Ecosyste.ms: Issues

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GitHub / RosettaCommons/RFdiffusion issues and pull requests

#318 - RFdiffusion small binder generation

Issue - State: open - Opened by kye0114 6 days ago

#317 - binder design

Issue - State: open - Opened by fanch1122 12 days ago - 3 comments

#316 - Query regarding metal-binding protein design

Issue - State: open - Opened by JavenGWY 17 days ago

#315 - RFdiffusion output chains are not separate

Issue - State: open - Opened by UTH-Arnav 20 days ago

#312 - Chain identity and index

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

#311 - VHH and scFV type binder prediction

Issue - State: open - Opened by seongguheo about 1 month ago - 1 comment

#310 - Cleft conditioner

Pull Request - State: closed - Opened by mnoyes68 about 1 month ago

#309 - Update Dockerfile to include numpy1.24.3

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

#308 - ValueError: Invalid shape in axis 0: 0.

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

#307 - questions for pAE compute

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

#306 - ModuleNotFoundError: No module named 'torchdata.datapipes'

Issue - State: open - Opened by Raef88 about 2 months ago - 3 comments

#305 - FileNotFoundError - sym_rots.npz

Issue - State: open - Opened by 0xpsi 2 months ago

#303 - Enforcing a fold on designed binder

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

#302 - Enforcing constraints on generated design

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

#301 - Beta-pairing Binder Design Script?

Issue - State: open - Opened by amelie-iska 2 months ago

#299 - the chainA of design_ppi_X.pdb file in output all is GGGGGG....

Issue - State: open - Opened by RyanYip-Kat 3 months ago - 2 comments

#298 - binder design

Issue - State: open - Opened by enco1218 3 months ago

#297 - binder design shell script error

Issue - State: open - Opened by ppxwwtaking 3 months ago - 1 comment

#295 - Draft: Cleft conditioner

Pull Request - State: closed - Opened by mnoyes68 3 months ago

#294 - Position-independent distances

Issue - State: open - Opened by Tomoeee889 3 months ago

#292 - How to partially diffuse a homo-oligomer?

Issue - State: open - Opened by Lyang556 3 months ago

#291 - fine-tuning

Issue - State: open - Opened by Ryosuke-254 3 months ago

#290 - AssertionError: ('B', 1) is not in pdb file!

Issue - State: open - Opened by alymakhlouf 4 months ago - 5 comments

#288 - [Bug?] Missing Padding Mask for Batch Mode

Issue - State: open - Opened by Oxer11 4 months ago

#287 - When design enzyme

Issue - State: open - Opened by DM0815 4 months ago - 1 comment

#286 - Update model_runners.py

Pull Request - State: open - Opened by brianloyal 4 months ago

#285 - Trouble understanding `con_ref_idx0`

Issue - State: closed - Opened by kjczarne 4 months ago - 1 comment

#284 - SVD error

Issue - State: open - Opened by soumadwip 4 months ago

#283 - Run error

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

#282 - Gap-filling with RFdiffusion

Issue - State: closed - Opened by kjczarne 5 months ago - 4 comments

#281 - bug

Issue - State: open - Opened by Ryosuke-254 5 months ago - 1 comment

#278 - Enable running with T < 15

Pull Request - State: closed - Opened by prihoda 6 months ago

#277 - Fix Torch CPU support in SE3Transformer

Pull Request - State: closed - Opened by prihoda 6 months ago

#276 - How to generate compact binders?

Issue - State: open - Opened by bzhousd 6 months ago - 1 comment

#275 - Partial diffusion with sequences does not work

Issue - State: open - Opened by gezmi 6 months ago

#272 - Problem about design_ppi_scaffolded.sh in the example

Issue - State: open - Opened by kn301BE 6 months ago - 8 comments

#263 - diffuser.T is being ignored

Issue - State: open - Opened by markf94 7 months ago - 2 comments

#259 - Using sequence in potentials

Issue - State: closed - Opened by geraseva 8 months ago - 2 comments

#257 - FileNotFoundError:

Issue - State: open - Opened by Ryosuke-254 8 months ago - 3 comments

#253 - use user HOME dir for cache, config, models

Pull Request - State: open - Opened by EricDeveaud 8 months ago - 1 comment

#251 - why default pdb db is set to examples/input_pdbs/1qys.pdb

Issue - State: open - Opened by EricDeveaud 8 months ago - 2 comments

#249 - Fixed Dockerfile numpy version bug

Pull Request - State: open - Opened by AlexTaguchi 8 months ago - 1 comment

#241 - pyRosetta not found for Fold conditioning design

Issue - State: open - Opened by 363892878a 9 months ago - 3 comments

#238 - Traceback (most recent call last)

Issue - State: open - Opened by AIM132 10 months ago - 3 comments

#221 - Issue with controlling motif scaffold length?

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

#214 - Partial diffusion errors

Issue - State: open - Opened by ibalafkir 11 months ago - 8 comments

#209 - Error When Setup

Issue - State: open - Opened by xinran1129305 11 months ago - 1 comment

#183 - Not working with CUDA 11.1

Issue - State: open - Opened by crazyNi about 1 year ago - 4 comments

#169 - Where to find documentation about contigmap.contigs?

Issue - State: open - Opened by JaktensTid about 1 year ago - 1 comment

#137 - How to use the trb file in combination with ProteinMPNN

Issue - State: open - Opened by wangdoc2002 over 1 year ago - 5 comments

#116 - CUDA not working

Issue - State: closed - Opened by ChengkuiZhao over 1 year ago

#115 - Got wrong Amino Acid

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

#115 - Got wrong Amino Acid

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

#114 - How to generate a binder when using Docker

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

#114 - How to generate a binder when using Docker

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

#113 - No pAE_interaction<10

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

#113 - No pAE_interaction<10

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

#109 - ModuleNotFoundError: No module named 'pyrsistent'

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

#107 - Modifying Binder Length when using fold conditioning

Issue - State: open - Opened by okanders over 1 year ago - 3 comments

#107 - Modifying Binder Length when using fold conditioning

Issue - State: open - Opened by okanders over 1 year ago - 3 comments

#105 - Is it possible to run RFdiffusion without the GPU?

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

#105 - Is it possible to run RFdiffusion without the GPU?

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

#104 - How to do self-conditioning?

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

#103 - chain break doesn't work as expected

Issue - State: open - Opened by bzhousd over 1 year ago - 5 comments

#103 - chain break doesn't work as expected

Issue - State: open - Opened by bzhousd over 1 year ago - 5 comments

#101 - conda issue: ResolvePackageNotFound

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

#100 - 'no viable alternative at input' when designing binders

Issue - State: closed - Opened by jbrydon2 over 1 year ago - 5 comments

#100 - 'no viable alternative at input' when designing binders

Issue - State: closed - Opened by jbrydon2 over 1 year ago - 5 comments

#97 - Contigmap in Motif Scaffolding

Issue - State: open - Opened by plvdac1 over 1 year ago - 5 comments

#96 - Added p53 scaffolding example

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

#96 - Added p53 scaffolding example

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

#95 - Is conda a hard requirement?

Issue - State: open - Opened by kuoirad over 1 year ago - 3 comments

#94 - Deep Learning Binder Results

Issue - State: open - Opened by okanders over 1 year ago - 10 comments

#93 - Using motif scaffolds for binder design

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

#91 - fine-tuning method

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

#90 - Fixed incorrect variable name in contig parsing

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

#89 - Adding p53 helix scaffold method to repository

Issue - State: closed - Opened by ttessie2 over 1 year ago - 1 comment

#89 - Adding p53 helix scaffold method to repository

Issue - State: closed - Opened by ttessie2 over 1 year ago - 1 comment

#88 - PAE interaction score

Issue - State: open - Opened by Najy-Yusuf over 1 year ago - 4 comments

#87 - Naming contigs in colab notebook

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

#86 - Using non-protein targets for binder design

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

#85 - Doubts regarding binder design results

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

#83 - updating rosetta-ci scripts to fix design_ppi_scaffolded test

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

#82 - updating rosetta-ci scripts to fix design_ppi_scaffolded test

Pull Request - State: closed - Opened by lyskov over 1 year ago - 3 comments

#81 - Update install instructions for model directory location.

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

#80 - Help with error: no such file or directory /models/Base_ckpt.pt

Issue - State: closed - Opened by ttessie2 over 1 year ago - 5 comments