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Rosetta 3 - Applications

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Sticky topic Sticky: FAQ
by admin » Mon, 2010-08-30 04:18
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17,566 by admin
Fri, 2015-09-04 16:17
Normal topic Ligand Docking with ROSETTA
by sc19 » Thu, 2022-07-14 01:32
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1,043 by sc19
Thu, 2022-07-14 01:34
Normal topic Errors about rifdock step 15
by ng98 » Thu, 2024-02-01 17:41
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383 by ng98
Thu, 2024-02-01 17:41
Normal topic Using abinition to predict a new (previously unsolved) structure.
by ac.research » Mon, 2017-01-09 00:59
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1,402 by ac.research
Mon, 2017-01-09 00:59
Normal topic metalloprotein ab initio with glutamic acid
by inorgchem » Tue, 2020-06-16 20:45
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772 by inorgchem
Tue, 2020-06-16 20:45
Normal topic Writing down properties for new atom types
by Corvin » Tue, 2021-01-12 04:30
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786 by Corvin
Wed, 2021-01-13 04:00
Normal topic Relax in membrane pull my protein out of the membrane
by Martin Floor » Wed, 2022-01-26 07:46
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1,102 by Martin Floor
Wed, 2022-01-26 07:46
Normal topic Silent File Scores Missing: RNA Protein Complex Predition
by axio23 » Fri, 2023-06-16 05:45
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460 by axio23
Fri, 2023-06-16 05:45
Normal topic clashes created with enzdes
by listofdina » Mon, 2021-08-02 06:51
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834 by listofdina
Mon, 2021-08-02 06:51
Normal topic snugdock: constrained backbone
by mahendra » Mon, 2022-11-14 02:51
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1,850 by mahendra
Mon, 2022-11-14 02:51
Normal topic Reproduce Robetta's ddg values of interface alanine scan using Rosetta?
by cossio » Mon, 2015-01-19 07:14
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2,795 by cossio
Mon, 2015-01-19 07:14
Normal topic DDG_monomer ΔΔG question
by asbelx » Fri, 2018-04-20 03:31
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1,223 by asbelx
Fri, 2018-04-20 03:33
Normal topic Global Docking with carbohydrates
by ChiauShu » Sat, 2020-08-22 20:16
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1,004 by ChiauShu
Sat, 2020-08-22 20:16
Normal topic Creating fragment files for proteins less than 27 aa in length
by Poladu » Tue, 2021-01-26 07:50
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912 by Poladu
Tue, 2021-01-26 07:50
Normal topic Antibody Structure Prediction - Error on antibody_H3 step: "Option matching -antibody:remodel not found in command line"
by ramon-arg » Mon, 2023-07-24 17:56
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376 by ramon-arg
Mon, 2023-07-24 17:56
Normal topic Flex_ddG crashes when attempting to move 2 chains (e.g. chains_to_move = A,C)
by jcampecino » Wed, 2020-05-13 12:22
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1,141 by jcampecino
Wed, 2020-05-13 12:22
Normal topic comparative modelling of a complex
by sdh_h » Sun, 2017-12-17 06:07
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1,134 by sdh_h
Sun, 2017-12-17 06:07
Normal topic Metal Ion in symmetric design
by tschiex » Wed, 2020-07-08 05:28
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943 by tschiex
Wed, 2020-07-08 05:28
Normal topic denovo_density don't output a pdb file
by ylwang » Sun, 2018-11-18 17:51
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1,113 by ylwang
Sun, 2018-11-18 17:51
Normal topic mp_transform optimize with franklin2019 scoring
by benhardy » Thu, 2020-05-28 08:35
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1,319 by benhardy
Thu, 2020-05-28 08:45
Normal topic Remodel's problem in treatment with non-protein residues
by Corvin » Mon, 2021-12-13 09:07
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1,029 by Corvin
Mon, 2021-12-13 09:07
Normal topic Error with xml script
by almeida85 » Tue, 2023-03-28 01:53
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661 by almeida85
Tue, 2023-05-16 01:00
Normal topic Can remodel really handle multiple insertions in one simulation?
by lanselibai » Sat, 2019-12-28 12:51
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946 by lanselibai
Sat, 2019-12-28 12:51
Normal topic minimize_ppi.mpi.linuxgccrelease doesn't use jd2?
by e3lm » Tue, 2022-05-17 11:58
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1,058 by e3lm
Tue, 2022-05-17 11:58
Normal topic Error with SapScoreMetric (SimpleMetric sap_score not found in basic::datacache::DataMap)
by Seongsung » Fri, 2023-11-24 05:09
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313 by Seongsung
Fri, 2023-11-24 13:14
Normal topic Patch to impose tetrahedral geometry on backbone O atom
by georg » Thu, 2021-04-08 09:30
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810 by georg
Thu, 2021-04-08 09:31
Normal topic RemodelMover and Input Pose
by ozyo » Tue, 2020-12-29 09:41
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948 by ozyo
Tue, 2020-12-29 09:41
Normal topic I need help with cst file the paper: De Novo Computational Design of Retro-Aldol Enzymes
by Wenithor » Thu, 2022-01-06 12:20
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1,168 by Wenithor
Thu, 2022-01-06 12:20
Normal topic Simple_cycpep_predict with crosslinker BBMB
by Ken » Tue, 2023-05-09 08:52
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535 by Ken
Tue, 2023-05-09 08:52
Normal topic Pepspec Anchor Dock
by Soler » Fri, 2020-09-18 08:09
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1,080 by Soler
Fri, 2020-09-18 08:09
Normal topic Symmetry definition question
by mrconde96 » Sun, 2022-10-02 05:34
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1,436 by mrconde96
Sun, 2022-10-02 05:34
Normal topic Problem with Scoring function and PlaceStub mover
by a-eatemadi@razi... » Sat, 2018-04-07 09:22
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1,227 by a-eatemadi@razi...
Sat, 2018-04-07 09:24
Normal topic What is interface_cutoff_distance? And why did my residues outside this value get designed?
by chrisHKL » Fri, 2020-02-28 14:52
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1,113 by chrisHKL
Fri, 2020-02-28 14:52
Normal topic clustering output file has few structures
by fabiotrovato » Mon, 2020-08-17 11:37
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818 by fabiotrovato
Mon, 2020-08-17 11:37
Normal topic Error Run Blueprint File
by ileanexis » Thu, 2024-03-07 10:28
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192 by ileanexis
Thu, 2024-03-07 10:28
Normal topic Domain insertion with Non-CAA
by mwfranklin » Mon, 2017-01-16 12:30
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1,855 by mwfranklin
Mon, 2017-01-16 12:30
Normal topic Segment File Gen - no ouput
by CATarr » Wed, 2019-10-09 19:05
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953 by CATarr
Wed, 2019-10-09 19:05
Normal topic RosettaAntibody - No matching templates for CDR1
by agctomer » Tue, 2021-01-19 22:45
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1,006 by agctomer
Tue, 2021-01-19 22:45
Normal topic Generating the 3-mer and 9-mer fragments
by Prasoon » Wed, 2022-02-09 09:04
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1,286 by Prasoon
Wed, 2022-02-09 09:04
Normal topic Memory Leak in FragmentPicker.cxx11thread application
by Corvin » Tue, 2023-07-11 06:04
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384 by Corvin
Thu, 2023-07-13 05:30
Normal topic Flexpepdock I_hb scoring term
by mbakalar » Fri, 2018-08-31 13:05
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1,208 by mbakalar
Fri, 2018-08-31 13:06
Normal topic General question regarding ligand-docking
by Alison_Yajie » Thu, 2020-05-07 09:48
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861 by Alison_Yajie
Thu, 2020-05-07 09:48
Normal topic Modelling of multi-component symmetrical structures
by LanMei » Wed, 2020-10-07 09:58
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1,068 by LanMei
Wed, 2020-10-07 09:58
Normal topic Molecular Replacement with multiple chains
by brspurri » Fri, 2011-06-10 08:25
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2,217 by brspurri
Mon, 2014-04-21 06:47
Normal topic wallpaper symmetry definition file
by aaj » Fri, 2016-02-26 08:40
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1,490 by aaj
Fri, 2016-02-26 08:40
Normal topic pMHC modelling
by Roberto » Thu, 2022-08-04 07:11
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867 by Roberto
Thu, 2022-08-04 07:11
Normal topic Interesting scoring performance in flexpepdock against random peptides
by ziqi1234 » Fri, 2017-12-08 07:52
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1,212 by ziqi1234
Fri, 2017-12-08 07:52
Normal topic An error with score app
by Genta » Tue, 2019-10-29 18:46
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8,624 by Genta
Tue, 2019-10-29 18:46
Normal topic How do I compare the results of InterfaceAnalyzer using different trimers as input?
by franz72 » Sun, 2023-08-06 10:10
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394 by franz72
Sun, 2023-08-06 10:10
Normal topic antibody.mpi.linuxgccrelease some antibodies failing to model
by drewaight » Mon, 2020-11-02 17:07
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1,277 by drewaight
Mon, 2020-11-02 17:07
Normal topic Rosetta DARc suboptimal dockings
by ddhoyo » Mon, 2021-10-11 06:18
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771 by ddhoyo
Mon, 2021-10-11 06:18
Normal topic Snugdock Error: The sequence position requested was greater than the number of residues
by stannowitz » Tue, 2023-01-17 07:37
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1,200 by stannowitz
Tue, 2023-01-17 23:48
Normal topic SecundaryStructure Filter
by Soler » Sun, 2021-11-21 22:20
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892 by Soler
Sun, 2021-11-21 22:20
Normal topic how to control alignment for energy_based_clustering
by xfradera » Tue, 2023-02-28 10:13
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1,908 by xfradera
Tue, 2023-02-28 10:13
Normal topic DNA Interface design
by zadie1118 » Wed, 2011-06-22 07:05
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2,230 by zadie1118
Mon, 2014-04-21 06:47
Normal topic Rosetta remodel - including an RNA ligand
by daniloboskovic » Fri, 2020-04-10 04:24
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1,028 by daniloboskovic
Fri, 2020-04-10 04:24
Normal topic Fragment library (vall file) from Robetta?
by alex » Sun, 2017-02-19 08:12
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1,704 by alex
Sun, 2017-02-19 08:12
Normal topic using piper-flexpepdock
by syntekabio2019 » Thu, 2019-12-12 01:22
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1,392 by syntekabio2019
Thu, 2019-12-12 01:22
Normal topic Ab Initio folding with HEM ligand molecule
by jseco » Fri, 2021-03-05 06:49
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831 by jseco
Mon, 2021-03-08 03:40
Normal topic Dimeric interface redesign
by kjs1728 » Mon, 2022-05-02 21:57
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909 by kjs1728
Mon, 2022-05-02 21:57
Normal topic Match: Outputs with 0 hits for cst and clashes with sidechains
by uka147 » Wed, 2023-11-08 06:11
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321 by uka147
Thu, 2023-11-09 01:36
Normal topic Error when using Remodel on a protein with a chemically bound ligand
by Pappmaschee » Wed, 2020-12-16 09:23
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1,199 by Pappmaschee
Wed, 2020-12-16 09:23
Normal topic simple_cycpep_predict with N-term acetylation
by Ken » Fri, 2021-12-17 09:49
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1,053 by Ken
Fri, 2021-12-17 09:49
Normal topic dG_separated values comparison
by almeida85 » Mon, 2023-04-24 03:34
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624 by almeida85
Tue, 2023-05-16 01:02
Normal topic FlexPepDocking
by jlawrie » Tue, 2020-09-15 12:52
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970 by jlawrie
Tue, 2020-09-15 12:52
Normal topic Macrocycle from a C-terminal amidated peptide
by almeida85 » Thu, 2022-08-18 07:53
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1,046 by almeida85
Thu, 2022-08-18 07:53
Normal topic Problems met when do H3_modeling in the antibody design protocol
by ng98 » Sun, 2024-05-12 18:40
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232 by ng98
Sun, 2024-05-12 18:56
Normal topic csrosetta.org login
by jfeuva » Tue, 2014-12-09 14:49
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24,469 by jfeuva
Tue, 2014-12-09 14:49
Normal topic Zero residues error in docking
by cjy318 » Tue, 2020-07-28 19:47
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1,180 by cjy318
Tue, 2020-07-28 19:47
Normal topic Params for a stapled helix peptide
by e3lm » Thu, 2022-05-26 12:55
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939 by e3lm
Thu, 2022-05-26 12:55
Normal topic Secondary Matching build_sets Error
by enmirts » Wed, 2018-03-28 10:33
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1,164 by enmirts
Wed, 2018-03-28 10:34
Normal topic multi ligand docking using rosetta script
by syntekabio2019 » Tue, 2021-04-13 19:31
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854 by syntekabio2019
Tue, 2021-04-13 19:31
Normal topic Per residue total score
by johnnytam100 » Wed, 2022-07-13 21:57
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813 by johnnytam100
Wed, 2022-07-13 21:57
Normal topic rosetta remodel and designing helix extension
by dhirajks » Thu, 2018-12-13 19:34
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1,280 by dhirajks
Thu, 2018-12-13 19:34
Normal topic constraints in Rosetta ligand docking (AddorRemoveMatchCsts, Addconstraints Mover, and ConstraintSetMover)
by rohi » Mon, 2021-01-11 13:32
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1,060 by rohi
Mon, 2021-01-11 13:58
Normal topic Can anybody suggests some flags to run Rifdock?
by Hyunmi Song » Sun, 2022-01-23 16:45
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1,392 by Hyunmi Song
Sun, 2022-01-23 16:45
Normal topic FlexPepDock bug? Constraints do not appear in total_score?
by nrollins » Mon, 2021-07-26 14:29
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815 by nrollins
Mon, 2021-07-26 14:29
Normal topic Ligand Rotamer Control in Macther
by Hirbond » Tue, 2022-10-25 13:01
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1,826 by Hirbond
Wed, 2022-10-26 12:57
Normal topic FloppyTail as a rosettascripts file
by tiagogomes89 » Mon, 2015-01-19 02:45
0
1,464 by tiagogomes89
Mon, 2015-01-19 02:45
Normal topic Fewer than expected structures in clustering output
by fabiotrovato » Thu, 2020-08-20 00:59
0
872 by fabiotrovato
Thu, 2020-08-20 00:59
Normal topic Benchmarking Rosetta DDG Methods
by sareeves96 » Fri, 2022-07-29 09:55
0
1,003 by sareeves96
Fri, 2022-07-29 09:55
Normal topic Creation of crystal_complex.pdb for docking
by HBenson » Mon, 2024-03-11 08:57
0
226 by HBenson
Mon, 2024-03-11 08:57
Normal topic Ligand docking with constraint
by Alison_Yajie » Wed, 2020-06-24 12:34
0
911 by Alison_Yajie
Wed, 2020-06-24 12:34
Normal topic Question with rosetta AbPredict tutorial
by terabithia2011 » Mon, 2021-01-25 09:24
0
877 by terabithia2011
Mon, 2021-01-25 09:24
Normal topic Rosetta Matcher not recognizing protonation forms of CST files like CYZ, HIS_D, etc
by Hirbond » Tue, 2022-03-01 13:16
0
1,156 by Hirbond
Tue, 2022-03-01 13:16
Normal topic Symmetry definition file versions
by Jeff Qu » Tue, 2021-09-28 09:53
0
833 by Jeff Qu
Tue, 2021-09-28 09:53
Normal topic RosettaCM Ignoring Ligand
by Delfosse57 » Sun, 2022-12-04 12:05
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4,018 by Delfosse57
Sun, 2022-12-04 12:05
Normal topic The problems on pdb renumbering
by Sunyp_IM » Sun, 2017-08-20 06:39
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2,303 by Sunyp_IM
Sun, 2017-08-20 06:39
Normal topic Comparing a prediction to the native structure and calculate RMSD for RNA
by danwolf_33 » Thu, 2023-02-09 09:32
0
2,024 by danwolf_33
Thu, 2023-02-09 09:34
Normal topic behind threading protocol
by fred » Tue, 2011-10-25 05:37
0
2,282 by fred
Mon, 2014-04-21 06:47
Normal topic application for affinity optimization
by wentlewi » Fri, 2020-03-13 03:24
0
1,048 by wentlewi
Fri, 2020-03-13 03:24
Normal topic FastRelax Refinement severe clashes
by Victor Tobiasson » Thu, 2021-05-20 06:55
0
905 by Victor Tobiasson
Thu, 2021-05-20 06:55
Normal topic Does antibody_numbering_converter support camelid antibody?
by mxp » Tue, 2020-07-07 01:21
0
935 by mxp
Tue, 2020-07-07 01:21
Normal topic problem in using "zinc_site_redesign" tool
by Isomerase » Mon, 2022-03-28 01:19
0
804 by Isomerase
Mon, 2022-03-28 01:19
Normal topic extract docking pose from ligand docking silent file
by Ruska322 » Sat, 2019-09-07 05:21
0
1,094 by Ruska322
Sat, 2019-09-07 05:21
Normal topic How to apply cartesian_ddg to multi-metric enzyme?
by Wang Zhe » Wed, 2021-12-08 10:07
0
994 by Wang Zhe
Wed, 2021-12-08 10:07
Normal topic Protein Protein Docking with Linker
by mrinal » Mon, 2023-03-20 15:58
0
870 by mrinal
Mon, 2023-03-20 15:58
Normal topic Urgent issue: Error with submitting a new Rosetta-Vienna RNP-ddG job
by eyaaaan » Sun, 2022-08-07 22:03
0
945 by eyaaaan
Tue, 2022-08-09 21:59
Normal topic Model GFP chromophore(cro) using NCAA or NC backbone method?
by lei » Thu, 2024-04-04 06:23
0
201 by lei
Thu, 2024-04-04 06:23
Normal topic How many iterations of remodel is enough?
by daniloboskovic » Thu, 2020-07-16 08:07
0
884 by daniloboskovic
Thu, 2020-07-16 08:14

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