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Rosetta 3 - Applications

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Normal topic rosetta 3.3 - antibody
by ron amon » Mon, 2014-07-21 00:44
1
2,100 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
2,462 by rmoretti
Wed, 2015-03-25 11:33
Normal topic Incorporating iron-sulfur cluster into ROSETTA applications
by Derek Smith » Thu, 2014-08-14 23:12
1
2,267 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
1,860 by rmoretti
Tue, 2015-11-24 16:16
Normal topic SnugDock Partners parameter
by tyang39 » Fri, 2022-07-08 10:02
1
211 by rmoretti
Fri, 2022-07-08 10:27
Normal topic Relax with RDC data gives segmentation fault
by sn » Mon, 2018-07-23 11:39
1
1,241 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
803 by leygkn
Tue, 2020-09-22 22:46
Normal topic Packstat application output
by Vedasheersh » Mon, 2017-07-03 02:45
1
1,653 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
612 by nannemdp
Mon, 2021-09-27 14:22
Normal topic ambiguous constraints
by shrutikhare » Mon, 2014-05-12 04:42
1
2,939 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
2,726 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
1,234 by rmoretti
Tue, 2018-04-10 15:29
Normal topic ProteinInterfaceDesign algorithm questions
by tsztain » Mon, 2019-02-18 14:10
1
1,346 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
1,064 by danpf
Wed, 2019-10-16 13:03
Normal topic Add missing residues in loop modeling
by exchhattu » Thu, 2013-06-20 17:38
1
3,240 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
1,957 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
1,477 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
700 by rmoretti
Tue, 2021-05-18 07:21
Normal topic Snugdock_error
by luicui » Thu, 2017-02-09 21:06
1
1,394 by smlewis
Thu, 2017-02-09 21:50
Normal topic Interface Analyzer Segmentation Fault
by h_trasatti » Tue, 2017-02-21 12:48
1
1,885 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
890 by danpf
Tue, 2020-07-14 10:27
Normal topic cluster error
by sudhar » Fri, 2011-06-17 05:58
1
2,539 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Using different number of 9-mers (UPDATED)
by JadAbbass » Mon, 2017-08-28 07:20
1
1,537 by rmoretti
Mon, 2017-09-04 10:33
Normal topic docking with capping groups
by xavierfradera » Sun, 2018-11-04 16:17
1
1,163 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
740 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
1,170 by rmoretti
Fri, 2018-08-03 08:16
Normal topic RosettaMatch
by xingqing326 » Mon, 2019-07-22 13:14
1
1,371 by rmoretti
Mon, 2019-08-26 12:57
Normal topic InterfaceAnalyzer -resfile
by gw » Wed, 2011-11-02 16:01
1
2,544 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
683 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
1,558 by smlewis
Thu, 2016-12-08 15:50
Normal topic dssp
by MA » Thu, 2017-10-05 09:34
1
1,426 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
508 by dgm3
Fri, 2021-12-31 17:42
Normal topic How to calculate dG?
by yperez » Mon, 2012-10-22 07:28
1
2,532 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
2,472 by jarod
Mon, 2014-04-21 06:47
Normal topic splitfile.py
by saladi » Fri, 2018-03-30 10:31
1
1,384 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
888 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
1,028 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
1,788 by rmoretti
Thu, 2014-10-23 13:55
Normal topic Homology modelling applies alignment wrong
by bernhardcl » Thu, 2015-08-06 09:39
1
1,732 by bernhardcl
Tue, 2015-08-11 09:11
Normal topic comparative modeling of a homodimer
by banshee » Mon, 2017-01-09 18:34
1
1,968 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
702 by bjharris
Fri, 2021-01-22 17:34
Normal topic duplex RNA
by amir_tagh » Thu, 2021-08-05 06:34
1
638 by everyday847
Mon, 2021-08-16 10:43
Normal topic Ligand creation
by Prasanth Kumar » Fri, 2013-08-02 09:48
1
2,141 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Ligand docking: ERROR: set_atom_base: atoms must be bonded!
by mengzhang » Mon, 2014-05-12 12:36
1
2,301 by rmoretti
Mon, 2014-05-12 15:08
Normal topic radius of gyration as constrain
by dhirajks » Sat, 2018-05-05 23:00
1
1,337 by smlewis
Mon, 2018-05-07 11:42
Normal topic AbinitioRelax Disulfide Bonds are not being retained
by brspurri » Wed, 2011-09-28 13:55
1
3,937 by parmef
Mon, 2014-04-21 06:47
Normal topic Antibody Modelling
by luicui » Mon, 2017-01-23 21:30
1
1,871 by smlewis
Mon, 2017-02-06 20:46
Normal topic blast database error
by jessye » Sun, 2017-12-03 23:59
1
1,443 by smlewis
Mon, 2017-12-04 12:18
Normal topic Comparative modeling
by MRH » Mon, 2013-08-19 23:08
1
2,156 by smlewis
Mon, 2014-04-21 06:48
Normal topic SymDock with constraints
by felipet » Thu, 2015-05-14 09:01
1
2,738 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
1,125 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
979 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
823 by vmulligan
Thu, 2020-05-21 18:33
Normal topic trouble in floppytail modelling
by ytao » Thu, 2013-06-27 13:15
1
2,135 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
3,368 by lanselibai
Tue, 2015-02-24 02:36
Normal topic Enzyme Design - Score File
by nwhoppe » Thu, 2016-04-07 15:11
1
1,763 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
1,234 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
1,211 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
1,332 by matteoferla
Tue, 2020-08-04 09:30
Normal topic score and relax
by Prasanth Kumar » Thu, 2013-05-02 05:09
1
2,948 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic JD2 MPI
by jrcf » Wed, 2015-10-28 14:45
1
1,907 by rmoretti
Sat, 2015-10-31 08:57
Normal topic RosettaLigand Docking
by Dinesh Kumar » Mon, 2018-01-15 20:54
1
1,758 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
1,446 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
1,149 by aloshbau
Fri, 2020-01-10 16:48
Normal topic pepspec anchor dock
by Andre Serobian » Tue, 2020-07-28 05:51
1
841 by Andre Serobian
Tue, 2020-07-28 23:26
Normal topic Surface Docking Crash (continued)
by dkozuch » Tue, 2017-09-12 06:18
1
1,311 by rmoretti
Tue, 2017-10-10 10:08
Normal topic AbinitioRelax - Error with flags
by jmschu » Wed, 2018-11-21 17:36
1
1,668 by rmoretti
Fri, 2018-11-23 07:59
Normal topic error mesages from RosettaDock
by AlanZhao » Mon, 2011-03-21 11:42
1
2,220 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to run my openmp programe in rosetta3.3?
by lihowe » Mon, 2012-02-27 23:43
1
2,087 by smlewis
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
674 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
1,645 by rmoretti
Fri, 2016-06-17 10:24
Normal topic Problem with AtomPair constraint
by jarek » Tue, 2012-10-09 07:28
1
2,065 by smlewis
Mon, 2014-04-21 06:47
Normal topic Representing Cross-linked nitrogens
by jjlee2 » Sat, 2011-11-26 18:42
1
2,138 by smlewis
Mon, 2014-04-21 06:47
Normal topic modeling 4 linkers between 2 domains
by pdbb » Thu, 2013-05-16 08:23
1
2,111 by smlewis
Mon, 2014-04-21 06:47
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
1,768 by rmoretti
Tue, 2015-01-13 07:44
Normal topic cluster.linuxgccrelease Killed error
by samuelrpita » Fri, 2015-11-20 05:56
1
1,993 by rmoretti
Tue, 2015-11-24 16:07
Normal topic loop design for Conformational bias
by dhirajks » Thu, 2019-05-09 21:22
1
1,173 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
1,456 by xinmiaohe
Fri, 2020-01-31 08:23
Normal topic score_jd2.linuxgccrelease documentation
by fglaser » Mon, 2011-08-01 04:08
1
3,512 by smlewis
Mon, 2014-04-21 06:47
Normal topic profit program in antibody design
by tzhou » Tue, 2013-10-15 23:29
1
2,493 by rmoretti
Mon, 2014-04-21 06:48
Normal topic how to generate Fragments using up to 2001 structures only
by oppopomoz » Sat, 2015-07-25 00:43
1
1,729 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
1,047 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
856 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
967 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
1,259 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
617 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
902 by rmoretti
Tue, 2022-10-04 07:57
Normal topic antibody protocol fails
by hamedkhakzad » Mon, 2019-08-19 07:43
1
1,035 by smlewis
Tue, 2019-10-22 09:45
Normal topic Rosetta_scripts error, Got some signal... It is:6
by jhm13c » Fri, 2017-04-14 14:05
1
1,705 by rmoretti
Sat, 2017-04-15 13:30
Normal topic Relax with multiple small molecules
by jharamesh » Sun, 2019-05-26 19:34
1
1,262 by rmoretti
Mon, 2019-06-24 15:19
Normal topic Ddg filter threshold value?
by chrisHKL » Fri, 2020-02-28 15:01
1
872 by rmoretti
Wed, 2020-03-04 09:56
Normal topic shape complementarity
by holdenj » Fri, 2022-07-15 13:24
1
232 by rmoretti
Fri, 2022-07-15 13:50
Normal topic Script for loop modeling: how to define loop sequence
by batch2k » Thu, 2014-10-30 12:58
1
1,859 by jadolfbr
Fri, 2014-10-31 08:45
Normal topic "install_dependencies.pl" script: an optimization of HDD space during nr-pfilt data extracting and formatting stage
by Corvin » Thu, 2019-10-10 02:20
1
1,082 by danpf
Thu, 2019-10-10 09:55
Normal topic How to select docked models
by Sunyp_IM » Mon, 2020-06-22 00:50
1
781 by ssrb
Mon, 2020-06-22 13:12
Normal topic Rosetta DNA - Protein-DNA scoring function and binding energy
by tanoramb » Tue, 2012-05-08 14:00
1
4,151 by smlewis
Mon, 2014-04-21 06:47
Normal topic Error with FlexPepDock
by aloshbau » Sat, 2013-08-10 11:51
1
2,292 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Snugdock+ensembledock usage
by Anouk » Mon, 2014-09-22 08:09
1
2,601 by jadolfbr
Mon, 2014-10-20 13:42
Normal topic Should I trust the score output from relax used with a protein complex?
by cossio » Thu, 2015-05-07 06:08
1
1,794 by rmoretti
Mon, 2015-05-25 12:37
Normal topic C-termini remodelling of dimeric structure removes second chain
by LeonhardJS » Wed, 2021-10-13 06:23
1
543 by LeonhardJS
Fri, 2021-11-12 01:20
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