee 11 months ago - 5 comments

#62 - Failed to find 6azb_A in *_pdb.ffindex

Issue - State: open - Opened by BigMary2001 11 months ago - 2 comments

#59 - Stuck at "Running hhsearch"

Issue - State: closed - Opened by denizkavi 11 months ago - 1 comment

#58 - No module named 'hydra'

Issue - State: open - Opened by cron-weasley 11 months ago - 4 comments

#56 - "sequence ss_pred contains no residues" Error

Issue - State: closed - Opened by denizkavi 11 months ago - 1 comment

#55 - bad prediction for a homodimer

Issue - State: open - Opened by lucl13 11 months ago - 4 comments

#54 - Output PDB file formatting potentially invalid for proper ligand parsing

Issue - State: open - Opened by amorehead 11 months ago - 3 comments

#52 - How can the results of inference be visualized?

Issue - State: closed - Opened by MedicalAGI 11 months ago

#51 - remove build strings from env to make it more portable and add UI

Pull Request - State: open - Opened by duerrsimon 11 months ago - 1 comment

#50 - Are there any methods to relax the small molecule and protein complex?

Issue - State: closed - Opened by simonkim1347 11 months ago - 2 comments

#49 - Fix some bugs in data handling code

Pull Request - State: closed - Opened by jnooree 11 months ago

#48 - Size limitations based on memory allocation

Issue - State: open - Opened by gulseva 11 months ago - 2 comments

#47 - Minor bug affecting expanding multi-MSAs

Issue - State: closed - Opened by milafternoon 11 months ago - 3 comments

#46 - Failed to generate 3D coordinates for small molecule

Issue - State: open - Opened by Amy-Fernandez 11 months ago - 1 comment

#45 - How to produce the top 5 proteins/complexes?

Issue - State: open - Opened by syanle 11 months ago

#44 - SignalP required?

Issue - State: closed - Opened by CMargreitter 11 months ago - 2 comments

#43 - API for unnatural amino acid

Issue - State: open - Opened by LesongWei 11 months ago - 1 comment

#42 - Small fasta sequences cause error

Issue - State: open - Opened by tydingcw 11 months ago - 1 comment

#41 - Small molecule without protein causes error

Issue - State: open - Opened by tydingcw 11 months ago - 1 comment

#40 - More than one bond in the covale_inputs section

Issue - State: open - Opened by pstansfeld 11 months ago - 2 comments

#39 - Custom Template Database

Issue - State: open - Opened by fabgonzal 11 months ago

#38 - OSError after python -m rf2aa.run_inference --config-name protein

Issue - State: open - Opened by PiotrP95 11 months ago - 1 comment

#37 - The code stops at the protein example.

Issue - State: open - Opened by YOtani11517 11 months ago - 5 comments

#36 - Error in python -m rf2aa.run_inference --config-name protein_sm

Issue - State: open - Opened by xie-yun-ai 11 months ago - 2 comments

#35 - Error in homodimer prediction

Issue - State: closed - Opened by Garhorne0813 11 months ago - 2 comments

#34 - Error in the protein example

Issue - State: open - Opened by xie-yun-ai 11 months ago - 6 comments

#32 - Error in the protein example

Issue - State: open - Opened by ILUT1 11 months ago - 4 comments

#31 - BLAST (SS assignment) pipeline fails for certain inputs

Issue - State: open - Opened by amorehead 11 months ago - 6 comments

#30 - `expand_multi_msa()` fails for certain inputs

Issue - State: closed - Opened by amorehead 11 months ago - 1 comment

#29 - added license

Pull Request - State: closed - Opened by r-krishna 11 months ago

#28 - psipred terminated

Issue - State: closed - Opened by leodoned 11 months ago - 3 comments

#27 - Excellent work + small question -- smiles format

Issue - State: closed - Opened by Samuel-gwb 11 months ago - 2 comments
Labels: question

#26 - adding support for multi-GPU inference

Issue - State: open - Opened by Garhorne0813 11 months ago - 4 comments
Labels: enhancement

#25 - Is it possible to use the RF2AA in the colab note?

Issue - State: open - Opened by g00dtw0 11 months ago - 4 comments
Labels: enhancement, help wanted

#23 - terminated when run in conda environment

Issue - State: open - Opened by masterwhook 11 months ago - 3 comments

#22 - CUDA out of memory while running the 'nucleic_acid' example

Issue - State: closed - Opened by wjk1214 11 months ago - 2 comments

#20 - Installation issues

Issue - State: open - Opened by XuanZhou001 11 months ago - 5 comments
Labels: question

#19 - Is it possible to share your training data to the public?

Issue - State: open - Opened by lkfo415579 11 months ago
Labels: enhancement

#18 - Questions about the database

Issue - State: open - Opened by mh8859 11 months ago - 5 comments
Labels: question

#17 - Error while running the protein example

Issue - State: open - Opened by abhinavb22 11 months ago - 10 comments

#16 - added back sm complex example

Pull Request - State: closed - Opened by r-krishna 12 months ago

#15 - Add minimum and recommended hardware requirements to readme.md

Issue - State: open - Opened by jorgecomas 12 months ago - 5 comments
Labels: question

#14 - Training code availability?

Issue - State: open - Opened by amorehead 12 months ago
Labels: enhancement

#12 - Bug in merge_inputs.py

Issue - State: closed - Opened by CYP152N1 12 months ago - 5 comments
Labels: bug

#11 - Update merge_inputs.py

Pull Request - State: closed - Opened by CYP152N1 12 months ago - 3 comments

#10 - bugs (?) in make_msa.sh

Issue - State: open - Opened by komatsuna-san 12 months ago - 4 comments
Labels: bug

#9 - Fix `hhdb` value in base.yaml

Pull Request - State: closed - Opened by amorehead 12 months ago

#8 - run error about apptainer

Issue - State: open - Opened by Takk522 12 months ago - 6 comments

#7 - make_msa.sh error (signalp6, hhblits, hhfilter)

Issue - State: closed - Opened by blacktanktop 12 months ago - 9 comments

#6 - Using pre-calculated msa

Issue - State: open - Opened by gezmi 12 months ago - 3 comments
Labels: enhancement

#5 - About Conda Environment

Issue - State: open - Opened by Maikuraky 12 months ago - 22 comments
Labels: question

#4 - No such file or directory: 'pdb100_2022Apr19/pdb100_2022Apr19_pdb.ffindex'

Issue - State: closed - Opened by blauemond 12 months ago - 4 comments

#3 - squashfs image was compressed with lz4, if it failed to run

Issue - State: closed - Opened by blacktanktop 12 months ago - 8 comments

#2 - License

Issue - State: closed - Opened by exs-hkenlay 12 months ago - 5 comments

#1 - Multimer

Pull Request - State: closed - Opened by r-krishna 12 months ago