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Rosetta 3 - Applications

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Normal topic Error Interface analyser
by jrcf » Thu, 2017-06-22 12:55
1
1,353 by smlewis
Thu, 2017-06-22 13:31
Normal topic Relaxing protein-RNA complexes
by rkirchdo » Fri, 2018-08-03 08:50
1
1,119 by rmoretti
Fri, 2018-08-24 11:28
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
2,477 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
1,488 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
843 by daniloboskovic
Tue, 2020-02-25 08:28
Normal topic FlexPepDock in RosettaScripts keeps running
by gw » Tue, 2012-08-21 12:31
1
2,200 by smlewis
Mon, 2014-04-21 06:47
Normal topic Relax with a ligand is messing up the coordinates of the ligand
by brspurri » Sat, 2015-01-24 12:39
1
2,333 by rmoretti
Mon, 2015-01-26 12:15
Normal topic Difference between movemap and -pivot_residues
by aloshbau » Wed, 2016-02-24 13:21
1
1,693 by rmoretti
Wed, 2016-02-24 14:39
Normal topic weights for pH_protocol
by fmerino » Wed, 2017-04-26 07:14
1
1,544 by rmoretti
Thu, 2017-04-27 07:10
Normal topic broker domain insertion
by dhirajks » Sun, 2018-05-06 12:55
1
1,103 by rmoretti
Fri, 2018-05-18 12:28
Normal topic The relax qustion of Rosetta VIP
by asbelx » Mon, 2019-06-10 07:52
1
922 by rmoretti
Mon, 2019-06-24 14:42
Normal topic Help with enzyme design files
by Wenithor » Thu, 2021-04-29 10:33
1
491 by rmoretti
Thu, 2021-04-29 10:44
Normal topic Flexible peptide docking with flexible receptor backbone
by tevang » Fri, 2012-09-14 11:18
1
2,333 by smlewis
Mon, 2014-04-21 06:47
Normal topic Antibody Docking application
by Maryam_tabasinezhad » Sat, 2015-09-05 09:58
1
1,884 by jadolfbr
Wed, 2015-09-09 12:35
Normal topic Modelling at defined pH - for pmutscan - pH:mode not working
by cagfa1 » Tue, 2022-03-15 04:05
1
184 by Rituparna_Saman...
Wed, 2022-03-23 11:21
Normal topic error--rosetta fragment‐based refinement protocol for refinement against EM density
by gsuchunli » Mon, 2016-07-25 13:35
1
1,904 by gsuchunli
Mon, 2016-07-25 13:56
Normal topic MPdocking I_sc
by jrcf » Mon, 2017-07-31 16:10
1
1,382 by rmoretti
Thu, 2017-08-03 09:29
Normal topic Membrane Abinitio modeling error
by jkyan007 » Thu, 2020-10-29 03:30
1
648 by noahC_noahDo
Tue, 2020-11-17 10:35
Normal topic Fastrelax problem
by Pernille » Tue, 2014-06-17 08:59
1
1,674 by Pernille
Fri, 2014-06-20 00:17
Normal topic 'standard.wts' does not exist
by almeida85 » Mon, 2020-09-14 02:26
1
717 by rmoretti
Mon, 2020-09-14 06:36
Normal topic Rosetta Holes
by zsun12 » Wed, 2015-09-30 11:40
1
3,179 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
1,091 by danpf
Fri, 2020-02-21 18:37
Normal topic Problem with mpirun/mpiexec
by ahansel » Fri, 2020-07-10 08:37
1
2,283 by rmoretti
Fri, 2020-07-10 09:59
Normal topic Comparative Modeling Tutorial
by code_Monkey » Thu, 2021-03-04 12:35
1
537 by rmoretti
Fri, 2021-03-05 09:35
Normal topic Pepspec error
by almeida85 » Mon, 2022-05-02 04:07
1
94 by almeida85
Mon, 2022-05-02 05:05
Normal topic fold and dock protocol not working
by ytao » Mon, 2012-11-26 15:33
1
2,018 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
2,119 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
1,631 by rmoretti
Fri, 2016-09-09 07:47
Normal topic creating a model using a base pdb and extending a chain
by rlwoltz » Fri, 2013-07-12 15:35
1
2,249 by nawsad
Mon, 2014-04-21 06:48
Normal topic rosetta 3.3 - antibody
by ron amon » Mon, 2014-07-21 00:44
1
1,973 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
2,306 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
1,215 by rmoretti
Mon, 2017-03-06 12:39
Normal topic input file for loop modeling
by Negarsardar » Tue, 2019-04-16 10:21
1
995 by rmoretti
Tue, 2019-04-16 11:07
Normal topic Place ligand in a pocket
by sn » Fri, 2017-09-15 12:53
1
1,419 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
895 by smlewis
Mon, 2019-09-16 12:22
Normal topic Filtering while clustering
by David Hoover » Wed, 2011-03-30 07:03
1
2,189 by smlewis
Mon, 2014-04-21 06:47
Normal topic Relax with RDC data gives segmentation fault
by sn » Mon, 2018-07-23 11:39
1
1,123 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
663 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
2,128 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
1,738 by rmoretti
Tue, 2015-11-24 16:16
Normal topic ProteinInterfaceDesign algorithm questions
by tsztain » Mon, 2019-02-18 14:10
1
1,207 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
932 by danpf
Wed, 2019-10-16 13:03
Normal topic Packstat application output
by Vedasheersh » Mon, 2017-07-03 02:45
1
1,517 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
384 by nannemdp
Mon, 2021-09-27 14:22
Normal topic ambiguous constraints
by shrutikhare » Mon, 2014-05-12 04:42
1
2,813 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
2,586 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
1,113 by rmoretti
Tue, 2018-04-10 15:29
Normal topic Add missing residues in loop modeling
by exchhattu » Thu, 2013-06-20 17:38
1
3,108 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
1,841 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
1,363 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
533 by rmoretti
Tue, 2021-05-18 07:21
Normal topic Snugdock_error
by luicui » Thu, 2017-02-09 21:06
1
1,277 by smlewis
Thu, 2017-02-09 21:50
Normal topic Question on restraining receptor symmetry when docking ligand
by subha » Fri, 2018-07-06 21:59
1
1,056 by rmoretti
Fri, 2018-08-03 08:16
Normal topic RosettaMatch
by xingqing326 » Mon, 2019-07-22 13:14
1
1,230 by rmoretti
Mon, 2019-08-26 12:57
Normal topic InterfaceAnalyzer -resfile
by gw » Wed, 2011-11-02 16:01
1
2,416 by smlewis
Mon, 2014-04-21 06:47
Normal topic Interface Analyzer Segmentation Fault
by h_trasatti » Tue, 2017-02-21 12:48
1
1,759 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
764 by danpf
Tue, 2020-07-14 10:27
Normal topic cluster error
by sudhar » Fri, 2011-06-17 05:58
1
2,414 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
1,417 by rmoretti
Mon, 2017-09-04 10:33
Normal topic docking with capping groups
by xavierfradera » Sun, 2018-11-04 16:17
1
1,031 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
610 by rmoretti
Wed, 2020-12-02 07:27
Normal topic Pre-packing a model for SWA loop building
by franfdez » Sun, 2014-07-27 02:16
2
2,422 by franfdez
Mon, 2014-07-28 01:04
Normal topic PIKAA in resfile does not mutate Cys in disulfide bond to specified residue
by attesor » Fri, 2014-03-14 07:53
2
2,754 by attesor
Mon, 2014-06-16 07:34
Normal topic Write error during saving of PDB-file after working with it in the Rosetta through Unix terminal
by Corvin » Thu, 2019-04-25 01:20
2
1,515 by Corvin
Wed, 2019-06-12 00:04
Normal topic Segmentation Fault in Rosetta CM Hybridize
by yliang20 » Mon, 2022-06-06 17:25
2
102 by yliang20
Tue, 2022-06-07 08:36
Normal topic flexpepdock flag "-packing:unboundrot"
by gw » Mon, 2011-07-11 12:23
2
3,319 by Ora Schueler-Furman
Mon, 2014-04-21 06:47
Normal topic Symmetry definition for coiled-coil dimer and trimer
by kszczepaniak » Fri, 2013-10-11 05:33
2
5,058 by kszczepaniak
Mon, 2014-04-21 06:48
Normal topic Use "loopmodel.linuxgccrelease" CCD to build missing residue positions
by lanselibai » Sun, 2014-10-12 09:00
2
2,804 by lanselibai
Mon, 2014-10-13 10:10
Normal topic antibody modeling error
by mxp » Mon, 2019-09-16 18:29
2
1,254 by mxp
Mon, 2019-09-23 01:40
Normal topic Building loop extensions in a membrane protein with Remodel
by benhardy » Tue, 2020-06-02 08:21
2
1,311 by benhardy
Sun, 2020-09-20 11:15
Normal topic Missing atoms and cannot find atom pose when refining ligand position with EM density
by BuddySphinx » Mon, 2018-12-31 16:22
2
2,230 by e3lm
Tue, 2021-09-14 10:02
Normal topic A problem with "make_fragments.pl" script dependencies
by Corvin » Fri, 2019-08-16 04:30
2
1,657 by Corvin
Tue, 2019-08-27 00:46
Normal topic RMS determination using Rosetta 3.3
by adraney » Thu, 2011-12-08 12:44
2
2,706 by mark.wilson
Mon, 2014-04-21 06:47
Normal topic regarding extracting silent file - renamed tag
by shrutikhare » Thu, 2014-04-17 01:19
2
2,109 by shrutikhare
Fri, 2014-04-18 23:11
Normal topic creating compound task mover
by aaj » Wed, 2016-02-24 04:48
2
1,982 by aaj
Wed, 2016-02-24 07:37
Normal topic Strong bias in sampling observed in RosettaDock
by chenna » Thu, 2020-08-27 22:23
2
910 by chenna
Tue, 2021-10-12 20:51
Normal topic GrowLigand
by allan.ferrari » Sat, 2019-10-19 05:32
2
1,381 by allan.ferrari
Tue, 2019-11-05 16:52
Normal topic kinematic loop modeling multiple input: possible?
by a_s_a » Thu, 2011-05-12 09:33
2
2,723 by a_s_a
Mon, 2014-04-21 06:47
Normal topic RoseTTaFold
by ozsolomon » Thu, 2021-10-07 05:27
2
755 by ozsolomon
Thu, 2021-10-07 14:25
Normal topic Regarding the efficiency of the new low resolution ligand-docking movement “Transform”.
by Martin Floor » Mon, 2017-05-15 09:19
2
1,957 by Martin Floor
Mon, 2017-05-15 11:13
Normal topic The question about ligand score function
by asbelx » Sun, 2018-06-17 02:07
2
2,305 by asbelx
Mon, 2018-06-18 22:34
Normal topic Number of max allowed mutations from WT sequence
by mouung » Fri, 2020-09-04 02:33
2
1,030 by amorin
Fri, 2021-02-12 08:53
Normal topic Problems running pmut in parallel with openmpi
by RMJ » Fri, 2012-09-21 06:25
2
3,398 by RMJ
Mon, 2014-04-21 06:47
Normal topic Syntax for python-based (.py) command line on cluster
by lanselibai » Fri, 2014-11-14 09:32
2
4,498 by lanselibai
Thu, 2014-11-20 02:15
Normal topic Error from clean_pdb.py
by code_Monkey » Mon, 2021-03-01 17:00
2
700 by code_Monkey
Thu, 2021-03-04 12:14
Normal topic refining crystal structure using phenix without CIF file
by banshee » Fri, 2016-09-09 01:14
2
2,422 by banshee
Mon, 2016-09-12 23:41
Normal topic Generate fragment locally
by deltag » Wed, 2012-02-01 06:26
2
2,931 by deltag
Mon, 2014-04-21 06:47
Normal topic select_best_unique_ligand_poses output
by ast » Thu, 2013-07-11 02:33
2
2,735 by ast
Mon, 2014-04-21 06:48
Normal topic Remodel: neighbor cutoff
by felipet » Wed, 2014-07-16 08:11
2
2,093 by felipet
Thu, 2014-07-17 10:13
Normal topic Total score problems with high-res ddg_monomer
by jklesmith » Tue, 2015-03-10 15:54
2
2,814 by jennifer
Fri, 2015-03-27 05:56
Normal topic KeyError: 'subject-id' in antibody modelling
by bogac » Mon, 2017-03-06 02:00
2
2,296 by bogac
Tue, 2017-03-07 02:11
Normal topic Membrane homology modeling loop building gives very strange outputs
by chelsell » Tue, 2014-09-30 14:46
2
2,535 by chelsell
Wed, 2014-10-08 12:25
Normal topic The usage of antibody_H3.linuxgccrelease
by Sunyp_IM » Thu, 2020-05-28 22:50
2
1,133 by Sunyp_IM
Thu, 2020-06-04 08:20
Normal topic getting a3m files
by alonwenger » Wed, 2021-12-15 02:38
2
570 by alonwenger
Sat, 2021-12-18 12:32
Normal topic How to eliminate "NUL"s when scoring PDBs?
by lanselibai » Tue, 2014-10-14 10:04
2
2,355 by lanselibai
Fri, 2014-10-17 03:36
Normal topic How to scan double mutations in RosettaScripts?
by msardejani » Mon, 2016-12-12 16:52
2
1,857 by msardejani
Mon, 2016-12-12 17:48
Normal topic FlexPepDock Concatenation
by cam11 » Mon, 2014-08-11 07:39
2
2,206 by cam11
Wed, 2014-08-13 10:06
Normal topic does the loop kinetic support MPI now?
by albumns » Fri, 2012-10-26 06:31
2
1,998 by smlewis
Mon, 2014-04-21 06:47
Normal topic score_jd2.mpi.linuxgccrelease failed
by fred » Wed, 2014-03-26 13:54
2
4,443 by fred
Tue, 2014-04-01 08:24
Normal topic Homology Modeling-no PDB output
by jlawrie » Wed, 2020-08-12 06:30
2
1,048 by jlawrie
Wed, 2020-08-12 08:56
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