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Rosetta 3 - Applications

Topic / Topic starter Replies Viewssort ascending Last post
Normal topic AddHelixSequenceConstraints Mover
by Negarsardar » Thu, 2019-05-30 03:17
2
952 by vmulligan
Thu, 2019-06-13 14:59
Normal topic Coupled Moves crash with Membrane Protein - residue_edge is undefined for root vertex
by benhardy » Mon, 2020-06-15 09:33
3
950 by benhardy
Fri, 2020-06-19 07:55
Normal topic Coding denovo prediction from density maps in PyRosetta
by ahmadkhalifa » Tue, 2018-04-10 11:43
1
945 by rmoretti
Tue, 2018-04-10 15:29
Normal topic ligand docking with MPI
by Ruska322 » Wed, 2019-09-04 03:47
2
943 by Ruska322
Fri, 2019-09-06 07:13
Normal topic Relaxing protein-RNA complexes
by rkirchdo » Fri, 2018-08-03 08:50
1
941 by rmoretti
Fri, 2018-08-24 11:28
Normal topic Centroid mode minimization
by Martin Floor » Tue, 2020-01-21 07:34
2
940 by Martin Floor
Tue, 2020-01-21 11:15
Normal topic Ligand docking cannot open the protein file
by swarekwood » Tue, 2017-10-17 08:17
1
939 by rmoretti
Tue, 2017-10-17 09:03
Normal topic relax.linuxgccrelease in multiple processors
by jpfuenzalidawx » Thu, 2021-01-14 14:07
5
937 by jadolfbr
Fri, 2021-01-15 08:06
Normal topic Remodel: the pose does not have residue with chain=H, PDBnum=114
by lanselibai » Wed, 2019-12-25 13:35
1
936 by lanselibai
Fri, 2019-12-27 09:38
Normal topic broker domain insertion
by dhirajks » Sun, 2018-05-06 12:55
1
936 by rmoretti
Fri, 2018-05-18 12:28
Normal topic missing atom number 5 atom name CB
by ajaniharesh » Fri, 2019-04-26 12:08
1
928 by rmoretti
Fri, 2019-04-26 12:13
Normal topic Relax with multiple small molecules
by jharamesh » Sun, 2019-05-26 19:34
1
922 by rmoretti
Mon, 2019-06-24 15:19
Normal topic How does the label in pdb files looks like when using ResiduePDBInfoHasLabel?
by johnnytam100 » Fri, 2019-08-16 00:25
1
921 by JackMaguire
Fri, 2019-08-16 07:41
Normal topic Is native.pdb necess for fragment_picker?
by ylwang » Thu, 2020-03-12 00:57
2
919 by ylwang
Thu, 2020-03-12 20:42
Normal topic Prevention of the negatively charged Nitrogen protonation by coupled_moves
by Corvin » Wed, 2020-11-18 02:56
4
919 by Corvin
Wed, 2020-11-25 02:58
Normal topic Rosetta_cm Partial Threading Removing Parts of Sequence
by gszwabowski » Thu, 2019-06-20 12:30
1
913 by rmoretti
Mon, 2019-06-24 13:43
Normal topic Question on restraining receptor symmetry when docking ligand
by subha » Fri, 2018-07-06 21:59
1
912 by rmoretti
Fri, 2018-08-03 08:16
Normal topic Using abinition to predict a new (previously unsolved) structure.
by ac.research » Mon, 2017-01-09 00:59
0
905 by ac.research
Mon, 2017-01-09 00:59
Normal topic RosettaCM or FastRelax?
by Tianyang89 » Wed, 2020-09-23 07:46
3
899 by danpf
Thu, 2020-09-24 13:44
Normal topic Rosetta scripts crash in CM workflow
by jlburkhead » Tue, 2019-12-03 22:55
1
896 by danpf
Fri, 2020-02-21 18:37
Normal topic The usage of antibody_H3.linuxgccrelease
by Sunyp_IM » Thu, 2020-05-28 22:50
2
889 by Sunyp_IM
Thu, 2020-06-04 08:20
Normal topic Can't generate a cst file to use with ddg_monomer application
by ctqwong » Sat, 2021-03-13 03:53
6
889 by ctqwong
Thu, 2021-03-18 02:04
Normal topic change number of output pose files written out (default=50) in ligand docking XML script
by hdelrisco » Fri, 2019-10-18 13:50
2
888 by hdelrisco
Fri, 2019-10-18 17:16
Normal topic can anyone help me correct this script to do alanine scanning
by xinmiaohe » Mon, 2019-08-26 17:23
1
887 by xinmiaohe
Mon, 2019-08-26 18:16
Normal topic Threading with Ligand
by ekwan » Thu, 2018-12-06 15:10
1
885 by rmoretti
Fri, 2019-03-29 13:21
Normal topic loop design for Conformational bias
by dhirajks » Thu, 2019-05-09 21:22
1
885 by jadolfbr
Fri, 2019-05-10 07:53
Normal topic VH-VL Orientation in antibody
by sujigeorge1979 » Mon, 2019-06-17 01:23
1
883 by jeliazkov
Mon, 2019-06-17 06:03
Normal topic Protein Protein Docking with Constraints
by ajaniharesh » Wed, 2019-04-10 07:26
1
881 by rmoretti
Thu, 2019-05-09 15:40
Normal topic Usage of the TaskOperations "RestrictToCDRsAndNeighbors"
by johnnytam100 » Wed, 2019-04-10 02:58
1
880 by rmoretti
Wed, 2019-07-10 10:10
Normal topic PlaceStub filter
by a-eatemadi@razi... » Wed, 2017-11-15 04:19
0
872 by a-eatemadi@razi...
Mon, 2017-12-04 23:52
Normal topic OptimizeMembranePositionMover - This element is not expected
by bjharris » Wed, 2020-07-01 23:21
2
864 by bjharris
Thu, 2020-07-02 11:09
Normal topic docking with capping groups
by xavierfradera » Sun, 2018-11-04 16:17
1
862 by maral.adeli-kou...
Wed, 2020-01-22 12:41
Normal topic Any progress on getting intermediate structures during a design?
by broomsday » Mon, 2020-03-16 06:46
2
856 by vmulligan
Tue, 2020-03-17 11:35
Normal topic Error with Formatdb of legacy blast when running "install_dependencies.pl"?
by Danielsebas » Mon, 2019-09-16 09:30
2
856 by Danielsebas
Tue, 2019-09-17 01:03
Normal topic Membrane ab-initio modelling of a beta-strand
by hzhekova » Mon, 2019-06-10 14:22
1
850 by rmoretti
Mon, 2019-06-24 14:39
Normal topic issues about cstfile in RosettaMatch
by Nicole Deng » Fri, 2020-12-18 05:44
3
846 by He Xiao
Sun, 2021-04-11 19:29
Normal topic Sampling a wider range of RMSD of poses by Rosetta Dock
by johnnytam100 » Tue, 2019-05-21 22:28
1
844 by johnnytam100
Thu, 2019-05-23 20:52
Normal topic PDB moves after relaxing
by Hr13b » Fri, 2018-07-27 13:12
1
844 by smlewis
Fri, 2018-07-27 13:32
Normal topic input file for loop modeling
by Negarsardar » Tue, 2019-04-16 10:21
1
841 by rmoretti
Tue, 2019-04-16 11:07
Normal topic "Angle constraint: 0-length bonds" error
by purvi24 » Sun, 2019-07-28 10:09
1
840 by rmoretti
Mon, 2019-08-26 12:49
Normal topic Abinitio the Broker protocol
by ac.research » Sun, 2019-03-24 03:56
1
839 by rmoretti
Fri, 2019-04-05 00:18
Normal topic How to freeze ligand during FastRelax?
by dnamkr » Thu, 2020-01-02 14:53
1
839 by aloshbau
Fri, 2020-01-10 16:48
Normal topic ProteinInterfaceMS
by rbjacob » Wed, 2018-10-24 11:31
1
838 by rmoretti
Wed, 2018-11-21 15:10
Normal topic protein interction design
by Negarsardar » Wed, 2019-05-15 12:01
1
835 by rmoretti
Wed, 2019-07-10 09:24
Normal topic Predicting the part of protein strcutrue
by ksy141 » Tue, 2018-10-16 11:47
1
832 by jadolfbr
Fri, 2018-11-09 14:28
Normal topic hybrid approach - comparative and ab initio modelling
by eprates » Wed, 2019-03-20 11:58
1
829 by rmoretti
Fri, 2019-03-29 09:45
Normal topic Can rosetta generate a centroid model based on the rna sequence?
by yels » Fri, 2021-03-26 04:06
7
829 by yels
Wed, 2021-03-31 18:31
Normal topic BUG REPORT: Remodel Resfile ERROR: LEU was added more than once?
by daniloboskovic » Wed, 2020-04-29 01:17
2
820 by daniloboskovic
Wed, 2020-04-29 05:51
Normal topic make_fragments.pl error
by almeida85 » Mon, 2020-08-31 04:39
2
820 by almeida85
Tue, 2020-09-01 01:29
Normal topic pmut_scan_parallel
by G Mustafa » Wed, 2018-10-17 05:41
0
817 by G Mustafa
Wed, 2018-10-17 05:41
Normal topic nstruct vs. trials?
by chrisHKL » Mon, 2020-03-02 13:22
2
816 by chrisHKL
Wed, 2020-03-04 10:49
Normal topic Rosetta Antibody Design: Error with foldtree: problem with the fold_tree:biggest_label != num_jump 2 1
by cm21 » Wed, 2020-05-20 08:55
2
813 by cm21
Wed, 2020-05-20 11:22
Normal topic "core.kinematics.FoldTree" error upon running RAbD
by Sunyp_IM » Fri, 2020-06-26 17:27
2
804 by Sunyp_IM
Fri, 2020-06-26 20:57
Normal topic How to create a native file for Protein-Protein docking
by Kotimedidhi » Fri, 2020-06-19 08:58
2
795 by Kotimedidhi
Mon, 2020-06-22 16:19
Normal topic backrub application, resfile, and pivot_residues
by tylerborrman » Tue, 2016-12-06 14:46
0
794 by tylerborrman
Tue, 2016-12-06 14:46
Normal topic debug rosetta_scripts FunFolDes run
by tatsiana.bylund » Sun, 2019-08-18 23:17
1
792 by neelamraju.srid...
Wed, 2020-11-18 05:47
Normal topic ligand_docking ligand preparation
by Alison_Yajie » Thu, 2020-05-21 10:21
2
790 by Alison_Yajie
Wed, 2020-06-24 12:38
Normal topic how to generate the whole molecule that contains all the symmetric chains
by Sunyp_IM » Sun, 2017-12-10 19:43
0
789 by Sunyp_IM
Sun, 2017-12-10 19:43
Normal topic How to design the anitgen-antibody interface
by Sunyp_IM » Tue, 2017-12-12 18:44
0
788 by Sunyp_IM
Tue, 2017-12-12 18:44
Normal topic kcenters_clustering_of_fragments
by bjharris » Mon, 2019-07-01 16:16
1
785 by bjharris
Wed, 2020-07-01 23:25
Normal topic Modelling temperature dependent RNA structures
by tuleshwori » Tue, 2020-05-19 01:16
2
780 by tuleshwori
Thu, 2020-05-21 02:08
Normal topic Homology Modeling-no PDB output
by jlawrie » Wed, 2020-08-12 06:30
2
777 by jlawrie
Wed, 2020-08-12 08:56
Normal topic "install_dependencies.pl" script: an optimization of HDD space during nr-pfilt data extracting and formatting stage
by Corvin » Thu, 2019-10-10 02:20
1
775 by danpf
Thu, 2019-10-10 09:55
Normal topic how to "rescore" the models using lowest energy model from rosetta run as native, for RMSD vs Score plot?
by Danielsebas » Tue, 2019-09-24 03:51
1
771 by smlewis
Tue, 2019-09-24 12:43
Normal topic antibody.linuxgccrelease- output models don't have the same sequence as the input fasta
by agctomer » Thu, 2021-01-21 15:35
4
767 by agctomer
Sun, 2021-01-31 01:06
Normal topic Error with RosettaAntibodyDesign when running antibody_designer.linuxgccrelease
by bdzhh » Tue, 2019-09-17 17:02
1
765 by jadolfbr
Thu, 2019-09-19 08:53
Normal topic The relax qustion of Rosetta VIP
by asbelx » Mon, 2019-06-10 07:52
1
764 by rmoretti
Mon, 2019-06-24 14:42
Normal topic Scoring docking error
by almeida85 » Wed, 2020-09-02 01:32
2
763 by almeida85
Wed, 2020-09-02 06:14
Normal topic FlexPepDock Multi chain receptor
by evo_umich » Mon, 2018-04-02 12:13
0
762 by evo_umich
Mon, 2018-04-02 12:13
Normal topic RosettaAntibodyDesign] How can I use run_relax and run_snugdock as part of my command and workflow?
by brspurri » Thu, 2020-05-14 11:15
2
756 by brspurri
Thu, 2020-05-14 12:24
Normal topic Docking-I_sc values do not correlate
by jlawrie » Wed, 2020-08-12 08:08
2
755 by jlawrie
Wed, 2020-08-12 08:57
Normal topic not knowing which one of three ways to run rosettascript
by xinmiaohe » Tue, 2020-10-13 13:52
2
755 by xinmiaohe
Mon, 2020-10-19 13:18
Normal topic Number of max allowed mutations from WT sequence
by mouung » Fri, 2020-09-04 02:33
2
752 by amorin
Fri, 2021-02-12 08:53
Normal topic denovo modelling on a virus-coat protein dimer
by aseem121 » Wed, 2019-10-16 06:55
1
748 by danpf
Wed, 2019-10-16 13:03
Normal topic AddHelixSequenceConstraints Mover2
by Negarsardar » Sat, 2019-06-01 01:54
1
747 by vmulligan
Thu, 2019-06-13 15:01
Normal topic antibody protocol fails
by hamedkhakzad » Mon, 2019-08-19 07:43
1
735 by smlewis
Tue, 2019-10-22 09:45
Normal topic minimize_with_cst and convert_to_cst_file for ddG_monomer issues/confusion
by Kharlamov1317a » Mon, 2020-09-21 08:46
1
733 by Kharlamov1317a
Wed, 2020-10-07 08:26
Normal topic LoopModeler mover unable to determine cut point
by gszwabowski » Mon, 2020-06-01 13:12
1
731 by matteoferla
Thu, 2020-07-02 07:27
Normal topic DDG_monomer ΔΔG question
by asbelx » Fri, 2018-04-20 03:31
0
730 by asbelx
Fri, 2018-04-20 03:33
Normal topic Can I use rosetta binaries built in one linux system to another linux system?
by Danielsebas » Wed, 2019-09-18 06:49
1
722 by rmoretti
Wed, 2019-09-18 10:36
Normal topic Successful RosettaCM?
by jlawrie » Wed, 2020-08-19 06:53
2
721 by jlawrie
Thu, 2020-08-20 11:00
Normal topic Robetta ab initio - TrRosetta for membrane proteins
by benhardy » Wed, 2020-09-30 08:42
0
718 by benhardy
Wed, 2020-09-30 08:42
Normal topic RNA modeling with step wise Monte Carlo error
by szcshr123 » Mon, 2020-12-07 18:08
3
710 by everyday847
Wed, 2020-12-09 21:46
Normal topic How to analyse multiple silent files from "Abinitiorelax" output to find best models?
by Danielsebas » Tue, 2019-09-10 10:01
1
706 by smlewis
Mon, 2019-09-16 12:22
Normal topic RosettaScripts filter BuriedUnsatHbonds2 missing still
by zdaw » Fri, 2020-12-11 12:39
3
706 by zdaw
Tue, 2020-12-15 15:38
Normal topic Issue with Rosetta LinkResidues Script
by adityapadhi » Wed, 2019-11-20 22:00
1
705 by JackMaguire
Fri, 2019-11-22 13:45
Normal topic DDG and interaction score problem
by a-eatemadi@razi... » Mon, 2018-04-09 22:54
0
702 by a-eatemadi@razi...
Mon, 2018-04-09 22:54
Normal topic fixing sequence during grafting in antibody_designer
by COM » Fri, 2020-01-24 11:38
1
701 by jadolfbr
Tue, 2020-01-28 09:13
Normal topic Protein-Protein Docking or Comparative Modeling
by Morrian_Lynn » Wed, 2020-01-29 19:01
1
697 by danpf
Fri, 2020-02-21 18:23
Normal topic Error when trying docking protocol with different ligand
by scyphs » Wed, 2020-08-05 04:37
2
695 by scyphs
Mon, 2020-08-10 08:09
Normal topic get an increased energy after energy minimization when using different score functions for repacking and energy minimization
by xinmiaohe » Fri, 2020-02-07 11:59
1
691 by xinmiaohe
Fri, 2020-02-07 13:52
Normal topic Docking-RMS value nan
by jlawrie » Wed, 2020-08-12 07:03
2
689 by jlawrie
Wed, 2020-08-12 07:27
Normal topic Dock two domains using topology broker
by sn » Thu, 2017-10-05 17:07
0
688 by sn
Thu, 2017-10-05 17:07
Normal topic Rosetta antibody- modeling in the presense of an antigen
by agctomer » Mon, 2021-02-01 03:19
4
688 by nannemdp
Wed, 2021-02-03 08:52
Normal topic Interesting scoring performance in flexpepdock against random peptides
by ziqi1234 » Fri, 2017-12-08 07:52
0
687 by ziqi1234
Fri, 2017-12-08 07:52
Normal topic Adding positional restraints to pure RNA system in DRRAFTER and rna_denovo
by zharmad » Fri, 2019-08-23 01:16
1
684 by everyday847
Fri, 2019-08-23 04:08
Normal topic Do partner1 and partner2 in mover BackrubDD mean chain1 and chain2 respectively?
by johnnytam100 » Fri, 2019-08-23 21:10
1
682 by rmoretti
Mon, 2019-08-26 12:03
Normal topic Problem with Scoring function and PlaceStub mover
by a-eatemadi@razi... » Sat, 2018-04-07 09:22
0
679 by a-eatemadi@razi...
Sat, 2018-04-07 09:24
Normal topic rosetta remodel and designing helix extension
by dhirajks » Thu, 2018-12-13 19:34
0
678 by dhirajks
Thu, 2018-12-13 19:34
Normal topic comparative modelling of a complex
by sdh_h » Sun, 2017-12-17 06:07
0
674 by sdh_h
Sun, 2017-12-17 06:07
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