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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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7,620 by admin
Fri, 2015-09-04 16:17
Normal topic Python2 script in Rosetta3.13
by ddhoyo » Wed, 2021-09-15 04:05
1
58 by matteoferla
Wed, 2021-09-15 06:04
Normal topic Repacker vs minimization
by Elijah_Hix » Fri, 2021-07-02 07:25
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93 by Elijah_Hix
Fri, 2021-07-02 07:25
Normal topic FlexPepDock ab initio: behavior without fragment files
by nrollins » Mon, 2021-07-26 14:16
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104 by nrollins
Mon, 2021-07-26 14:16
Normal topic FlexPepDock bug? Constraints do not appear in total_score?
by nrollins » Mon, 2021-07-26 14:29
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115 by nrollins
Mon, 2021-07-26 14:29
Normal topic clashes created with enzdes
by listofdina » Mon, 2021-08-02 06:51
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127 by listofdina
Mon, 2021-08-02 06:51
Normal topic How to Perform point mutations with NCAA
by Subhrodeep Saha » Tue, 2021-06-22 02:05
1
135 by vmulligan
Thu, 2021-06-24 13:23
Normal topic setup_RosettaCM.py
by browns02 » Mon, 2021-06-28 07:13
2
137 by browns02
Tue, 2021-06-29 11:41
Normal topic Topobuilder segmentation fault
by tatsiana.bylund » Mon, 2021-08-09 07:10
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142 by tatsiana.bylund
Mon, 2021-08-09 07:10
Normal topic Blast error for rosetta antibody: No argument value given for Query file
by dngusdnr1 » Tue, 2021-06-08 17:30
1
150 by taylorjones
Wed, 2021-06-09 16:38
Normal topic Patch to impose tetrahedral geometry on backbone O atom
by georg » Thu, 2021-04-08 09:30
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151 by georg
Thu, 2021-04-08 09:31
Normal topic rosetta_cm segfault
by browns02 » Fri, 2021-07-09 13:35
2
152 by rmoretti
Fri, 2021-07-09 15:05
Normal topic Stepwise Monte Carlo - errors with ResidueTypeSet and Disulfides
by user42 » Wed, 2021-07-21 20:34
1
156 by everyday847
Fri, 2021-07-30 13:26
Normal topic Issues with modifying dock.xml for multiple ligand docking
by DGR95 » Fri, 2021-05-14 12:51
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159 by DGR95
Fri, 2021-05-14 12:51
Normal topic FastRelax Refinement severe clashes
by Victor Tobiasson » Thu, 2021-05-20 06:55
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159 by Victor Tobiasson
Thu, 2021-05-20 06:55
Normal topic duplex RNA
by amir_tagh » Thu, 2021-08-05 06:34
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162 by everyday847
Mon, 2021-08-16 10:43
Normal topic What is an SS0 predictor?
by ojmel » Fri, 2021-04-02 14:25
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178 by ojmel
Mon, 2021-04-12 07:50
Normal topic hpatch commands and how to identify patches
by Bianca Oliva » Thu, 2021-04-29 04:02
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178 by Bianca Oliva
Thu, 2021-04-29 04:02
Normal topic D-amino acids tripeptide docking.
by sam_dc » Sat, 2021-07-03 08:48
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183 by vmulligan
Tue, 2021-07-06 08:27
Normal topic multi ligand docking using rosetta script
by syntekabio2019 » Tue, 2021-04-13 19:31
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185 by syntekabio2019
Tue, 2021-04-13 19:31
Normal topic Segfault with Pepspec
by almeida85 » Thu, 2021-02-11 02:56
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185 by almeida85
Thu, 2021-02-11 02:56
Normal topic PDB Clustering
by code_Monkey » Mon, 2021-04-05 10:40
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189 by code_Monkey
Mon, 2021-04-05 10:40
Normal topic Writing down properties for new atom types
by Corvin » Tue, 2021-01-12 04:30
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194 by Corvin
Wed, 2021-01-13 04:00
Normal topic Ab Initio folding with HEM ligand molecule
by jseco » Fri, 2021-03-05 06:49
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205 by jseco
Mon, 2021-03-08 03:40
Normal topic RosettaCM/hybridize
by kywei » Wed, 2021-04-28 09:56
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205 by vmulligan
Wed, 2021-04-28 12:59
Normal topic Help with enzyme design files
by Wenithor » Thu, 2021-04-29 10:33
1
206 by rmoretti
Thu, 2021-04-29 10:44
Normal topic Question with rosetta AbPredict tutorial
by terabithia2011 » Mon, 2021-01-25 09:24
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209 by terabithia2011
Mon, 2021-01-25 09:24
Normal topic residue_energy_breakdown of a protein-ligand complex.
by sam_dc » Tue, 2021-05-18 04:45
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211 by rmoretti
Tue, 2021-05-18 07:21
Normal topic Design of multimeric protein
by ldlamini » Mon, 2021-01-11 07:23
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226 by ldlamini
Mon, 2021-01-11 07:23
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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230 by Poladu
Tue, 2021-01-26 07:50
Normal topic RosettaAntibody - No matching templates for CDR1
by agctomer » Tue, 2021-01-19 22:45
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234 by agctomer
Tue, 2021-01-19 22:45
Normal topic Modelling humanized camelid like antibody
by terabithia2011 » Tue, 2021-01-26 10:12
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235 by terabithia2011
Tue, 2021-01-26 10:12
Normal topic NCAA attached at two points
by tsztain » Wed, 2021-06-16 15:20
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237 by matteoferla
Sat, 2021-06-19 03:07
Normal topic Generalized KIC loop closure affects downstream residues without perturbations
by chenna » Mon, 2021-04-26 02:16
2
239 by chenna
Wed, 2021-04-28 07:18
Normal topic Filling the missing loops
by code_Monkey » Tue, 2021-04-27 07:44
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239 by code_Monkey
Tue, 2021-04-27 12:11
Normal topic flexpepdcok of lipid conjugated peptide with glyco protein.
by ravi.thakkkar369 » Fri, 2020-12-18 13:00
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240 by ravi.thakkkar369
Fri, 2020-12-18 13:00
Normal topic different value of score from rna_denovo and rna_score?
by yikanzhang » Wed, 2021-02-03 07:17
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245 by CameronJA
Tue, 2021-06-15 20:02
Normal topic Disulfide Bonds in Loop Modeling
by code_Monkey » Mon, 2021-05-03 08:27
2
250 by code_Monkey
Thu, 2021-05-06 07:14
Normal topic r_frag_quality
by ii_cnr » Mon, 2021-04-12 03:06
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251 by ii_cnr
Mon, 2021-04-12 23:44
Normal topic Should I be stripping water molecules from my input structure for Rosetta Design?
by chrisHKL » Wed, 2021-03-24 14:22
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253 by smlewis
Wed, 2021-03-24 14:59
Normal topic How to use base_pair_constraint for RNA as a constraint term?
by yels » Sat, 2021-04-03 01:19
1
254 by everyday847
Sun, 2021-04-04 12:48
Normal topic RemodelMover and Input Pose
by ozyo » Tue, 2020-12-29 09:41
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259 by ozyo
Tue, 2020-12-29 09:41
Normal topic Bug Report - Encoding issue
by daniloboskovic » Tue, 2020-08-04 07:02
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268 by daniloboskovic
Tue, 2020-08-04 07:02
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
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277 by Corvin
Wed, 2020-12-30 09:21
Normal topic Docking Analysis and Metrics in RosettaLigand.
by sam_dc » Tue, 2021-04-20 03:54
1
279 by rmoretti
Tue, 2021-04-20 13:27
Normal topic Element 'trRosettaProtocol': This element is not expected.
by csaylan » Tue, 2021-04-20 14:21
2
280 by csaylan
Tue, 2021-04-20 16:13
Normal topic metalloprotein ab initio with glutamic acid
by inorgchem » Tue, 2020-06-16 20:45
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282 by inorgchem
Tue, 2020-06-16 20:45
Normal topic core.optimization.LineMinimizer: [ ERROR ] Inaccurate G!
by aralz » Thu, 2021-02-11 00:46
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283 by aralz
Thu, 2021-02-11 00:46
Normal topic constraints in Rosetta ligand docking (AddorRemoveMatchCsts, Addconstraints Mover, and ConstraintSetMover)
by rohi » Mon, 2021-01-11 13:32
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284 by rohi
Mon, 2021-01-11 13:58
Normal topic Pepspec Anchor Dock
by Soler » Wed, 2020-09-16 19:08
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286 by Soler
Wed, 2020-09-16 19:08
Normal topic GeneralizedKIC loop closure error
by chenna » Sat, 2021-04-10 00:21
2
289 by chenna
Mon, 2021-04-12 22:08
Normal topic Comparative Modeling Tutorial
by code_Monkey » Thu, 2021-03-04 12:35
1
290 by rmoretti
Fri, 2021-03-05 09:35
Normal topic clustering output file has few structures
by fabiotrovato » Mon, 2020-08-17 11:37
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298 by fabiotrovato
Mon, 2020-08-17 11:37
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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304 by Pappmaschee
Wed, 2020-12-16 09:23
Normal topic Side-chain grafting at the fixed protein and position
by Kazu » Wed, 2020-05-20 08:49
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313 by Kazu
Wed, 2020-05-20 08:49
Normal topic Fewer than expected structures in clustering output
by fabiotrovato » Thu, 2020-08-20 00:59
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314 by fabiotrovato
Thu, 2020-08-20 00:59
Normal topic Global Docking with carbohydrates
by ChiauShu » Sat, 2020-08-22 20:16
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318 by ChiauShu
Sat, 2020-08-22 20:16
Normal topic How many iterations of remodel is enough?
by daniloboskovic » Thu, 2020-07-16 08:07
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319 by daniloboskovic
Thu, 2020-07-16 08:14
Normal topic zero standard deviation of I_sc in protein-protein docking
by rohi » Fri, 2020-07-03 22:19
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324 by rohi
Fri, 2020-07-03 22:20
Normal topic Scoring after HBNet
by HHL_SIUC » Wed, 2020-07-01 10:49
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329 by HHL_SIUC
Wed, 2020-07-01 10:49
Normal topic Error from clean_pdb.py
by code_Monkey » Mon, 2021-03-01 17:00
2
329 by code_Monkey
Thu, 2021-03-04 12:14
Normal topic [Solved] Resetting a pose with RigidBodyTransMover
by bjharris » Wed, 2021-01-13 14:01
1
332 by bjharris
Fri, 2021-01-22 17:34
Normal topic Does antibody_numbering_converter support camelid antibody?
by mxp » Tue, 2020-07-07 01:21
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334 by mxp
Tue, 2020-07-07 01:21
Normal topic FlexPepDocking
by jlawrie » Tue, 2020-09-15 12:52
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335 by jlawrie
Tue, 2020-09-15 12:52
Normal topic Ligand docking with constraint
by Alison_Yajie » Wed, 2020-06-24 12:34
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336 by Alison_Yajie
Wed, 2020-06-24 12:34
Normal topic General question regarding ligand-docking
by Alison_Yajie » Thu, 2020-05-07 09:48
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338 by Alison_Yajie
Thu, 2020-05-07 09:48
Normal topic ligand_docking: ligand preparation
by Alison_Yajie » Thu, 2020-07-02 07:05
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342 by Alison_Yajie
Thu, 2020-07-02 07:10
Normal topic Metal Ion in symmetric design
by tschiex » Wed, 2020-07-08 05:28
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342 by tschiex
Wed, 2020-07-08 05:28
Normal topic RosettaLigand ERROR: Error in core::conformation::check_good_cutpoint_neighbour()
by sam_dc » Thu, 2021-03-25 09:32
2
345 by sam_dc
Mon, 2021-04-12 07:24
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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346 by Sunyp_IM
Thu, 2020-06-04 05:54
Normal topic antibody H3 modelling protocol for nanobody gives "[ ERROR ] Inaccurate G!" messages
by AlfredoKCL » Sun, 2021-02-28 16:42
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349 by AlfredoKCL
Mon, 2021-03-01 04:07
Normal topic Protein Ensemble RosettaLigand Docking
by sam_dc » Fri, 2021-03-26 10:18
2
350 by sam_dc
Fri, 2021-03-26 12:04
Normal topic Residue selector
by Alison_Yajie » Wed, 2020-06-17 19:57
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352 by Alison_Yajie
Thu, 2020-06-18 09:47
Normal topic protein relax
by Alison_Yajie » Tue, 2020-05-19 08:29
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358 by Alison_Yajie
Tue, 2020-05-19 08:29
Normal topic polymer docking using rosetta scripts
by syntekabio2019 » Fri, 2020-11-27 01:51
1
359 by rmoretti
Fri, 2020-11-27 10:47
Normal topic Rosetta Ligand Ensemble
by malfonsoprieto » Wed, 2021-05-26 10:21
3
361 by vizcarra
Thu, 2021-08-26 10:16
Normal topic Using Rmsd RosettaScripts filter with alignment files
by bjharris » Sun, 2020-11-08 15:51
1
363 by rmoretti
Sun, 2020-11-08 18:56
Normal topic RosettaAntibody3 - How can I model an extended H3?
by brspurri » Fri, 2020-08-28 09:11
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363 by brspurri
Fri, 2020-08-28 09:11
Normal topic ligand_docking: ligand preparation
by Alison_Yajie » Thu, 2020-05-21 09:42
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363 by Alison_Yajie
Thu, 2020-05-21 09:42
Normal topic appropriate sampling for protein docking to a multi chain assembly
by SWM » Fri, 2020-01-24 11:22
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363 by SWM
Fri, 2020-01-24 11:22
Normal topic Extracting top score PIPER models
by almeida85 » Mon, 2020-08-31 07:17
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364 by almeida85
Mon, 2020-08-31 07:17
Normal topic Undesirable behaviour of PoseFromSFRBuilder regarding Hydrogen atoms
by Corvin » Wed, 2020-12-02 04:00
1
366 by rmoretti
Wed, 2020-12-02 07:27
Normal topic Zero residues error in docking
by cjy318 » Tue, 2020-07-28 19:47
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370 by cjy318
Tue, 2020-07-28 19:47
Normal topic Modelling of multi-component symmetrical structures
by LanMei » Wed, 2020-10-07 09:58
0
384 by LanMei
Wed, 2020-10-07 09:58
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
388 by chrisHKL
Fri, 2020-02-28 14:52
Normal topic NCAA Rotamers for Cyclosporin
by marinok » Mon, 2020-09-28 14:11
0
394 by marinok
Mon, 2020-09-28 14:11
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
0
397 by jcampecino
Wed, 2020-05-13 12:22
Normal topic antibody.mpi.linuxgccrelease some antibodies failing to model
by drewaight » Mon, 2020-11-02 17:07
0
398 by drewaight
Mon, 2020-11-02 17:07
Normal topic Can remodel really handle multiple insertions in one simulation?
by lanselibai » Sat, 2019-12-28 12:51
0
402 by lanselibai
Sat, 2019-12-28 12:51
Normal topic [Solved] RosettaAntibody3 - Grafting step is failing to detect H3 from the input sequence
by brspurri » Mon, 2021-01-04 16:46
1
404 by brspurri
Mon, 2021-01-18 18:14
Normal topic score is 0 in the output? - RosettaScripts
by chrisHKL » Thu, 2020-03-05 09:33
0
405 by chrisHKL
Thu, 2020-03-05 12:58
Normal topic Comparative Modeling Templates for Protein with Multiple Domains
by Morrian_Lynn » Wed, 2020-03-04 10:42
0
410 by Morrian_Lynn
Wed, 2020-03-04 10:42
Normal topic Modeling-Using RosettaCM
by jlawrie » Wed, 2020-08-12 08:46
1
414 by jlawrie
Wed, 2020-08-12 08:47
Normal topic Input structure
by Soler » Mon, 2020-09-28 13:18
1
420 by ssrb
Tue, 2020-09-29 12:37
Normal topic ligand_docking tutorial help: do crystal_complex.pdb files need to be prepped before using with <InterfaceScoreCalculator>
by DGR95 » Fri, 2021-04-16 19:26
4
421 by DGR95
Wed, 2021-04-28 16:13
Normal topic RosettaAntibody3 core.pose.util error
by linhhoang157 » Tue, 2020-07-28 12:40
0
421 by linhhoang157
Tue, 2020-07-28 12:40
Normal topic Pepspec Anchor Dock
by Soler » Fri, 2020-09-18 08:09
0
425 by Soler
Fri, 2020-09-18 08:09
Normal topic Membrane Abinitio modeling error
by jkyan007 » Thu, 2020-10-29 03:30
1
428 by noahC_noahDo
Tue, 2020-11-17 10:35
Normal topic trRosetta protocol Segmentation Fault
by nc-ring » Wed, 2021-04-28 11:57
5
431 by nc-ring
Tue, 2021-05-04 12:26
Normal topic Use membrane or non-membrane weights in RosettaCM for a hexon in virus capsid?
by lanselibai » Sat, 2020-04-11 02:10
0
433 by lanselibai
Sat, 2020-04-11 02:10

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