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Rosetta 3 - Applications

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Normal topic Creating model of 89-90 residues by ab initio methodology-help
by krlitros87 » Sun, 2014-05-25 12:12
1
1,780 by rmoretti
Mon, 2014-05-26 09:29
Normal topic Membrane ab-initio modelling of a beta-strand
by hzhekova » Mon, 2019-06-10 14:22
1
1,023 by rmoretti
Mon, 2019-06-24 14:39
Normal topic density scoring
by Tianyang89 » Sat, 2020-08-29 04:54
1
912 by danpf
Sun, 2020-08-30 22:23
Normal topic Is it possible to restart the ddg_monomer.linuxgccrelease?
by lanselibai » Mon, 2015-09-07 03:46
1
1,622 by rmoretti
Wed, 2015-09-09 12:01
Normal topic Rosetta failed in making score.fsc
by josdee » Sun, 2017-02-05 21:58
1
1,391 by smlewis
Mon, 2017-02-06 06:57
Normal topic different value of score from rna_denovo and rna_score?
by yikanzhang » Wed, 2021-02-03 07:17
1
522 by CameronJA
Tue, 2021-06-15 20:02
Normal topic Alanine Scanning
by gjbartlett » Mon, 2013-08-05 07:02
1
3,036 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Enzyme Design with additional covalent backbone bonds
by mwfranklin » Wed, 2016-08-03 10:23
1
1,930 by rmoretti
Mon, 2016-09-05 11:29
Normal topic Getting error with Rosetta "antibody.linuxgccrelease" command
by Sunyp_IM » Mon, 2017-08-07 19:40
1
1,951 by smlewis
Tue, 2017-08-15 23:19
Normal topic can anyone help me correct this script to do alanine scanning
by xinmiaohe » Mon, 2019-08-26 17:23
1
1,087 by xinmiaohe
Mon, 2019-08-26 18:16
Normal topic ERROR: unrecognized residue name 'GLY_p:RepulsiveOnly'
by smiruthi » Mon, 2011-12-12 14:27
1
2,341 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Files for Spatial Constraints
by Derek » Tue, 2016-04-12 01:00
1
1,476 by Derek
Wed, 2016-04-27 01:31
Normal topic Partial Active Site Design for a Novel Substrate
by Derek » Wed, 2017-05-17 19:41
1
1,276 by rmoretti
Thu, 2017-05-18 13:51
Normal topic Calbur vs Energy Based Clustering
by Swillard » Sun, 2018-07-01 13:24
1
1,385 by rmoretti
Fri, 2018-08-03 08:26
Normal topic kcenters_clustering_of_fragments
by bjharris » Mon, 2019-07-01 16:16
1
987 by bjharris
Wed, 2020-07-01 23:25
Normal topic Enzyme design output silent file and score file
by deltag » Fri, 2012-09-28 13:07
1
1,970 by rmoretti
Mon, 2014-04-21 06:47
Normal topic number of structures in homology modeling for cluster analysis
by pdbb » Fri, 2013-04-12 08:52
1
2,220 by smlewis
Mon, 2014-04-21 06:47
Normal topic ddg_monomer "ERROR: seqpos >= 1"
by cossio » Fri, 2015-10-02 12:20
1
1,795 by rmoretti
Fri, 2015-10-02 12:30
Normal topic manually defining CDRs in antibody modelling
by gard.nelson » Fri, 2020-07-10 13:31
1
747 by brspurri
Wed, 2021-01-20 08:11
Normal topic Flexible docking using rosetta density-fitting for DNA
by helm » Thu, 2012-06-14 23:43
1
2,276 by smlewis
Mon, 2014-04-21 06:47
Normal topic ProteinInterfaceMS
by rbjacob » Wed, 2018-10-24 11:31
1
1,011 by rmoretti
Wed, 2018-11-21 15:10
Normal topic polymer docking using rosetta scripts
by syntekabio2019 » Fri, 2020-11-27 01:51
1
632 by rmoretti
Fri, 2020-11-27 10:47
Normal topic FloppyTail options error
by DmitriiN » Fri, 2016-11-11 02:54
1
1,388 by smlewis
Fri, 2016-11-11 08:33
Normal topic LoopModeler mover unable to determine cut point
by gszwabowski » Mon, 2020-06-01 13:12
1
941 by matteoferla
Thu, 2020-07-02 07:27
Normal topic docking with constraints
by talavera » Tue, 2013-05-07 01:50
1
3,558 by rmoretti
Mon, 2014-04-21 06:47
Normal topic ArchiveManager -- spinning down
by Marius1987 » Fri, 2016-12-23 03:10
1
1,365 by smlewis
Fri, 2016-12-23 07:04
Normal topic Abinitio error: std::out_of_range: basic_string
by Harley Worthy » Tue, 2017-10-31 15:20
1
1,634 by Harley Worthy
Thu, 2017-11-02 08:53
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
985 by smlewis
Tue, 2019-09-24 12:43
Normal topic problem when exact pdb from silent file
by wenchangyu2008 » Mon, 2011-04-18 00:42
1
2,670 by wenchangyu2008
Mon, 2014-04-21 06:47
Normal topic PDB moves after relaxing
by Hr13b » Fri, 2018-07-27 13:12
1
984 by smlewis
Fri, 2018-07-27 13:32
Normal topic can remodel add loops in one chain in multichain PDB structure?
by ksteczk » Fri, 2020-05-01 06:26
1
821 by matteoferla
Mon, 2020-05-04 01:43
Normal topic Binding energy contribution broken down by residue
by brspurri » Tue, 2013-07-23 12:47
1
2,359 by rmoretti
Mon, 2014-04-21 06:48
Normal topic score_jd2 errors out with: ERROR: [ERROR] Error opening RBSeg file 'batch_000065_000059'
by sn » Fri, 2017-03-24 12:26
1
1,364 by rmoretti
Fri, 2017-03-24 13:39
Normal topic protein interction design
by Negarsardar » Wed, 2019-05-15 12:01
1
1,002 by rmoretti
Wed, 2019-07-10 09:24
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
857 by xinmiaohe
Fri, 2020-02-07 13:52
Normal topic Protein-DNA Docking using RosettaScripts?
by brspurri » Fri, 2013-06-07 09:06
1
3,894 by rmoretti
Mon, 2014-04-21 06:48
Normal topic RosettaCM/hybridize
by kywei » Wed, 2021-04-28 09:56
1
488 by vmulligan
Wed, 2021-04-28 12:59
Normal topic Ab-initio modeling on part of the protein
by xiayanlawrence » Thu, 2013-12-19 07:45
1
2,967 by rmoretti
Mon, 2014-04-21 06:48
Normal topic latest version of rosetta unable to build models
by pramod » Mon, 2014-11-03 11:31
1
2,161 by rmoretti
Tue, 2014-11-04 10:33
Normal topic RosettaRemodel: ERROR: 'Replacing' an atom which doesn't currently exist.
by kamau » Fri, 2017-12-01 08:42
1
1,216 by kamau
Wed, 2017-12-13 14:31
Normal topic Adding 'virtual' residues for N- and C-terminal optimisation
by Derek Smith » Thu, 2014-08-14 23:18
1
1,838 by jadolfbr
Fri, 2014-10-31 09:00
Normal topic Adding positional restraints to pure RNA system in DRRAFTER and rna_denovo
by zharmad » Fri, 2019-08-23 01:16
1
856 by everyday847
Fri, 2019-08-23 04:08
Normal topic VH-VL Orientation in antibody
by sujigeorge1979 » Mon, 2019-06-17 01:23
1
1,133 by jeliazkov
Mon, 2019-06-17 06:03
Normal topic Standalone alanine scanning protocol
by exchhattu » Thu, 2011-10-13 19:40
1
4,852 by smlewis
Mon, 2014-04-21 06:47
Normal topic hybrid approach - comparative and ab initio modelling
by eprates » Wed, 2019-03-20 11:58
1
967 by rmoretti
Fri, 2019-03-29 09:45
Normal topic Rosetta Remodel - Error in core::conformation::Conformation::residue(): The sequence position requested was 0.
by daniloboskovic » Fri, 2019-11-08 08:24
1
1,547 by Payne
Tue, 2022-06-21 07:25
Normal topic Holes output interpretation
by lah435 » Mon, 2012-06-04 15:02
1
2,016 by smlewis
Mon, 2014-04-21 06:47
Normal topic Loopmodel with DNA has no energy score
by Nicky_Learning_... » Sun, 2015-05-10 19:31
1
1,801 by rmoretti
Mon, 2015-05-25 12:30
Normal topic extract docking pose from ligand docking silent file
by Ruska322 » Sat, 2019-09-07 05:21
0
677 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
200 by Wang Zhe
Wed, 2021-12-08 10:07
Normal topic How many iterations of remodel is enough?
by daniloboskovic » Thu, 2020-07-16 08:07
0
473 by daniloboskovic
Thu, 2020-07-16 08:14
Normal topic backrub application, resfile, and pivot_residues
by tylerborrman » Tue, 2016-12-06 14:46
0
894 by tylerborrman
Tue, 2016-12-06 14:46
Normal topic Dock two domains using topology broker
by sn » Thu, 2017-10-05 17:07
0
786 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
0
497 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
0
198 by chemotaxis_123
Sun, 2022-01-02 16:01
Normal topic PDB Clustering
by code_Monkey » Mon, 2021-04-05 10:40
0
382 by code_Monkey
Mon, 2021-04-05 10:40
Normal topic FlexPepDock Multi chain receptor
by evo_umich » Mon, 2018-04-02 12:13
0
868 by evo_umich
Mon, 2018-04-02 12:13
Normal topic RNP structure prediction flags
by daniloboskovic » Fri, 2019-08-16 11:10
0
648 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
0
885 by benhardy
Wed, 2020-09-30 08:42
Normal topic Topobuilder segmentation fault
by tatsiana.bylund » Mon, 2021-08-09 07:10
0
505 by tatsiana.bylund
Mon, 2021-08-09 07:10
Normal topic RosettaAntibody3 - How can I model an extended H3?
by brspurri » Fri, 2020-08-28 09:11
0
500 by brspurri
Fri, 2020-08-28 09:11
Normal topic Scoring after HBNet
by HHL_SIUC » Wed, 2020-07-01 10:49
0
481 by HHL_SIUC
Wed, 2020-07-01 10:49
Normal topic Pepspec options
by shaunmk » Mon, 2015-04-27 02:33
0
1,325 by shaunmk
Mon, 2015-04-27 02:33
Normal topic Linker Building in scFv
by sam_dc » Sat, 2021-10-09 05:38
0
253 by sam_dc
Sat, 2021-10-09 05:38
Normal topic Finding lowest energy structure among generated structures
by Marius1987 » Sun, 2016-04-10 11:38
0
1,219 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
637 by Corvin
Thu, 2020-04-02 00:16
Normal topic help surface_docking peptide on ice
by engand93 » Wed, 2019-03-27 02:43
0
640 by engand93
Wed, 2019-03-27 02:43
Normal topic pmut_scan_parallel
by G Mustafa » Wed, 2018-10-17 05:41
0
967 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
523 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
272 by y_atsmonraz
Thu, 2021-11-18 03:01
Normal topic Problems with mpi version of antibody.linuxgccrelease
by Sunyp_IM » Thu, 2020-05-28 23:06
0
627 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
509 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
231 by memilton
Thu, 2021-12-16 09:09
Normal topic fragment_picker bug
by David Hoover » Wed, 2012-02-29 11:43
0
1,474 by David Hoover
Mon, 2014-04-21 06:47
Normal topic Helical Symmetry Axis
by Sandy » Tue, 2016-05-31 18:48
0
1,361 by Sandy
Tue, 2016-05-31 18:48
Normal topic RosettaAntibody3 core.pose.util error
by linhhoang157 » Tue, 2020-07-28 12:40
0
604 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
69 by tonycheng1688
Wed, 2022-05-25 10:23
Normal topic Design of multimeric protein
by ldlamini » Mon, 2021-01-11 07:23
0
404 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
245 by syntekabio2019
Thu, 2022-01-20 03:05
Normal topic new BUNS for FunFolDes run
by tatsiana.bylund » Wed, 2019-08-14 20:57
0
648 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
269 by nrollins
Mon, 2021-07-26 14:16
Normal topic Using GlycanDock and the Antibody Affinity Maturation protocol.
by tbelec » Mon, 2022-02-28 12:37
0
204 by tbelec
Mon, 2022-02-28 12:37
Normal topic Docking protein complexes when constrained by oligomer symmetry
by msk » Tue, 2014-06-03 11:09
0
1,186 by msk
Tue, 2014-06-03 11:09
Normal topic Extracting top score PIPER models
by almeida85 » Mon, 2020-08-31 07:17
0
571 by almeida85
Mon, 2020-08-31 07:17
Normal topic How to design the anitgen-antibody interface
by Sunyp_IM » Tue, 2017-12-12 18:44
0
888 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
777 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
451 by rohi
Fri, 2020-07-03 22:20
Normal topic Segfault with Pepspec
by almeida85 » Thu, 2021-02-11 02:56
0
358 by almeida85
Thu, 2021-02-11 02:56
Normal topic snugdock run error: Sequence for partner1 does not match first member of ensemble1
by pagumaaaaa » Fri, 2022-03-25 01:21
0
103 by pagumaaaaa
Fri, 2022-03-25 01:21
Normal topic Side-chain grafting at the fixed protein and position
by Kazu » Wed, 2020-05-20 08:49
0
454 by Kazu
Wed, 2020-05-20 08:49
Normal topic core.pose.util: [ ERROR ] Can't find residue type 'UNK' in type set of mode fa_standard
by AlfredoKCL » Sat, 2020-11-07 18:21
0
669 by AlfredoKCL
Sat, 2020-11-07 18:21
Normal topic cartesian_ddg crashes when the mutfile contains multiple mutations to non-canonical residues
by ValentinaSora » Sun, 2020-05-24 12:32
0
694 by ValentinaSora
Sun, 2020-05-24 12:32
Normal topic Symmetric assembly and output reconstruction
by felipet » Wed, 2014-07-02 10:23
0
1,090 by felipet
Wed, 2014-07-02 10:23
Normal topic Error Implementing Match Style Constraints
by pwging13 » Thu, 2019-12-19 09:53
0
626 by pwging13
Thu, 2019-12-19 09:53
Normal topic Can't find RosettaRemodel in Rosetta 3.4
by petrikigor » Mon, 2012-12-03 13:56
0
1,478 by petrikigor
Mon, 2014-04-21 06:47
Normal topic Weighted scores??
by sizhang » Wed, 2018-12-05 15:22
0
669 by sizhang
Wed, 2018-12-05 15:22
Normal topic flexpepdcok of lipid conjugated peptide with glyco protein.
by ravi.thakkkar369 » Fri, 2020-12-18 13:00
0
395 by ravi.thakkkar369
Fri, 2020-12-18 13:00
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
0
1,890 by fglaser
Mon, 2014-04-21 06:47
Normal topic DNA-protein docking
by ksteczk » Sat, 2020-04-11 11:23
0
809 by ksteczk
Sat, 2020-04-11 11:23
Normal topic Pepspec Anchor Dock
by Soler » Wed, 2020-09-16 19:08
0
422 by Soler
Wed, 2020-09-16 19:08
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