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Rosetta 3 - Applications

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Normal topic I need help with cst file the paper: De Novo Computational Design of Retro-Aldol Enzymes
by Wenithor » Thu, 2022-01-06 12:20
0
1,009 by Wenithor
Thu, 2022-01-06 12:20
Normal topic Simple_cycpep_predict with crosslinker BBMB
by Ken » Tue, 2023-05-09 08:52
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418 by Ken
Tue, 2023-05-09 08:52
Normal topic Pepspec Anchor Dock
by Soler » Fri, 2020-09-18 08:09
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1,005 by Soler
Fri, 2020-09-18 08:09
Normal topic Symmetry definition question
by mrconde96 » Sun, 2022-10-02 05:34
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1,336 by mrconde96
Sun, 2022-10-02 05:34
Normal topic Problem with Scoring function and PlaceStub mover
by a-eatemadi@razi... » Sat, 2018-04-07 09:22
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1,160 by a-eatemadi@razi...
Sat, 2018-04-07 09:24
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
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990 by chrisHKL
Fri, 2020-02-28 14:52
Normal topic clustering output file has few structures
by fabiotrovato » Mon, 2020-08-17 11:37
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749 by fabiotrovato
Mon, 2020-08-17 11:37
Normal topic Domain insertion with Non-CAA
by mwfranklin » Mon, 2017-01-16 12:30
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1,749 by mwfranklin
Mon, 2017-01-16 12:30
Normal topic Segment File Gen - no ouput
by CATarr » Wed, 2019-10-09 19:05
0
892 by CATarr
Wed, 2019-10-09 19:05
Normal topic RosettaAntibody - No matching templates for CDR1
by agctomer » Tue, 2021-01-19 22:45
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905 by agctomer
Tue, 2021-01-19 22:45
Normal topic Generating the 3-mer and 9-mer fragments
by Prasoon » Wed, 2022-02-09 09:04
0
1,166 by Prasoon
Wed, 2022-02-09 09:04
Normal topic Memory Leak in FragmentPicker.cxx11thread application
by Corvin » Tue, 2023-07-11 06:04
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267 by Corvin
Thu, 2023-07-13 05:30
Normal topic Flexpepdock I_hb scoring term
by mbakalar » Fri, 2018-08-31 13:05
0
1,129 by mbakalar
Fri, 2018-08-31 13:06
Normal topic General question regarding ligand-docking
by Alison_Yajie » Thu, 2020-05-07 09:48
0
784 by Alison_Yajie
Thu, 2020-05-07 09:48
Normal topic Modelling of multi-component symmetrical structures
by LanMei » Wed, 2020-10-07 09:58
0
957 by LanMei
Wed, 2020-10-07 09:58
Normal topic Alanine Scanning
by gjbartlett » Mon, 2013-08-05 07:02
1
3,621 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
2,480 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
2,524 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
1,650 by xinmiaohe
Mon, 2019-08-26 18:16
Normal topic Creating model of 89-90 residues by ab initio methodology-help
by krlitros87 » Sun, 2014-05-25 12:12
1
2,247 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
1,516 by rmoretti
Mon, 2019-06-24 14:39
Normal topic density scoring
by Tianyang89 » Sat, 2020-08-29 04:54
1
1,749 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
2,101 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
1,910 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
1,080 by CameronJA
Tue, 2021-06-15 20:02
Normal topic ProteinInterfaceMS
by rbjacob » Wed, 2018-10-24 11:31
1
1,523 by rmoretti
Wed, 2018-11-21 15:10
Normal topic polymer docking using rosetta scripts
by syntekabio2019 » Fri, 2020-11-27 01:51
1
1,168 by rmoretti
Fri, 2020-11-27 10:47
Normal topic Files for Spatial Constraints
by Derek » Tue, 2016-04-12 01:00
1
1,944 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
1,773 by rmoretti
Thu, 2017-05-18 13:51
Normal topic Calbur vs Energy Based Clustering
by Swillard » Sun, 2018-07-01 13:24
1
1,846 by rmoretti
Fri, 2018-08-03 08:26
Normal topic kcenters_clustering_of_fragments
by bjharris » Mon, 2019-07-01 16:16
1
1,494 by bjharris
Wed, 2020-07-01 23:25
Normal topic number of structures in homology modeling for cluster analysis
by pdbb » Fri, 2013-04-12 08:52
1
2,634 by smlewis
Mon, 2014-04-21 06:47
Normal topic ddg_monomer "ERROR: seqpos >= 1"
by cossio » Fri, 2015-10-02 12:20
1
2,253 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
1,251 by brspurri
Wed, 2021-01-20 08:11
Normal topic docking with constraints
by talavera » Tue, 2013-05-07 01:50
1
4,035 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Fragment Files
by nkemjika » Fri, 2011-07-22 15:11
1
3,059 by dgront
Mon, 2014-04-21 06:47
Normal topic FloppyTail options error
by DmitriiN » Fri, 2016-11-11 02:54
1
1,832 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
1,548 by matteoferla
Thu, 2020-07-02 07:27
Normal topic Holes output interpretation
by lah435 » Mon, 2012-06-04 15:02
1
2,474 by smlewis
Mon, 2014-04-21 06:47
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
1,838 by rmoretti
Fri, 2017-03-24 13:39
Normal topic protein interction design
by Negarsardar » Wed, 2019-05-15 12:01
1
1,464 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
1,368 by xinmiaohe
Fri, 2020-02-07 13:52
Normal topic Inquiry about MPI-Rosetta: Issue with -nstruct Parameter
by serena » Wed, 2024-01-24 00:59
1
118 by rmoretti
Wed, 2024-01-24 08:46
Normal topic ArchiveManager -- spinning down
by Marius1987 » Fri, 2016-12-23 03:10
1
1,835 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
2,204 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
1,573 by smlewis
Tue, 2019-09-24 12:43
Normal topic cluster docked pdbs
by kwu030 » Wed, 2023-06-14 22:48
1
515 by rmoretti
Wed, 2023-06-28 12:36
Normal topic PDB moves after relaxing
by Hr13b » Fri, 2018-07-27 13:12
1
1,464 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
1,419 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
2,809 by rmoretti
Mon, 2014-04-21 06:48
Normal topic relax VS. backrub
by jiongzhang » Mon, 2012-07-02 14:52
1
2,576 by smlewis
Mon, 2014-04-21 06:47
Normal topic Protein-DNA Docking using RosettaScripts?
by brspurri » Fri, 2013-06-07 09:06
1
4,446 by rmoretti
Mon, 2014-04-21 06:48
Normal topic RosettaCM/hybridize
by kywei » Wed, 2021-04-28 09:56
1
1,022 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
3,452 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
2,829 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
1,692 by kamau
Wed, 2017-12-13 14:31
Normal topic ERROR: ResidueType::add_ring: Requested atoms don't exist in this ResidueType!
by walidabualafia » Thu, 2023-07-20 09:44
1
351 by rmoretti
Thu, 2023-07-20 10:08
Normal topic Adding 'virtual' residues for N- and C-terminal optimisation
by Derek Smith » Thu, 2014-08-14 23:18
1
2,320 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
1,379 by everyday847
Fri, 2019-08-23 04:08
Normal topic Loopmodel with DNA has no energy score
by Nicky_Learning_... » Sun, 2015-05-10 19:31
1
2,276 by rmoretti
Mon, 2015-05-25 12:30
Normal topic VH-VL Orientation in antibody
by sujigeorge1979 » Mon, 2019-06-17 01:23
1
1,733 by jeliazkov
Mon, 2019-06-17 06:03
Normal topic Surface accessible residue as a constraint.
by arthuc01 » Fri, 2012-03-09 23:27
1
2,276 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
1,467 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
3,162 by Payne
Tue, 2022-06-21 07:25
Normal topic Should I be stripping water molecules from my input structure for Rosetta Design?
by chrisHKL » Wed, 2021-03-24 14:22
1
1,098 by smlewis
Wed, 2021-03-24 14:59
Normal topic Disulfidize- "Extra content at the end of the document"
by ldlamini » Tue, 2022-05-17 02:37
1
1,095 by rmoretti
Tue, 2022-05-17 07:29
Normal topic Loop modeling: KIC with fragments producing unusual models
by kamau » Mon, 2015-06-01 12:06
1
2,235 by rmoretti
Sat, 2015-06-20 20:07
Normal topic RosettaMatch outputs
by mwfranklin » Tue, 2016-10-11 11:46
1
2,233 by rmoretti
Fri, 2016-10-14 08:56
Normal topic Problem passing a list of PDB files to minimize_with_cst
by dolevrahat » Sun, 2018-11-18 16:13
1
1,835 by rmoretti
Wed, 2018-11-21 15:31
Normal topic FlexPepDock in RosettaScripts keeps running
by gw » Tue, 2012-08-21 12:31
1
2,607 by smlewis
Mon, 2014-04-21 06:47
Normal topic FloppyTail vs. Remodel for linkers
by attesor » Mon, 2014-07-07 08:36
1
2,301 by smlewis
Mon, 2014-07-07 11:58
Normal topic Error in Loop modeling and other queries
by ashu4487 » Wed, 2016-05-11 18:23
1
2,223 by rmoretti
Fri, 2016-06-17 10:15
Normal topic "Angle constraint: 0-length bonds" error
by purvi24 » Sun, 2019-07-28 10:09
1
1,583 by rmoretti
Mon, 2019-08-26 12:49
Normal topic Instructing design scripts to use noncanonical AA instead of canonical
by zcrook » Tue, 2014-11-25 10:43
1
2,110 by rmoretti
Wed, 2014-11-26 07:51
Normal topic Modeling the structure of camel single domain antibody
by Sunyp_IM » Mon, 2018-01-08 00:34
1
2,258 by Sunyp_IM
Mon, 2018-01-08 00:55
Normal topic Usage of the TaskOperations "RestrictToCDRsAndNeighbors"
by johnnytam100 » Wed, 2019-04-10 02:58
1
1,595 by rmoretti
Wed, 2019-07-10 10:10
Normal topic Remodel: the pose does not have residue with chain=H, PDBnum=114
by lanselibai » Wed, 2019-12-25 13:35
1
2,170 by lanselibai
Fri, 2019-12-27 09:38
Normal topic score application
by Hongtham » Tue, 2014-12-23 06:38
1
2,013 by rmoretti
Fri, 2015-01-02 11:06
Normal topic Membrane Abinitio modeling
by bharat_46010 » Mon, 2017-03-13 22:39
1
1,723 by benhardy
Wed, 2020-09-30 04:24
Normal topic missing atom number 5 atom name CB
by ajaniharesh » Fri, 2019-04-26 12:08
1
1,829 by rmoretti
Fri, 2019-04-26 12:13
Normal topic fixing sequence during grafting in antibody_designer
by COM » Fri, 2020-01-24 11:38
1
1,381 by jadolfbr
Tue, 2020-01-28 09:13
Normal topic the results obtained after docking using RosettaDock and ZDOCK
by aha » Thu, 2024-01-04 21:13
1
212 by rmoretti
Thu, 2024-01-11 14:39
Normal topic molfile_to_params script error
by pablogalazdavison » Tue, 2015-07-07 21:22
1
2,471 by rmoretti
Tue, 2015-07-14 14:59
Normal topic Threading with Ligand
by ekwan » Thu, 2018-12-06 15:10
1
1,560 by rmoretti
Fri, 2019-03-29 13:21
Normal topic Error with RosettaAntibodyDesign when running antibody_designer.linuxgccrelease
by bdzhh » Tue, 2019-09-17 17:02
1
1,452 by jadolfbr
Thu, 2019-09-19 08:53
Normal topic problem when exact pdb from silent file
by wenchangyu2008 » Mon, 2011-04-18 00:42
1
3,150 by wenchangyu2008
Mon, 2014-04-21 06:47
Normal topic Flexible peptide docking with flexible receptor backbone
by tevang » Fri, 2012-09-14 11:18
1
2,734 by smlewis
Mon, 2014-04-21 06:47
Normal topic Ligand docking at specific orientation
by ShiranBZ » Mon, 2020-04-13 20:46
1
1,200 by matteoferla
Mon, 2020-05-04 02:02
Normal topic Old Knotfind algorithm
by Martin Floor » Thu, 2022-09-22 07:28
1
1,086 by rmoretti
Fri, 2022-09-23 09:38
Normal topic Docking on mpi.
by Pernille » Mon, 2014-07-28 08:40
1
2,964 by rmoretti
Mon, 2014-08-04 14:51
Normal topic ROSETTALIGAND: How to prepare data to plot ROC curves using rosettaligand docking result???
by Ryhon Wang » Mon, 2016-01-04 22:36
1
3,080 by rmoretti
Tue, 2016-01-05 08:35
Normal topic Mutating phosphorylated residues to "canonical" residues and vice versa
by ValentinaSora » Mon, 2019-05-20 05:58
1
2,184 by rmoretti
Wed, 2019-07-10 09:22
Normal topic remodel ERROR: unrecognized mm_atom_type_name RGU
by daniloboskovic » Sat, 2020-02-22 11:55
1
1,454 by daniloboskovic
Tue, 2020-02-25 08:28
Normal topic Symmetric docking with multiple chains as asymmetric unit
by sarah29 » Tue, 2013-11-05 20:24
1
3,206 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Constraint generator
by Alison_Yajie » Wed, 2020-06-17 20:14
1
1,163 by Alison_Yajie
Wed, 2020-06-17 20:35
Normal topic PyIgClassify cannot renumber and label CDRs my Nanobody-Antigen complex for RabD
by WBNeT » Fri, 2023-07-07 10:58
1
404 by jadolfbr
Mon, 2023-07-10 09:05
Normal topic Ligand Docking with ARLS
by cam11 » Thu, 2016-06-23 09:34
1
2,150 by rmoretti
Thu, 2016-06-23 10:55
Normal topic Error Interface analyser
by jrcf » Thu, 2017-06-22 12:55
1
1,853 by smlewis
Thu, 2017-06-22 13:31
Normal topic Relaxing protein-RNA complexes
by rkirchdo » Fri, 2018-08-03 08:50
1
1,606 by rmoretti
Fri, 2018-08-24 11:28
Normal topic error--rosetta fragment‐based refinement protocol for refinement against EM density
by gsuchunli » Mon, 2016-07-25 13:35
1
2,372 by gsuchunli
Mon, 2016-07-25 13:56
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