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Rosetta 3 - Applications

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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
0
903 by chrisHKL
Fri, 2020-02-28 14:52
Normal topic clustering output file has few structures
by fabiotrovato » Mon, 2020-08-17 11:37
0
691 by fabiotrovato
Mon, 2020-08-17 11:37
Normal topic Domain insertion with Non-CAA
by mwfranklin » Mon, 2017-01-16 12:30
0
1,670 by mwfranklin
Mon, 2017-01-16 12:30
Normal topic Segment File Gen - no ouput
by CATarr » Wed, 2019-10-09 19:05
0
839 by CATarr
Wed, 2019-10-09 19:05
Normal topic RosettaAntibody - No matching templates for CDR1
by agctomer » Tue, 2021-01-19 22:45
0
835 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
0
1,050 by Prasoon
Wed, 2022-02-09 09:04
Normal topic Memory Leak in FragmentPicker.cxx11thread application
by Corvin » Tue, 2023-07-11 06:04
0
184 by Corvin
Thu, 2023-07-13 05:30
Normal topic Interesting scoring performance in flexpepdock against random peptides
by ziqi1234 » Fri, 2017-12-08 07:52
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1,064 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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5,175 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
0
179 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
0
1,089 by drewaight
Mon, 2020-11-02 17:07
Normal topic Rosetta DARc suboptimal dockings
by ddhoyo » Mon, 2021-10-11 06:18
0
615 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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950 by stannowitz
Tue, 2023-01-17 23:48
Normal topic wallpaper symmetry definition file
by aaj » Fri, 2016-02-26 08:40
0
1,355 by aaj
Fri, 2016-02-26 08:40
Normal topic pMHC modelling
by Roberto » Thu, 2022-08-04 07:11
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623 by Roberto
Thu, 2022-08-04 07:11
Normal topic Fragment library (vall file) from Robetta?
by alex » Sun, 2017-02-19 08:12
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1,565 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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1,176 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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692 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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759 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
0
89 by uka147
Thu, 2023-11-09 01:36
Normal topic SecundaryStructure Filter
by Soler » Sun, 2021-11-21 22:20
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752 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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1,730 by xfradera
Tue, 2023-02-28 10:13
Normal topic Rosetta remodel - including an RNA ligand
by daniloboskovic » Fri, 2020-04-10 04:24
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910 by daniloboskovic
Fri, 2020-04-10 04:24
Normal topic csrosetta.org login
by jfeuva » Tue, 2014-12-09 14:49
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24,348 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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965 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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756 by e3lm
Thu, 2022-05-26 12:55
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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1,026 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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832 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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342 by almeida85
Tue, 2023-05-16 01:02
Normal topic FlexPepDocking
by jlawrie » Tue, 2020-09-15 12:52
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832 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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771 by almeida85
Thu, 2022-08-18 07:53
Normal topic FlexPepDock bug? Constraints do not appear in total_score?
by nrollins » Mon, 2021-07-26 14:29
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650 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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1,625 by Hirbond
Wed, 2022-10-26 12:57
Normal topic Secondary Matching build_sets Error
by enmirts » Wed, 2018-03-28 10:33
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1,055 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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709 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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644 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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1,118 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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932 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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1,119 by Hyunmi Song
Sun, 2022-01-23 16:45
Normal topic membrane ab-initio modeling, is the quality comparable to comparative modeling of 20% id template?
by fglaser » Thu, 2011-04-07 07:57
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2,200 by fglaser
Mon, 2014-04-21 06:47
Normal topic Symmetry definition file versions
by Jeff Qu » Tue, 2021-09-28 09:53
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676 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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3,820 by Delfosse57
Sun, 2022-12-04 12:05
Normal topic FloppyTail as a rosettascripts file
by tiagogomes89 » Mon, 2015-01-19 02:45
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1,353 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
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729 by fabiotrovato
Thu, 2020-08-20 00:59
Normal topic Benchmarking Rosetta DDG Methods
by sareeves96 » Fri, 2022-07-29 09:55
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756 by sareeves96
Fri, 2022-07-29 09:55
Normal topic Ligand docking with constraint
by Alison_Yajie » Wed, 2020-06-24 12:34
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766 by Alison_Yajie
Wed, 2020-06-24 12:34
Normal topic Question with rosetta AbPredict tutorial
by terabithia2011 » Mon, 2021-01-25 09:24
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720 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
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844 by Hirbond
Tue, 2022-03-01 13:16
Normal topic Does antibody_numbering_converter support camelid antibody?
by mxp » Tue, 2020-07-07 01:21
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808 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
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657 by Isomerase
Mon, 2022-03-28 01:19
Normal topic The problems on pdb renumbering
by Sunyp_IM » Sun, 2017-08-20 06:39
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2,080 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
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1,752 by danwolf_33
Thu, 2023-02-09 09:34
Normal topic application for affinity optimization
by wentlewi » Fri, 2020-03-13 03:24
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912 by wentlewi
Fri, 2020-03-13 03:24
Normal topic FastRelax Refinement severe clashes
by Victor Tobiasson » Thu, 2021-05-20 06:55
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703 by Victor Tobiasson
Thu, 2021-05-20 06:55
Normal topic Folding and Docking using Symmetry
by danielles » Wed, 2012-09-12 11:32
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1,810 by danielles
Mon, 2014-04-21 06:47
Normal topic How many iterations of remodel is enough?
by daniloboskovic » Thu, 2020-07-16 08:07
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751 by daniloboskovic
Thu, 2020-07-16 08:14
Normal topic extract docking pose from ligand docking silent file
by Ruska322 » Sat, 2019-09-07 05:21
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947 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
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828 by Wang Zhe
Wed, 2021-12-08 10:07
Normal topic Protein Protein Docking with Linker
by mrinal » Mon, 2023-03-20 15:58
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614 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
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737 by eyaaaan
Tue, 2022-08-09 21:59
Normal topic PDB Clustering
by code_Monkey » Mon, 2021-04-05 10:40
0
683 by code_Monkey
Mon, 2021-04-05 10:40
Normal topic backrub application, resfile, and pivot_residues
by tylerborrman » Tue, 2016-12-06 14:46
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1,197 by tylerborrman
Tue, 2016-12-06 14:46
Normal topic Dock two domains using topology broker
by sn » Thu, 2017-10-05 17:07
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1,070 by sn
Thu, 2017-10-05 17:07
Normal topic "Residue 7 was disulfide bonded but had no partner" with antibody.linuxgccrelease
by Sunyp_IM » Thu, 2020-06-04 05:53
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790 by Sunyp_IM
Thu, 2020-06-04 05:54
Normal topic Protein design: Ligand binding between two units of a homodimer
by chemotaxis_123 » Sun, 2022-01-02 16:01
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830 by chemotaxis_123
Sun, 2022-01-02 16:01
Normal topic RNP structure prediction flags
by daniloboskovic » Fri, 2019-08-16 11:10
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895 by daniloboskovic
Fri, 2019-08-16 11:17
Normal topic Robetta ab initio - TrRosetta for membrane proteins
by benhardy » Wed, 2020-09-30 08:42
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1,272 by benhardy
Wed, 2020-09-30 08:42
Normal topic Topobuilder segmentation fault
by tatsiana.bylund » Mon, 2021-08-09 07:10
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1,072 by tatsiana.bylund
Mon, 2021-08-09 07:10
Normal topic Help to understand docking results
by rtorquato » Fri, 2022-11-25 12:05
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1,325 by rtorquato
Fri, 2022-11-25 12:05
Normal topic FlexPepDock Multi chain receptor
by evo_umich » Mon, 2018-04-02 12:13
0
1,158 by evo_umich
Mon, 2018-04-02 12:13
Normal topic Error with RNA_denovo
by zmfowler » Thu, 2022-07-14 05:34
0
643 by zmfowler
Thu, 2022-07-14 05:34
Normal topic Scoring after HBNet
by HHL_SIUC » Wed, 2020-07-01 10:49
0
766 by HHL_SIUC
Wed, 2020-07-01 10:49
Normal topic Pepspec options
by shaunmk » Mon, 2015-04-27 02:33
0
1,588 by shaunmk
Mon, 2015-04-27 02:33
Normal topic Linker Building in scFv
by sam_dc » Sat, 2021-10-09 05:38
0
698 by sam_dc
Sat, 2021-10-09 05:38
Normal topic RosettaAntibody3 - How can I model an extended H3?
by brspurri » Fri, 2020-08-28 09:11
0
769 by brspurri
Fri, 2020-08-28 09:11
Normal topic help surface_docking peptide on ice
by engand93 » Wed, 2019-03-27 02:43
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922 by engand93
Wed, 2019-03-27 02:43
Normal topic Error with docking_prepack_protocol while executing the tutorial "Docking Flexible Proteins"
by vitoralmeida1808 » Mon, 2023-11-06 09:43
0
55 by vitoralmeida1808
Mon, 2023-11-06 09:43
Normal topic pmut_scan_parallel
by G Mustafa » Wed, 2018-10-17 05:41
0
1,366 by G Mustafa
Wed, 2018-10-17 05:41
Normal topic ligand_docking: ligand preparation
by Alison_Yajie » Thu, 2020-05-21 09:42
0
872 by Alison_Yajie
Thu, 2020-05-21 09:42
Normal topic constraining different chains together in rosetta_cm
by y_atsmonraz » Thu, 2021-11-18 02:59
0
738 by y_atsmonraz
Thu, 2021-11-18 03:01
Normal topic Finding lowest energy structure among generated structures
by Marius1987 » Sun, 2016-04-10 11:38
0
1,494 by Marius1987
Sun, 2016-04-10 12:09
Normal topic What means "[ ERROR ] TIME_STAMP: AbrelaxMover: finished ...NO_BATCH S_0001."
by Corvin » Thu, 2020-04-02 00:16
0
912 by Corvin
Thu, 2020-04-02 00:16
Normal topic Helical Symmetry Axis
by Sandy » Tue, 2016-05-31 18:48
0
1,669 by Sandy
Tue, 2016-05-31 18:48
Normal topic RosettaAntibody3 core.pose.util error
by linhhoang157 » Tue, 2020-07-28 12:40
0
923 by linhhoang157
Tue, 2020-07-28 12:40
Normal topic IL-2 gets better binding with beta / gamma
by tonycheng1688 » Wed, 2022-05-25 10:23
0
772 by tonycheng1688
Wed, 2022-05-25 10:23
Normal topic Problems with mpi version of antibody.linuxgccrelease
by Sunyp_IM » Thu, 2020-05-28 23:06
0
998 by Sunyp_IM
Thu, 2020-05-28 23:07
Normal topic Protonating all possible sites: the problem in MOL2 file format or the innate Rosetta feature(bug)?
by Corvin » Wed, 2020-12-16 04:58
0
958 by Corvin
Wed, 2020-12-30 09:21
Normal topic Segfault error while running MR Rosetta in Phenix
by memilton » Thu, 2021-12-16 09:09
0
902 by memilton
Thu, 2021-12-16 09:09
Normal topic Docking HeparinSulfate to proteins using GlycanDock
by GebauerJ » Tue, 2022-08-16 07:44
0
741 by GebauerJ
Tue, 2022-08-16 07:44
Normal topic new BUNS for FunFolDes run
by tatsiana.bylund » Wed, 2019-08-14 20:57
0
908 by tatsiana.bylund
Wed, 2019-08-14 20:57
Normal topic FlexPepDock ab initio: behavior without fragment files
by nrollins » Mon, 2021-07-26 14:16
0
598 by nrollins
Mon, 2021-07-26 14:16
Normal topic Setting pivots points for GenKIC
by almeida85 » Tue, 2022-10-25 02:32
0
1,548 by almeida85
Tue, 2022-10-25 02:32
Normal topic Design of multimeric protein
by ldlamini » Mon, 2021-01-11 07:23
0
792 by ldlamini
Mon, 2021-01-11 07:23
Normal topic ligand dock into HEM containg pdb
by syntekabio2019 » Thu, 2022-01-20 03:05
0
913 by syntekabio2019
Thu, 2022-01-20 03:05
Normal topic non-zero ddG of binding even without mutations
by top-gun98 » Wed, 2023-06-07 17:19
0
240 by top-gun98
Wed, 2023-06-07 17:19
Normal topic Using GlycanDock and the Antibody Affinity Maturation protocol.
by tbelec » Mon, 2022-02-28 12:37
0
1,014 by tbelec
Mon, 2022-02-28 12:37
Normal topic How to design the anitgen-antibody interface
by Sunyp_IM » Tue, 2017-12-12 18:44
0
1,145 by Sunyp_IM
Tue, 2017-12-12 18:44
Normal topic Symmetry mode in Remodel for N-terminal extension
by yvonne.chan2 » Mon, 2019-11-04 13:41
0
1,157 by yvonne.chan2
Mon, 2019-11-04 13:41
Normal topic zero standard deviation of I_sc in protein-protein docking
by rohi » Fri, 2020-07-03 22:19
0
747 by rohi
Fri, 2020-07-03 22:20
Normal topic Segfault with Pepspec
by almeida85 » Thu, 2021-02-11 02:56
0
608 by almeida85
Thu, 2021-02-11 02:56
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