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Rosetta 3 - Applications

Topic / Topic starter Repliessort ascending Views Last post
Normal topic domain:domain fusion
by felipet » Thu, 2017-06-15 13:13 		5
 5,782 by felipet
Fri, 2017-06-16 11:42
Normal topic Can the Rosetta Antibody Design (RAbD) protocol incorporate glycans?
by ccottrell » Tue, 2020-05-05 20:30 		5
 3,187 by jadolfbr
Wed, 2020-05-06 11:37
Normal topic RosettaScripts LinkResidues
by Yero » Fri, 2019-05-17 05:26 		5
 4,435 by Yero
Thu, 2019-07-18 01:39
Normal topic Parse error while reading in XML file in ROSETTA Scripts
by rweisse » Fri, 2014-08-29 03:24 		5
 9,757 by a-eatemadi@razi...
Sun, 2017-08-06 03:49
Normal topic Rosetta dock irmsd
by Pernille » Sun, 2015-04-26 13:51 		5
 7,264 by rmoretti
Mon, 2015-10-12 15:10
Normal topic snugdock(sequence position requested was greater than the number of residues in the pose)
by lei » Thu, 2023-01-12 01:40 		5
 2,919 by lei
Fri, 2023-01-20 08:11
Normal topic [TopologyBroker Exception]: BBTorsion at pos 468unitialized...unclaimed
by tevang » Wed, 2013-04-10 15:07 		5
 5,077 by rmoretti
Mon, 2014-04-21 06:47
Normal topic too many constraints result in no output pose
by Yao Wu » Sun, 2012-11-18 23:45 		5
 6,346 by smlewis
Mon, 2014-04-21 06:47
Normal topic extract_pdb application parse error with silent file
by staciekim » Tue, 2017-08-22 12:39 		5
 6,093 by rmoretti
Thu, 2017-08-24 08:19
Normal topic Local docking: "manually place the two proteins facing each other" ?
by mdeklotz » Fri, 2018-07-20 10:24 		5
 5,051 by dfcoelho
Tue, 2018-10-16 09:05
Normal topic ab initio protein prediction using homologs
by justin » Mon, 2012-02-13 07:52 		5
 5,995 by justin
Mon, 2014-04-21 06:47
Normal topic conway2016 correction on beta-nov15?
by attesor » Wed, 2017-03-15 05:26 		5
 4,680 by attesor
Thu, 2017-03-16 01:21
Normal topic rosetta protein protein docking start up
by vk » Fri, 2011-06-24 09:01 		5
 7,351 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to concatenate the 3-mer and 9-mer files for RosettaCM?
by lanselibai » Fri, 2020-05-08 05:38 		5
 3,552 by danpf
Tue, 2020-05-12 10:58
Normal topic Scoring functions: talaris2013 incompatible versions
by Smbat » Tue, 2020-10-13 06:18 		5
 3,388 by Astghik
Thu, 2020-10-15 00:48
Normal topic Is there a way to restrict memory usage of ddg_monomer?
by cossio » Fri, 2015-01-30 14:35 		5
 5,429 by rmoretti
Mon, 2015-02-09 12:04
Normal topic how to do alanine scanning
by xinmiaohe » Mon, 2019-08-26 17:40 		5
 5,480 by xinmiaohe
Fri, 2019-10-04 08:54
Normal topic Steric clashes in RNA minimization
by brianmlee » Tue, 2014-11-18 18:29 		5
 6,385 by brianmlee
Mon, 2014-11-24 19:40
Normal topic Symmetric Minimization
by aroop » Mon, 2012-12-17 11:45 		5
 4,922 by aroop
Mon, 2014-04-21 06:47
Normal topic How to minimize the decoys obtained from backrub?
by Vedasheersh » Wed, 2017-06-14 10:26 		5
 4,474 by SenyorDrew
Fri, 2017-06-30 09:47
Normal topic ndruns and nstruct in fixbb
by Anonymous » Tue, 2012-08-07 01:52 		5
 6,576 by Anonymous
Mon, 2014-04-21 06:47
Normal topic ddg_monomer conformational search...
by yperez » Wed, 2012-05-09 11:10 		5
 5,201 by yperez
Mon, 2014-04-21 06:47
Normal topic flexpep docking problem
by michael_luntan » Mon, 2011-04-18 17:15 		5
 5,940 by michael_luntan
Mon, 2014-04-21 06:47
Normal topic rosetta app
by MA » Wed, 2017-07-05 06:52 		5
 4,295 by smlewis
Tue, 2017-07-11 07:53
Normal topic trRosetta protocol Segmentation Fault
by nc-ring » Wed, 2021-04-28 11:57 		5
 2,992 by nc-ring
Tue, 2021-05-04 12:26
Normal topic problem creating lips4 file using run_lips.pl
by adva » Sun, 2015-02-15 06:22 		5
 7,813 by linucks
Mon, 2016-06-20 12:02
Normal topic Error with talaris2014.wts, which leads to a garbade scorefunction in loop modelling for protein-protein docking
by Corvin » Wed, 2019-06-19 08:40 		5
 4,396 by rmoretti
Tue, 2019-07-09 10:13
Normal topic a question about ligand docking
by yzhou » Wed, 2012-05-30 18:57 		5
 5,181 by yzhou
Mon, 2014-04-21 06:47
Normal topic How do you use two patches simulataneously with ab initio folding?
by smiruthi » Wed, 2011-12-21 15:24 		5
 5,604 by wangyr
Mon, 2014-04-21 06:47
Normal topic AbinitioRelax with native fragments
by ks » Mon, 2016-09-05 03:03 		5
 5,599 by ks
Mon, 2016-09-12 03:14
Normal topic RosettaCM Biological Assembly
by jrcf » Mon, 2015-10-26 11:01 		5
 7,586 by rmoretti
Tue, 2015-11-24 15:30
Normal topic pair energies across interface
by irini » Fri, 2012-02-10 09:17 		5
 5,235 by Anonymous
Mon, 2014-04-21 06:47
Normal topic matdes_design: ERROR]EXCN_utility_exit has been thrown from: src/core/io/silent/SilentFileData.cc line: 302
by siciliu » Fri, 2014-03-21 17:51 		5
 6,538 by siciliu
Thu, 2014-04-10 09:50
Normal topic Over-docking with FlexPepDock
by gw » Fri, 2012-07-20 13:10 		5
 5,877 by rmoretti
Mon, 2014-04-21 06:47
Normal topic RosettaMP: issue with generating .lips4 file
by ksy141 » Mon, 2019-01-21 17:17 		5
 3,743 by noahC_noahDo
Fri, 2020-11-20 11:29
Normal topic rna structure prediction
by cbala » Thu, 2011-04-14 07:42 		5
 6,113 by mkoohim
Mon, 2014-04-21 06:47
Normal topic Warning messages in Interface analyzer output
by Pernille » Wed, 2015-03-25 00:53 		4
 4,757 by rmoretti
Tue, 2015-03-31 08:20
Normal topic Changing scoring function for fixbb protocol
by mdyini » Sat, 2012-07-07 18:43 		4
 4,440 by mdyini
Mon, 2014-04-21 06:47
Normal topic Coverage of sequence space?
by johnnytam100 » Sun, 2019-04-21 23:25 		4
 3,841 by johnnytam100
Thu, 2019-04-25 19:28
Normal topic Thread target sequence
by duz » Thu, 2021-04-01 10:09 		4
 2,429 by duz
Mon, 2021-05-03 07:50
Normal topic Sequence design with mixed fixbb-relax protocol
by kszczepaniak » Thu, 2013-10-03 08:11 		4
 5,844 by fede
Wed, 2020-09-23 11:24
Normal topic Error when running Remodel with EnzDes constraint file to extend c-terminal
by Jeffrey_Chen » Thu, 2017-01-19 06:20 		4
 4,533 by dfcoelho
Tue, 2017-10-17 11:52
Normal topic Error while reading in silent file
by rweisse » Mon, 2015-04-20 00:31 		4
 5,773 by rmoretti
Thu, 2015-04-30 16:46
Normal topic conformational sampling of multi domain protein
by dhirajks » Tue, 2017-07-04 11:20 		4
 3,963 by jrporter
Wed, 2017-07-05 06:30
Normal topic select_best_unique_ligand_poses - Ligand docking
by subha » Thu, 2018-04-19 10:36 		4
 3,496 by subha
Fri, 2018-04-20 12:49
Normal topic antibody_numbering_converter cannot recognize the IMGT scheme
by cryosky » Sat, 2020-02-29 23:12 		4
 3,230 by jadolfbr
Sun, 2020-03-01 14:54
Normal topic Re: Glutamic acid protonation
by bharat_46010 » Fri, 2017-02-10 03:08 		4
 4,995 by rmoretti
Mon, 2017-02-20 08:09
Normal topic Positive scores with SymmDock in helical symmetry
by kxiao » Tue, 2014-02-11 07:37 		4
 4,842 by kxiao
Thu, 2014-06-05 08:37
Normal topic mr_protocols with symmetry and ligand
by jhm13c » Mon, 2017-02-27 11:59 		4
 3,979 by jhm13c
Thu, 2017-03-02 12:01
Normal topic Problem passing a list of PDB files to minimize_with_cst
by dolevrahat » Sun, 2018-11-18 16:13 		4
 2,031 by rmoretti
Thu, 2024-06-20 11:44
Normal topic When using "screening job files" in small molecule-docking I get: Residue type already exists in the cache Error
by Martin Floor » Thu, 2020-09-17 06:01 		4
 2,994 by Martin Floor
Tue, 2020-09-22 00:48
Normal topic Multiple ligands in enzyme design application
by yogeshkd » Mon, 2013-02-11 10:13 		4
 5,508 by yogeshkd
Mon, 2014-04-21 06:47
Normal topic Single Strand DNA (ssDNA) 3D structure prediction
by mkoohim » Fri, 2012-04-06 00:52 		4
 14,900 by smlewis
Mon, 2014-04-21 06:47
Normal topic Pepspec Errors running 3.4
by rrphenix » Tue, 2013-05-28 12:08 		4
 4,575 by rmoretti
Mon, 2014-04-21 06:47
Normal topic ddg_monomer: what is the meaning of "total score" and "score"?
by lanselibai » Tue, 2015-01-13 14:49 		4
 7,042 by rmoretti
Thu, 2015-04-16 11:23
Normal topic RosettaAntibody3 is failing with "Error: no input sequences were specified!"
by brspurri » Sun, 2020-08-16 16:16 		4
 2,953 by brspurri
Tue, 2020-08-18 09:57
Normal topic simple_cycpep_predict - Design mode - The base name "ARG" was added more than once
by almeida85 » Thu, 2022-08-04 02:57 		4
 1,933 by almeida85
Thu, 2022-08-11 00:58
Normal topic side chain repacking error
by malkeet.singh » Thu, 2017-12-07 04:49 		4
 4,331 by smlewis
Wed, 2017-12-13 09:54
Normal topic Any backrub expert?
by johnnytam100 » Fri, 2019-03-01 01:58 		4
 3,778 by johnnytam100
Sun, 2019-03-03 23:42
Normal topic Rosetta antibody- modeling in the presense of an antigen
by agctomer » Mon, 2021-02-01 03:19 		4
 2,300 by nannemdp
Wed, 2021-02-03 08:52
Normal topic relax protein with multi-conformer bound ligand
by xfradera » Thu, 2023-01-12 09:10 		4
 3,676 by rmoretti
Mon, 2023-02-06 15:06
Normal topic ddg_monomer and membrane proteins
by afmo » Tue, 2014-05-20 02:37 		4
 5,915 by afmo
Thu, 2014-05-22 01:19
Normal topic ddg_monomer: How the ddG is actually calculated based on the 50 trajectories? What scorefunction is used?
by lanselibai » Tue, 2015-02-24 02:38 		4
 6,548 by lanselibai
Sun, 2015-03-01 15:00
Normal topic make_rot_lib issue
by jarek » Thu, 2013-04-11 08:21 		4
 5,117 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to run simulations with non-canonical amino acids?
by Denise » Thu, 2017-06-08 07:50 		4
 4,340 by Denise
Thu, 2017-06-15 04:26
Normal topic rosetta.script segmentation fault
by felipet » Wed, 2013-10-02 10:41 		4
 6,285 by jadolfbr
Mon, 2014-04-21 06:48
Normal topic RosettaCM: An internal error has occurred when "Running the Hybridize mover"
by haom » Mon, 2020-06-15 05:56 		4
 2,632 by haom
Tue, 2020-06-16 05:55
Normal topic How to output all iteration structures from ddg_monomer?
by cossio » Fri, 2014-12-26 13:40 		4
 5,101 by cossio
Mon, 2015-01-19 07:10
Normal topic Can I assume the outputs from different runs are from a same batch?
by lanselibai » Mon, 2014-11-03 06:34 		4
 4,926 by lanselibai
Mon, 2014-11-03 13:15
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
 2,480 by agctomer
Sun, 2021-01-31 01:06
Normal topic Structure prediction using true distance and angle constraint
by maruhuang » Wed, 2019-08-21 02:29 		4
 2,752 by maruhuang
Thu, 2019-09-26 18:52
Normal topic ddg with ligands
by bhaines1 » Mon, 2011-12-05 14:32 		4
 5,850 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Filter for fixed-bb design using RosettaScript?
by chrisHKL » Fri, 2020-02-28 19:47 		4
 2,725 by vmulligan
Mon, 2020-03-02 13:40
Normal topic Backrub Params Files
by protos_heis » Tue, 2012-09-18 06:15 		4
 5,381 by protos_heis
Mon, 2014-04-21 06:47
Normal topic minirosetta: weird behavior
by fred » Wed, 2014-01-22 05:57 		4
 5,291 by fred
Mon, 2014-04-21 06:48
Normal topic Specifying resfile in rosetta scripts
by johnnytam100 » Mon, 2019-03-18 02:19 		4
 4,195 by rmoretti
Fri, 2019-03-29 09:30
Normal topic Problem readin .ccp4 map file
by jljbbc » Tue, 2011-05-03 11:29 		4
 5,984 by jljbbc
Mon, 2014-04-21 06:47
Normal topic building a protein-dna homology model via cm_rosetta
by y_atsmonraz » Wed, 2021-10-20 23:11 		4
 2,292 by y_atsmonraz
Tue, 2021-11-02 01:47
Normal topic RNA structure prediction
by emaghdam » Sat, 2014-02-08 01:30 		4
 6,066 by rmoretti
Mon, 2014-02-24 09:12
Normal topic How to specify only design surface residues and loops by RosettaScripts?
by johnnytam100 » Sun, 2019-04-07 21:47 		4
 3,353 by johnnytam100
Wed, 2019-04-10 02:48
Normal topic Unable to understand fragment picking tutorial points.
by Danielsebas » Thu, 2019-09-05 03:44 		4
 3,257 by danpf
Fri, 2019-09-06 11:29
Normal topic Relaxed proteins show higher clash score in molprobity results.
by Wang Zhe » Fri, 2021-12-03 04:32 		4
 3,406 by smlewis
Wed, 2021-12-08 13:02
Normal topic How to estimate the effect of a mutation on the binding energy?
by ltrabuco » Tue, 2011-02-15 08:02 		4
 5,699 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic Error while running "make_fragments.pl".....[blastpgp] ERROR: Arguments must start with '-'
by AG88 » Thu, 2011-11-03 01:25 		4
 7,903 by weitzner
Mon, 2014-04-21 06:47
Normal topic ligand_docking_analysis
by Prasanth Kumar » Thu, 2013-05-09 23:51 		4
 5,249 by rmoretti
Mon, 2014-04-21 06:47
Normal topic comparative modelling and broker
by felipet » Tue, 2013-02-05 08:33 		4
 4,505 by smlewis
Mon, 2014-04-21 06:47
Normal topic Docking Prepack protocol working or not ?
by MJG » Mon, 2017-04-03 08:02 		4
 4,218 by MJG
Tue, 2017-04-04 23:59
Normal topic null mutation with ddg_monomer
by fred » Fri, 2012-05-11 07:16 		4
 4,412 by fred
Mon, 2014-04-21 06:47
Normal topic Antibody modeling
by Maryam_tabasinezhad » Fri, 2015-09-04 11:00 		4
 5,172 by rmoretti
Wed, 2015-09-09 12:08
Normal topic fixbb with symmetry error
by Prasanth Kumar » Sun, 2014-01-26 10:56 		4
 5,667 by Prasanth Kumar
Mon, 2014-04-21 06:48
Normal topic fixbb algorithm reference?
by tylerborrman » Wed, 2015-09-23 10:20 		4
 5,510 by tylerborrman
Mon, 2015-09-28 09:30
Normal topic Prevention of the negatively charged Nitrogen protonation by coupled_moves
by Corvin » Wed, 2020-11-18 02:56 		4
 2,798 by Corvin
Wed, 2020-11-25 02:58
Normal topic Error with -patch_selectors
by subha » Tue, 2017-06-06 14:40 		4
 3,950 by subha
Fri, 2017-06-09 15:42
Normal topic favor native residue in fixBB design
by ast » Mon, 2012-12-10 06:00 		4
 4,986 by smlewis
Mon, 2014-04-21 06:47
Normal topic Loop modelling before peptide docking
by wsgosal » Tue, 2013-10-01 07:24 		4
 5,450 by wsgosal
Mon, 2014-04-21 06:48
Normal topic Options "-out:prefix" didn't work
by maruhuang » Tue, 2019-09-10 05:42 		4
 3,022 by danpf
Fri, 2020-02-21 18:32
Normal topic Segmentation Fault during prepacking
by Sunyp_IM » Fri, 2020-06-12 11:24 		4
 3,490 by Sunyp_IM
Thu, 2020-07-09 18:40
Normal topic Error about rifdocking step 15
by ng98 » Sun, 2024-01-21 16:30 		4
 725 by ng98
Tue, 2024-01-23 17:01
Normal topic Dimer of dimers
by smiruthi » Fri, 2011-04-15 10:41 		4
 7,309 by IAndre
Mon, 2014-04-21 06:47
Normal topic ligand dock question
by sacch » Sun, 2012-05-20 19:49 		4
 4,721 by sacch
Mon, 2014-04-21 06:47