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Rosetta 3 - Applications

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Normal topic I need some help for using pHDock applications(histidine protonation / pH-dependent binding)
by leygkn » Tue, 2020-09-22 18:40
1
1,149 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
2,579 by rmoretti
Fri, 2014-08-15 08:06
Normal topic Fixing part of a ligand in dock-design
by hssnzdh2 » Mon, 2015-11-23 17:14
1
2,186 by rmoretti
Tue, 2015-11-24 16:16
Normal topic SnugDock Partners parameter
by tyang39 » Fri, 2022-07-08 10:02
1
856 by rmoretti
Fri, 2022-07-08 10:27
Normal topic Holes output interpretation
by lah435 » Mon, 2012-06-04 15:02
1
2,402 by smlewis
Mon, 2014-04-21 06:47
Normal topic ProteinInterfaceDesign algorithm questions
by tsztain » Mon, 2019-02-18 14:10
1
1,676 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
1,353 by danpf
Wed, 2019-10-16 13:03
Normal topic Packstat application output
by Vedasheersh » Mon, 2017-07-03 02:45
1
1,976 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
1,109 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
3,901 by FJOM
Wed, 2023-05-03 07:21
Normal topic Standalone alanine scanning protocol
by exchhattu » Thu, 2011-10-13 19:40
1
5,350 by smlewis
Mon, 2014-04-21 06:47
Normal topic ambiguous constraints
by shrutikhare » Mon, 2014-05-12 04:42
1
3,277 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
3,058 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
1,507 by rmoretti
Tue, 2018-04-10 15:29
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
2,236 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
1,797 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
1,095 by rmoretti
Tue, 2021-05-18 07:21
Normal topic relax VS. backrub
by jiongzhang » Mon, 2012-07-02 14:52
1
2,507 by smlewis
Mon, 2014-04-21 06:47
Normal topic Snugdock_error
by luicui » Thu, 2017-02-09 21:06
1
1,664 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
238 by rmoretti
Tue, 2023-08-29 20:13
Normal topic Question on restraining receptor symmetry when docking ligand
by subha » Fri, 2018-07-06 21:59
1
1,460 by rmoretti
Fri, 2018-08-03 08:16
Normal topic RosettaMatch
by xingqing326 » Mon, 2019-07-22 13:14
1
1,725 by rmoretti
Mon, 2019-08-26 12:57
Normal topic ligand conformer generation for enzyme design
by bo » Mon, 2013-02-11 16:51
1
2,359 by smlewis
Mon, 2014-04-21 06:47
Normal topic placing a constraint during structure prediction
by cbala » Thu, 2011-04-07 08:54
1
3,126 by ic3reyes
Mon, 2014-04-21 06:47
Normal topic Interface Analyzer Segmentation Fault
by h_trasatti » Tue, 2017-02-21 12:48
1
2,194 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
1,225 by danpf
Tue, 2020-07-14 10:27
Normal topic Surface accessible residue as a constraint.
by arthuc01 » Fri, 2012-03-09 23:27
1
2,200 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
1,833 by rmoretti
Mon, 2017-09-04 10:33
Normal topic docking with capping groups
by xavierfradera » Sun, 2018-11-04 16:17
1
1,452 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
1,083 by rmoretti
Wed, 2020-12-02 07:27
Normal topic Destination of score.fsc file
by anirbanzz » Wed, 2011-04-20 23:30
1
2,760 by smlewis
Mon, 2014-04-21 06:47
Normal topic FlexPepDock in RosettaScripts keeps running
by gw » Tue, 2012-08-21 12:31
1
2,538 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
1,004 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
1,819 by smlewis
Thu, 2016-12-08 15:50
Normal topic dssp
by MA » Thu, 2017-10-05 09:34
1
1,721 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
1,131 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
320 by rmoretti
Fri, 2023-05-05 13:44
Normal topic problem with modelling of protein (140 and 150 residues respectively)
by krlitros87 » Wed, 2014-10-22 09:39
1
2,053 by rmoretti
Thu, 2014-10-23 13:55
Normal topic Homology modelling applies alignment wrong
by bernhardcl » Thu, 2015-08-06 09:39
1
1,994 by bernhardcl
Tue, 2015-08-11 09:11
Normal topic comparative modeling of a homodimer
by banshee » Mon, 2017-01-09 18:34
1
2,287 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
997 by bjharris
Fri, 2021-01-22 17:34
Normal topic duplex RNA
by amir_tagh » Thu, 2021-08-05 06:34
1
927 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
3,249 by nannemdp
Mon, 2022-11-28 09:39
Normal topic number of structures in homology modeling for cluster analysis
by pdbb » Fri, 2013-04-12 08:52
1
2,572 by smlewis
Mon, 2014-04-21 06:47
Normal topic Flexible peptide docking with flexible receptor backbone
by tevang » Fri, 2012-09-14 11:18
1
2,674 by smlewis
Mon, 2014-04-21 06:47
Normal topic splitfile.py
by saladi » Fri, 2018-03-30 10:31
1
1,669 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
1,172 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
1,625 by rmoretti
Tue, 2021-04-20 13:27
Normal topic Antibody Modelling
by luicui » Mon, 2017-01-23 21:30
1
2,150 by smlewis
Mon, 2017-02-06 20:46
Normal topic blast database error
by jessye » Sun, 2017-12-03 23:59
1
1,780 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
267 by skorro
Fri, 2023-07-28 12:20
Normal topic Ligand creation
by Prasanth Kumar » Fri, 2013-08-02 09:48
1
2,364 by rmoretti
Mon, 2014-04-21 06:48
Normal topic docking with constraints
by talavera » Tue, 2013-05-07 01:50
1
3,944 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Ligand docking: ERROR: set_atom_base: atoms must be bonded!
by mengzhang » Mon, 2014-05-12 12:36
1
2,547 by rmoretti
Mon, 2014-05-12 15:08
Normal topic radius of gyration as constrain
by dhirajks » Sat, 2018-05-05 23:00
1
1,622 by smlewis
Mon, 2018-05-07 11:42
Normal topic Executing the clean_pdb.py script
by Rkfoury » Fri, 2015-02-20 10:16
1
3,761 by lanselibai
Tue, 2015-02-24 02:36
Normal topic Enzyme Design - Score File
by nwhoppe » Thu, 2016-04-07 15:11
1
2,073 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
1,558 by rmoretti
Mon, 2019-06-24 13:43
Normal topic Filtering while clustering
by David Hoover » Wed, 2011-03-30 07:03
1
2,597 by smlewis
Mon, 2014-04-21 06:47
Normal topic Comparative modeling using a two chained template for a one chain structure
by ahmadkhalifa » Mon, 2017-12-18 11:00
1
1,517 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
1,678 by matteoferla
Tue, 2020-08-04 09:30
Normal topic Comparative modeling
by MRH » Mon, 2013-08-19 23:08
1
2,383 by smlewis
Mon, 2014-04-21 06:48
Normal topic SymDock with constraints
by felipet » Thu, 2015-05-14 09:01
1
3,034 by rmoretti
Mon, 2015-05-25 11:49
Normal topic Binding energy contribution broken down by residue
by brspurri » Tue, 2013-07-23 12:47
1
2,740 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Predicting the part of protein strcutrue
by ksy141 » Tue, 2018-10-16 11:47
1
1,431 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
1,269 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
1,116 by vmulligan
Thu, 2020-05-21 18:33
Normal topic Protein-DNA Docking using RosettaScripts?
by brspurri » Fri, 2013-06-07 09:06
1
4,319 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Blast error for rosetta antibody: No argument value given for Query file
by dngusdnr1 » Tue, 2021-06-08 17:30
1
1,097 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
1,924 by rmoretti
Fri, 2016-06-17 10:24
Normal topic JD2 MPI
by jrcf » Wed, 2015-10-28 14:45
1
2,237 by rmoretti
Sat, 2015-10-31 08:57
Normal topic RosettaLigand Docking
by Dinesh Kumar » Mon, 2018-01-15 20:54
1
2,091 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
1,847 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
1,464 by aloshbau
Fri, 2020-01-10 16:48
Normal topic pepspec anchor dock
by Andre Serobian » Tue, 2020-07-28 05:51
1
1,130 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
38 by Edward
Sat, 2023-11-25 05:17
Normal topic Surface Docking Crash (continued)
by dkozuch » Tue, 2017-09-12 06:18
1
1,583 by rmoretti
Tue, 2017-10-10 10:08
Normal topic AbinitioRelax - Error with flags
by jmschu » Wed, 2018-11-21 17:36
1
2,029 by rmoretti
Fri, 2018-11-23 07:59
Normal topic how to generate Fragments using up to 2001 structures only
by oppopomoz » Sat, 2015-07-25 00:43
1
2,023 by rmoretti
Thu, 2015-08-06 08:57
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
1,368 by rmoretti
Wed, 2019-09-18 10:36
Normal topic [Solved] RosettaAntibody3 - Grafting step is failing to detect H3 from the input sequence
by brspurri » Mon, 2021-01-04 16:46
1
1,219 by brspurri
Mon, 2021-01-18 18:14
Normal topic PDB file name too long to be handled by file system
by dave » Thu, 2019-08-08 03:10
1
1,276 by rmoretti
Mon, 2019-08-26 12:17
Normal topic minimize_with_cst and convert_to_cst_file for ddG_monomer issues/confusion
by Kharlamov1317a » Mon, 2020-09-21 08:46
1
1,736 by Kharlamov1317a
Wed, 2020-10-07 08:26
Normal topic Stepwise Monte Carlo - errors with ResidueTypeSet and Disulfides
by user42 » Wed, 2021-07-21 20:34
1
913 by everyday847
Fri, 2021-07-30 13:26
Normal topic Small molecule dimer/trimer/etc docking
by lukasz » Tue, 2022-10-04 06:49
1
1,530 by rmoretti
Tue, 2022-10-04 07:57
Normal topic ddg_monomer with -ddg::local_opt_only true, will it affect other chains that are close?
by cossio » Fri, 2014-12-26 13:11
1
2,037 by rmoretti
Tue, 2015-01-13 07:44
Normal topic cluster.linuxgccrelease Killed error
by samuelrpita » Fri, 2015-11-20 05:56
1
2,287 by rmoretti
Tue, 2015-11-24 16:07
Normal topic loop design for Conformational bias
by dhirajks » Thu, 2019-05-09 21:22
1
1,465 by jadolfbr
Fri, 2019-05-10 07:53
Normal topic error: Unable to open weights/patch file in using ddg_monomer.linuxgccrelease
by xinmiaohe » Thu, 2020-01-30 22:09
1
1,882 by xinmiaohe
Fri, 2020-01-31 08:23
Normal topic profit program in antibody design
by tzhou » Tue, 2013-10-15 23:29
1
2,777 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Repeatability of DDG calculation
by jennifer » Wed, 2015-04-08 05:29
0
1,553 by jennifer
Wed, 2015-04-08 05:29
Normal topic structure prediction
by MA » Wed, 2018-09-05 00:50
0
909 by MA
Wed, 2018-09-05 00:50
Normal topic Error reading in/out glycosylated silent file - "Can't create a polymer bond after residue due to incompatible type"
by amorin » Mon, 2021-09-27 12:16
0
821 by amorin
Mon, 2021-09-27 12:16
Normal topic remodel: what are the exact meanings of notations for secondary structure?
by lanselibai » Sat, 2015-01-17 04:53
0
1,456 by lanselibai
Sat, 2015-01-17 07:57
Normal topic DDG and interaction score problem
by a-eatemadi@razi... » Mon, 2018-04-09 22:54
0
1,149 by a-eatemadi@razi...
Mon, 2018-04-09 22:54
Normal topic score is 0 in the output? - RosettaScripts
by chrisHKL » Thu, 2020-03-05 09:33
0
893 by chrisHKL
Thu, 2020-03-05 12:58
Normal topic Issues with modifying dock.xml for multiple ligand docking
by DGR95 » Fri, 2021-05-14 12:51
0
690 by DGR95
Fri, 2021-05-14 12:51
Normal topic Include MHC alpha helices in loop modelling protocol for pMHC complex
by Roberto » Thu, 2022-08-04 07:22
0
701 by Roberto
Thu, 2022-08-04 07:22
Normal topic how to generate the whole molecule that contains all the symmetric chains
by Sunyp_IM » Sun, 2017-12-10 19:43
0
1,146 by Sunyp_IM
Sun, 2017-12-10 19:43
Normal topic ligand_docking: ligand preparation
by Alison_Yajie » Thu, 2020-07-02 07:05
0
834 by Alison_Yajie
Thu, 2020-07-02 07:10
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