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Rosetta 3 - Applications

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Normal topic error--rosetta fragment‐based refinement protocol for refinement against EM density
by gsuchunli » Mon, 2016-07-25 13:35
1
2,402 by gsuchunli
Mon, 2016-07-25 13:56
Normal topic MPdocking I_sc
by jrcf » Mon, 2017-07-31 16:10
1
1,987 by rmoretti
Thu, 2017-08-03 09:29
Normal topic Membrane Abinitio modeling error
by jkyan007 » Thu, 2020-10-29 03:30
1
1,178 by noahC_noahDo
Tue, 2020-11-17 10:35
Normal topic fold and dock protocol not working
by ytao » Mon, 2012-11-26 15:33
1
2,449 by smlewis
Mon, 2014-04-21 06:47
Normal topic submit_NGK.py not creating output files
by nkato2 » Wed, 2013-08-28 23:37
1
2,526 by rmoretti
Mon, 2014-04-21 06:48
Normal topic why is talaris2014 scoring fuction not used with ligand docking?
by banshee » Fri, 2016-09-09 01:19
1
2,154 by rmoretti
Fri, 2016-09-09 07:47
Normal topic Fastrelax problem
by Pernille » Tue, 2014-06-17 08:59
1
2,121 by Pernille
Fri, 2014-06-20 00:17
Normal topic 'standard.wts' does not exist
by almeida85 » Mon, 2020-09-14 02:26
1
1,313 by rmoretti
Mon, 2020-09-14 06:36
Normal topic Rosetta Holes
by zsun12 » Wed, 2015-09-30 11:40
1
4,123 by rmoretti
Mon, 2015-10-12 15:20
Normal topic Rosetta scripts crash in CM workflow
by jlburkhead » Tue, 2019-12-03 22:55
1
1,621 by danpf
Fri, 2020-02-21 18:37
Normal topic Problem with mpirun/mpiexec
by ahansel » Fri, 2020-07-10 08:37
1
3,721 by rmoretti
Fri, 2020-07-10 09:59
Normal topic Comparative Modeling Tutorial
by code_Monkey » Thu, 2021-03-04 12:35
1
1,043 by rmoretti
Fri, 2021-03-05 09:35
Normal topic Pepspec error
by almeida85 » Mon, 2022-05-02 04:07
1
1,228 by almeida85
Mon, 2022-05-02 05:05
Normal topic Rosetta DNA - Protein-DNA scoring function and binding energy
by tanoramb » Tue, 2012-05-08 14:00
1
4,583 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to pick fragments for a transmembrane protein
by tevang » Mon, 2012-05-28 06:52
1
2,275 by tevang
Mon, 2014-04-21 06:47
Normal topic Place ligand in a pocket
by sn » Fri, 2017-09-15 12:53
1
2,022 by rmoretti
Fri, 2017-09-15 13:11
Normal topic How to analyse multiple silent files from "Abinitiorelax" output to find best models?
by Danielsebas » Tue, 2019-09-10 10:01
1
1,439 by smlewis
Mon, 2019-09-16 12:22
Normal topic creating a model using a base pdb and extending a chain
by rlwoltz » Fri, 2013-07-12 15:35
1
2,706 by nawsad
Mon, 2014-04-21 06:48
Normal topic rosetta 3.3 - antibody
by ron amon » Mon, 2014-07-21 00:44
1
2,491 by rmoretti
Mon, 2014-07-21 10:51
Normal topic References where Rosetta is used to compute ddG of binding after mutation?
by cossio » Tue, 2015-03-17 05:13
1
2,935 by rmoretti
Wed, 2015-03-25 11:33
Normal topic Loop modeling/closure for many structures
by sn » Mon, 2017-03-06 11:25
1
1,719 by rmoretti
Mon, 2017-03-06 12:39
Normal topic input file for loop modeling
by Negarsardar » Tue, 2019-04-16 10:21
1
1,491 by rmoretti
Tue, 2019-04-16 11:07
Normal topic analyze_flex_ddG.py
by valebut » Tue, 2023-11-28 04:30
1
331 by Aleksandra Panfilova
Tue, 2023-11-28 05:34
Normal topic Fixing part of a ligand in dock-design
by hssnzdh2 » Mon, 2015-11-23 17:14
1
2,302 by rmoretti
Tue, 2015-11-24 16:16
Normal topic SnugDock Partners parameter
by tyang39 » Fri, 2022-07-08 10:02
1
1,040 by rmoretti
Fri, 2022-07-08 10:27
Normal topic Difference between relax and mimimize_with_cst
by basvandenberg » Thu, 2012-02-09 00:16
1
2,875 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Relax with RDC data gives segmentation fault
by sn » Mon, 2018-07-23 11:39
1
1,619 by rmoretti
Fri, 2018-08-03 07:54
Normal topic I need some help for using pHDock applications(histidine protonation / pH-dependent binding)
by leygkn » Tue, 2020-09-22 18:40
1
1,283 by leygkn
Tue, 2020-09-22 22:46
Normal topic Incorporating iron-sulfur cluster into ROSETTA applications
by Derek Smith » Thu, 2014-08-14 23:12
1
2,716 by rmoretti
Fri, 2014-08-15 08:06
Normal topic rosetta scores for mutated structures
by harshkhare » Wed, 2011-11-23 09:30
1
2,835 by rmoretti
Mon, 2014-04-21 06:47
Normal topic ambiguous constraints
by shrutikhare » Mon, 2014-05-12 04:42
1
3,408 by rmoretti
Mon, 2014-05-12 08:25
Normal topic How to build disulfide bond between two cysteine, i.e. change two "-SH" (sulfydryl) into "-S-S-"?
by lanselibai » Sat, 2015-01-17 11:19
1
3,168 by lanselibai
Wed, 2015-01-21 02:40
Normal topic Coding denovo prediction from density maps in PyRosetta
by ahmadkhalifa » Tue, 2018-04-10 11:43
1
1,623 by rmoretti
Tue, 2018-04-10 15:29
Normal topic Docking structures with ligands in cryo-EM maps
by galushin » Wed, 2012-07-11 12:40
1
4,601 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic ProteinInterfaceDesign algorithm questions
by tsztain » Mon, 2019-02-18 14:10
1
1,819 by rmoretti
Sun, 2019-08-25 19:15
Normal topic denovo modelling on a virus-coat protein dimer
by aseem121 » Wed, 2019-10-16 06:55
1
1,466 by danpf
Wed, 2019-10-16 13:03
Normal topic Packstat application output
by Vedasheersh » Mon, 2017-07-03 02:45
1
2,108 by rmoretti
Mon, 2017-07-03 09:17
Normal topic antibody - sequence position requested was 0
by jremmel » Mon, 2021-09-27 12:26
1
1,263 by nannemdp
Mon, 2021-09-27 14:22
Normal topic unable to generate the span file with "mp_span_from_pdb.default.linuxgccrelease" from a PDB file
by Sajjad » Wed, 2022-11-30 11:40
1
4,131 by FJOM
Wed, 2023-05-03 07:21
Normal topic Add missing residues in loop modeling
by exchhattu » Thu, 2013-06-20 17:38
1
3,655 by smlewis
Mon, 2014-04-21 06:48
Normal topic Output structures from docking_prepack_protocol: initial__*.pdb vs prepack__*.pdb, which one should I send to docking_protocol?
by cossio » Thu, 2015-02-05 07:10
1
2,343 by rmoretti
Mon, 2015-02-09 12:33
Normal topic Enzyme Design FlexBB Protocol Bug: DNA/RNA handling
by kettner » Fri, 2019-06-14 14:16
1
1,926 by rmoretti
Mon, 2019-06-24 13:46
Normal topic residue_energy_breakdown of a protein-ligand complex.
by sam_dc » Tue, 2021-05-18 04:45
1
1,304 by rmoretti
Tue, 2021-05-18 07:21
Normal topic Snugdock_error
by luicui » Thu, 2017-02-09 21:06
1
1,770 by smlewis
Thu, 2017-02-09 21:50
Normal topic FixedBB design output no beta strands
by tkoh » Fri, 2023-08-25 01:02
1
398 by rmoretti
Tue, 2023-08-29 20:13
Normal topic protein-protein docking
by cbala » Mon, 2011-04-18 09:15
1
2,644 by smlewis
Mon, 2014-04-21 06:47
Normal topic Using different number of 9-mers (UPDATED)
by JadAbbass » Mon, 2017-08-28 07:20
1
1,943 by rmoretti
Mon, 2017-09-04 10:33
Normal topic docking with capping groups
by xavierfradera » Sun, 2018-11-04 16:17
1
1,584 by maral.adeli-kou...
Wed, 2020-01-22 12:41
Normal topic Undesirable behaviour of PoseFromSFRBuilder regarding Hydrogen atoms
by Corvin » Wed, 2020-12-02 04:00
1
1,241 by rmoretti
Wed, 2020-12-02 07:27
Normal topic Question on restraining receptor symmetry when docking ligand
by subha » Fri, 2018-07-06 21:59
1
1,563 by rmoretti
Fri, 2018-08-03 08:16
Normal topic RosettaMatch
by xingqing326 » Mon, 2019-07-22 13:14
1
1,868 by rmoretti
Mon, 2019-08-26 12:57
Normal topic Interface Analyzer Segmentation Fault
by h_trasatti » Tue, 2017-02-21 12:48
1
2,308 by smlewis
Tue, 2017-02-21 14:10
Normal topic Warning: Fold tree is not set properly for density scoring
by ahansel » Mon, 2020-07-13 10:50
1
1,349 by danpf
Tue, 2020-07-14 10:27
Normal topic modeling missing linker in a protein
by Isaure de Beauchene » Fri, 2012-05-11 10:13
1
3,456 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to use base_pair_constraint for RNA as a constraint term?
by yels » Sat, 2021-04-03 01:19
1
1,110 by everyday847
Sun, 2021-04-04 12:48
Normal topic Design with limited number of aminoacids at given position
by sdh_h » Sun, 2016-12-04 03:44
1
1,926 by smlewis
Thu, 2016-12-08 15:50
Normal topic dssp
by MA » Thu, 2017-10-05 09:34
1
1,825 by rmoretti
Tue, 2017-10-10 09:54
Normal topic [LoopModelerMover] ERROR: Can't build a fold tree from a loop with an unspecified cut point.
by dgm3 » Sun, 2021-12-26 18:32
1
1,320 by dgm3
Fri, 2021-12-31 17:42
Normal topic Missing atoms, unable to fill in missing atoms
by kwu030 » Fri, 2023-05-05 13:41
1
491 by rmoretti
Fri, 2023-05-05 13:44
Normal topic loopmodel issue
by chiendarret » Fri, 2012-01-27 00:51
1
3,144 by smlewis
Mon, 2014-04-21 06:47
Normal topic No interface for protein - Interface Analyzer
by aloshbau » Tue, 2013-05-21 21:00
1
2,851 by jarod
Mon, 2014-04-21 06:47
Normal topic splitfile.py
by saladi » Fri, 2018-03-30 10:31
1
1,801 by rmoretti
Tue, 2018-04-10 15:34
Normal topic How can I model ligands in comparative modeling
by Morrian_Lynn » Thu, 2020-02-20 09:57
1
1,271 by danpf
Fri, 2020-02-21 17:05
Normal topic Docking Analysis and Metrics in RosettaLigand.
by sam_dc » Tue, 2021-04-20 03:54
1
1,860 by rmoretti
Tue, 2021-04-20 13:27
Normal topic problem with modelling of protein (140 and 150 residues respectively)
by krlitros87 » Wed, 2014-10-22 09:39
1
2,151 by rmoretti
Thu, 2014-10-23 13:55
Normal topic Homology modelling applies alignment wrong
by bernhardcl » Thu, 2015-08-06 09:39
1
2,090 by bernhardcl
Tue, 2015-08-11 09:11
Normal topic comparative modeling of a homodimer
by banshee » Mon, 2017-01-09 18:34
1
2,398 by rmoretti
Wed, 2017-01-11 13:00
Normal topic [Solved] Resetting a pose with RigidBodyTransMover
by bjharris » Wed, 2021-01-13 14:01
1
1,154 by bjharris
Fri, 2021-01-22 17:34
Normal topic duplex RNA
by amir_tagh » Thu, 2021-08-05 06:34
1
1,028 by everyday847
Mon, 2021-08-16 10:43
Normal topic Score.sc file showing total score 0 for all protein structures created
by aanshi » Wed, 2022-11-23 11:13
1
3,543 by nannemdp
Mon, 2022-11-28 09:39
Normal topic Ligand docking: ERROR: set_atom_base: atoms must be bonded!
by mengzhang » Mon, 2014-05-12 12:36
1
2,649 by rmoretti
Mon, 2014-05-12 15:08
Normal topic radius of gyration as constrain
by dhirajks » Sat, 2018-05-05 23:00
1
1,737 by smlewis
Mon, 2018-05-07 11:42
Normal topic Fragment Files
by nkemjika » Fri, 2011-07-22 15:11
1
3,092 by dgront
Mon, 2014-04-21 06:47
Normal topic Antibody Modelling
by luicui » Mon, 2017-01-23 21:30
1
2,259 by smlewis
Mon, 2017-02-06 20:46
Normal topic blast database error
by jessye » Sun, 2017-12-03 23:59
1
1,924 by smlewis
Mon, 2017-12-04 12:18
Normal topic RECCESS-Rosetta Segmentation Fault with nonnatural residues
by skorro » Tue, 2023-07-25 17:13
1
424 by skorro
Fri, 2023-07-28 12:20
Normal topic Ligand creation
by Prasanth Kumar » Fri, 2013-08-02 09:48
1
2,456 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Comparative modeling
by MRH » Mon, 2013-08-19 23:08
1
2,475 by smlewis
Mon, 2014-04-21 06:48
Normal topic SymDock with constraints
by felipet » Thu, 2015-05-14 09:01
1
3,157 by rmoretti
Mon, 2015-05-25 11:49
Normal topic Predicting the part of protein strcutrue
by ksy141 » Tue, 2018-10-16 11:47
1
1,538 by jadolfbr
Fri, 2018-11-09 14:28
Normal topic /database folder after running "install_dependencies.pl" size 657 GB?
by Danielsebas » Tue, 2019-09-03 03:32
1
1,395 by danpf
Tue, 2019-09-03 10:15
Normal topic Changing rosetta scoring to favour less hydrophobic areas
by daniloboskovic » Thu, 2020-05-21 03:03
1
1,226 by vmulligan
Thu, 2020-05-21 18:33
Normal topic trouble in floppytail modelling
by ytao » Thu, 2013-06-27 13:15
1
2,476 by ytao
Mon, 2014-04-21 06:48
Normal topic Executing the clean_pdb.py script
by Rkfoury » Fri, 2015-02-20 10:16
1
3,883 by lanselibai
Tue, 2015-02-24 02:36
Normal topic Enzyme Design - Score File
by nwhoppe » Thu, 2016-04-07 15:11
1
2,175 by rmoretti
Fri, 2016-04-08 07:39
Normal topic Rosetta_cm Partial Threading Removing Parts of Sequence
by gszwabowski » Thu, 2019-06-20 12:30
1
1,687 by rmoretti
Mon, 2019-06-24 13:43
Normal topic Comparative modeling using a two chained template for a one chain structure
by ahmadkhalifa » Mon, 2017-12-18 11:00
1
1,620 by rmoretti
Mon, 2018-01-15 16:14
Normal topic De novo water predictions using SPaDES
by MNP1986 » Mon, 2019-03-25 07:53
1
1,798 by matteoferla
Tue, 2020-08-04 09:30
Normal topic Surface Docking Crash (continued)
by dkozuch » Tue, 2017-09-12 06:18
1
1,684 by rmoretti
Tue, 2017-10-10 10:08
Normal topic AbinitioRelax - Error with flags
by jmschu » Wed, 2018-11-21 17:36
1
2,154 by rmoretti
Fri, 2018-11-23 07:59
Normal topic ERROR: unrecognized residue name 'GLY_p:RepulsiveOnly'
by smiruthi » Mon, 2011-12-12 14:27
1
2,806 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Blast error for rosetta antibody: No argument value given for Query file
by dngusdnr1 » Tue, 2021-06-08 17:30
1
1,256 by taylorjones
Wed, 2021-06-09 16:38
Normal topic No output with docking full protocol
by JulienO » Mon, 2016-05-30 02:16
1
2,040 by rmoretti
Fri, 2016-06-17 10:24
Normal topic score and relax
by Prasanth Kumar » Thu, 2013-05-02 05:09
1
3,313 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic JD2 MPI
by jrcf » Wed, 2015-10-28 14:45
1
2,365 by rmoretti
Sat, 2015-10-31 08:57
Normal topic RosettaLigand Docking
by Dinesh Kumar » Mon, 2018-01-15 20:54
1
2,205 by rmoretti
Tue, 2018-01-16 07:24
Normal topic is it necessary to always run relax before any Rosetta
by mainzer » Fri, 2019-04-12 01:35
1
2,000 by rmoretti
Wed, 2019-07-10 09:47
Normal topic How to freeze ligand during FastRelax?
by dnamkr » Thu, 2020-01-02 14:53
1
1,597 by aloshbau
Fri, 2020-01-10 16:48
Normal topic pepspec anchor dock
by Andre Serobian » Tue, 2020-07-28 05:51
1
1,227 by Andre Serobian
Tue, 2020-07-28 23:26
Normal topic I want to refine my pdb file,but it has multiple breaks or has multiple loops missing resi
by Edward » Sat, 2023-11-25 04:58
1
326 by Edward
Sat, 2023-11-25 05:17
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