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Rosetta 3 - Applications

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Normal topic Homology Modelling with cofactors
by Derek Smith » Thu, 2015-07-09 08:24
3
3,920 by Derek Smith
Wed, 2016-02-03 05:47
Normal topic how to make "static" built binaries use multiple cpus like "mpi"?
by Danielsebas » Wed, 2019-09-18 06:41
3
2,003 by rmoretti
Wed, 2019-09-18 10:21
Normal topic Unable to locate the "compute_ddg.py" file and running the RosettaMP protocol
by Sajjad » Mon, 2022-11-28 14:09
3
3,930 by Sajjad
Wed, 2022-11-30 11:50
Normal topic Problems incorporating nucleotides (GTP/GDP) into the modeling process for RosettaCM
by ajkal » Fri, 2017-04-14 08:44
3
2,986 by rmoretti
Thu, 2017-04-20 13:59
Normal topic strange effect in: SymDock.linuxgccrelease
by ast » Tue, 2013-06-11 11:05
3
3,379 by ast
Mon, 2014-04-21 06:48
Normal topic make fragment
by zadie1118 » Thu, 2012-08-30 07:45
3
4,610 by smlewis
Mon, 2014-04-21 06:47
Normal topic Docking to TM protein plus lipid bilayer
by renedominik » Tue, 2019-03-12 06:58
3
2,503 by renedominik
Tue, 2020-02-18 01:36
Normal topic ab initio
by malkeet.singh » Thu, 2018-05-10 05:34
3
2,791 by malkeet.singh
Mon, 2018-05-21 04:26
Normal topic  The error of InterfaceAnalyzer
by asbelx » Thu, 2017-12-21 19:04
3
3,225 by smlewis
Sat, 2017-12-23 15:56
Normal topic Missing common atom definitions in constraints
by ic3reyes » Sat, 2011-06-11 13:09
3
4,613 by smlewis
Mon, 2014-04-21 06:47
Normal topic comparative modeling of protein-ligand complex
by tevang » Mon, 2013-09-09 09:06
3
3,874 by rmoretti
Mon, 2014-04-21 06:48
Normal topic folding ectodomain in membrane ab initio
by freedman » Mon, 2015-05-25 21:09
3
3,394 by rmoretti
Fri, 2015-06-19 13:53
Normal topic sam.predict-2nd for make_fragments.pl script
by sumukh21 » Thu, 2011-02-17 12:29
3
4,277 by fukamitka
Mon, 2014-04-21 06:47
Normal topic proline patching problem
by xun » Tue, 2012-01-03 11:15
3
3,474 by xun
Mon, 2014-04-21 06:47
Normal topic Lammps or RosettaSurface
by StevPChem » Fri, 2016-06-10 10:13
3
3,373 by Anpu
Tue, 2018-09-25 18:53
Normal topic fragment_picker with fasta only
by gw » Tue, 2011-11-15 13:20
3
3,893 by gw
Mon, 2014-04-21 06:47
Normal topic Extract PDB structures from database
by cossio » Mon, 2018-01-29 09:30
3
3,027 by rmoretti
Fri, 2018-11-23 11:23
Normal topic Modeling of side-chains onto membrane ab initio cluster?
by akfried » Thu, 2011-06-23 04:03
3
3,568 by nkemjika
Mon, 2014-04-21 06:47
Normal topic How to perform abinitiorelax.mpi.linuxgccrelease in parallel mode with MPI
by kingljy » Sun, 2017-09-24 18:37
3
2,997 by rmoretti
Tue, 2017-10-10 09:58
Normal topic "Install_dependencies.pl" gives "Aborted" when downloading "nr" database?
by Danielsebas » Sat, 2019-09-14 08:53
3
1,682 by danpf
Mon, 2019-09-16 09:51
Normal topic problem with fixed_membrane option of membrane abinitio
by yescalona » Thu, 2013-01-17 15:42
3
3,110 by smlewis
Mon, 2014-04-21 06:47
Normal topic Does it make sense if I do backrub after sequence design?
by johnnytam100 » Thu, 2019-08-15 05:15
3
1,780 by johnnytam100
Fri, 2019-08-16 00:20
Normal topic RosettaCM or FastRelax?
by Tianyang89 » Wed, 2020-09-23 07:46
3
1,514 by danpf
Thu, 2020-09-24 13:44
Normal topic Syntax for the alignment file in "minirosetta comparative modeling"
by lanselibai » Thu, 2014-10-16 15:29
3
4,049 by lanselibai
Thu, 2014-10-23 03:26
Normal topic Constraints in RosettaCM
by kbuhr » Fri, 2015-07-31 06:55
3
3,646 by kbuhr
Mon, 2016-03-28 01:08
Normal topic Coupled Moves crash with Membrane Protein - residue_edge is undefined for root vertex
by benhardy » Mon, 2020-06-15 09:33
3
1,558 by benhardy
Fri, 2020-06-19 07:55
Normal topic Running RosettaHoles2
by weehee » Wed, 2013-02-13 09:35
3
3,204 by weehee
Mon, 2014-04-21 06:47
Normal topic Using Rosetta Docking for nucleic acids
by Adrien Guilhot » Thu, 2011-04-28 06:16
3
4,563 by Adrien Guilhot
Mon, 2014-04-21 06:47
Normal topic analysis of clustering
by loris.moretti » Thu, 2012-04-19 02:52
3
6,453 by rmoretti
Mon, 2014-04-21 06:47
Normal topic scoring input pdbs as the same as docking score
by hamedkhakzad » Fri, 2016-07-01 07:15
3
3,142 by rmoretti
Tue, 2016-07-12 09:05
Normal topic KIC with fragments versus Next generation KIC
by Loki01 » Fri, 2018-09-07 05:06
3
2,419 by smlewis
Mon, 2018-09-10 11:48
Normal topic Transmembrane helix fold-and-dock?
by sarah_b » Tue, 2020-05-12 02:09
3
1,715 by jkleman
Tue, 2020-05-19 15:02
Normal topic Missing CS-HM-Rosetta Binary files
by Marius1987 » Wed, 2016-02-10 05:52
3
3,415 by Marius1987
Mon, 2016-03-14 04:34
Normal topic Threading a sequence onto a template with ligands/metal ions included
by ajkal » Wed, 2017-04-19 11:53
3
3,001 by ahmadkhalifa
Sun, 2019-03-31 23:27
Normal topic Problems with always_constrained_relax_script
by wsgosal » Wed, 2013-05-29 04:39
3
4,294 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Rosetta make_fragments.pl error?
by Danielsebas » Mon, 2019-09-02 07:51
3
1,857 by Danielsebas
Thu, 2019-09-05 03:35
Normal topic De novo model-building guided by exprimental density data
by dee2711453 » Thu, 2016-03-10 17:28
3
3,087 by dee2711453
Fri, 2016-03-11 21:32
Normal topic The question of ligand docking with constraints
by asbelx » Mon, 2018-06-11 09:39
3
2,608 by rmoretti
Thu, 2018-06-28 12:58
Normal topic Adding water interactions when docking a ligand with Rosetta 3.7.
by brspurri » Thu, 2017-06-01 09:37
2
2,853 by brspurri
Thu, 2017-06-01 10:58
Normal topic Fold and Dock - chains not in contact
by arthuc01 » Wed, 2012-06-13 01:45
2
2,712 by smlewis
Mon, 2014-04-21 06:47
Normal topic Problem with SymmDock in helical symmetry
by mumdonar » Wed, 2013-09-18 03:59
2
3,486 by mumdonar
Mon, 2014-04-21 06:48
Normal topic where is generate_ligens.linuxgccrelease?
by Nicole Deng » Thu, 2020-12-03 00:00
2
1,164 by Nicole Deng
Fri, 2020-12-18 00:28
Normal topic D-amino acids tripeptide docking.
by sam_dc » Sat, 2021-07-03 08:48
2
944 by vmulligan
Tue, 2021-07-06 08:27
Normal topic Docking seems to not parse the -nstruct flag
by rosend » Tue, 2015-11-17 12:01
2
3,309 by rosend
Tue, 2015-11-17 12:12
Normal topic DDG_monomer application
by shadrinams » Mon, 2018-02-12 12:14
2
2,582 by shadrinams
Wed, 2018-03-14 07:46
Normal topic Error when trying docking protocol with different ligand
by scyphs » Wed, 2020-08-05 04:37
2
1,146 by scyphs
Mon, 2020-08-10 08:09
Normal topic Could not open file /Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/citations/rosetta_citations
by yliang20 » Wed, 2022-06-15 11:26
2
545 by yliang20
Wed, 2022-06-15 13:46
Normal topic where to look for positive sign for solution in mr-rosetta3.4?
by lchen » Tue, 2012-07-10 09:38
2
2,741 by lchen
Mon, 2014-04-21 06:47
Normal topic protein-ligand docking rescoring with interfaceAnalyzer
by syntekabio2019 » Sat, 2020-12-19 03:59
2
1,030 by syntekabio2019
Sun, 2020-12-20 21:10
Normal topic The Usage of motifgraft
by Sunyp_IM » Sun, 2017-11-19 20:22
2
2,767 by Sunyp_IM
Mon, 2017-11-20 19:20
Normal topic Chemically bound ligand connection error
by tsztain » Tue, 2019-01-01 18:40
2
1,814 by tsztain
Mon, 2019-02-18 09:55
Normal topic Speed problem when running RosettaLigand ligand docking
by Nicole Deng » Tue, 2019-10-08 04:29
2
1,731 by Nicole Deng
Tue, 2020-11-03 19:07
Normal topic symmetric fixbb design with design_hpatch
by sdh_h » Sat, 2013-02-02 01:48
2
2,550 by ronj
Mon, 2014-04-21 06:47
Normal topic Idealize in Rosetta 3.3
by jadolfbr » Tue, 2011-12-06 11:59
2
2,842 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic Element 'trRosettaProtocol': This element is not expected.
by csaylan » Tue, 2021-04-20 14:21
2
953 by csaylan
Tue, 2021-04-20 16:13
Normal topic homology modeling with threading says length mismatch between sequence and alignment
by rqliang » Thu, 2015-08-06 11:46
2
2,518 by jharamesh
Sat, 2015-08-08 19:51
Normal topic minimize_with_cst problems (ddg_monomer)
by alexn » Tue, 2011-09-20 13:46
2
3,153 by alexn
Mon, 2014-04-21 06:47
Normal topic Multiple Chain Comparative Modeling - End result is not even close to template structure
by eskici » Wed, 2012-08-29 08:09
2
3,417 by eskici
Mon, 2014-04-21 06:47
Normal topic Packstat score in InterfaceAnalyzer
by Vedasheersh » Fri, 2017-01-27 06:21
2
2,398 by smlewis
Fri, 2017-01-27 07:20
Normal topic Alanine Scanning for 1 Protein (no interface)
by mags33 » Fri, 2019-10-25 10:08
2
1,818 by mags33
Wed, 2019-11-06 09:35
Normal topic How to sort a Silent File based on RMSD
by JadAbbass » Sun, 2013-08-04 14:40
2
3,110 by lanselibai
Mon, 2014-10-06 15:30
Normal topic flexpepdock_score_only
by ays » Sun, 2014-09-21 06:17
2
2,263 by ays
Tue, 2014-09-30 08:31
Normal topic SPLINE EPR_DISTANCE Constraint Error
by mmw88 » Tue, 2018-09-18 14:39
2
1,974 by rmoretti
Thu, 2018-09-20 09:19
Normal topic RosettaAntibodyDesign] How can I use run_relax and run_snugdock as part of my command and workflow?
by brspurri » Thu, 2020-05-14 11:15
2
1,226 by brspurri
Thu, 2020-05-14 12:24
Normal topic Error in a new docking
by jrcf » Wed, 2017-05-17 19:26
2
3,418 by tingting
Tue, 2022-03-15 23:55
Normal topic Rosetta_cm Segmentation Fault
by gszwabowski » Thu, 2019-06-20 12:55
2
1,985 by gszwabowski
Wed, 2019-06-26 10:25
Normal topic Structure determination combining X-ray diffraction data and NMR chemical shift
by MajorID » Mon, 2011-10-17 19:55
2
3,392 by rmoretti
Mon, 2014-04-21 06:47
Normal topic cartfrag_overlap error while running hybridize protocol
by sn » Thu, 2017-12-21 10:24
2
1,814 by dnamkr
Mon, 2019-12-30 11:43
Normal topic Error: in membrane docking : Cannot split pose by membrane jump! Quitting...
by Astghik » Tue, 2020-11-24 05:27
2
1,133 by Astghik
Thu, 2020-12-03 02:35
Normal topic Fragment files for membrane_abinitio application
by sumukh21 » Tue, 2011-02-15 17:23
2
3,052 by sumukh21
Mon, 2014-04-21 06:47
Normal topic Rosetta Script for ddg_monomer protocol 16
by cossio » Thu, 2018-01-25 08:23
2
2,010 by cossio
Sun, 2018-03-11 09:12
Normal topic Protein Ensemble RosettaLigand Docking
by sam_dc » Fri, 2021-03-26 10:18
2
1,029 by sam_dc
Fri, 2021-03-26 12:04
Normal topic the meaning of total_score in docking
by libai2098 » Mon, 2011-03-21 05:46
2
4,148 by libai2098
Mon, 2014-04-21 06:47
Normal topic BUG REPORT: Remodel Resfile ERROR: LEU was added more than once?
by daniloboskovic » Wed, 2020-04-29 01:17
2
1,327 by daniloboskovic
Wed, 2020-04-29 05:51
Normal topic limit_cluster_size default value
by sacch » Thu, 2011-11-24 17:57
2
2,538 by sacch
Mon, 2014-04-21 06:47
Normal topic Docking-RMS value nan
by jlawrie » Wed, 2020-08-12 07:03
2
1,208 by jlawrie
Wed, 2020-08-12 07:27
Normal topic r_frag_quality
by ii_cnr » Mon, 2021-04-12 03:06
2
932 by ii_cnr
Mon, 2021-04-12 23:44
Normal topic ab initio modelling - what to do next?
by krlitros87 » Thu, 2014-10-16 13:05
2
2,973 by krlitros87
Wed, 2014-10-22 09:31
Normal topic score:weights for fixbb application in Rosetta 3.5
by tylerborrman » Tue, 2015-07-28 14:16
2
2,394 by tylerborrman
Wed, 2015-09-23 10:51
Normal topic Altering substrate specificity
by bp » Thu, 2016-12-22 02:45
2
2,223 by bp
Thu, 2016-12-22 07:54
Normal topic Model monomer to fit cryo density map of a filament
by BuddySphinx » Wed, 2018-12-12 18:58
2
1,643 by BuddySphinx
Sun, 2018-12-30 16:49
Normal topic flexpep docking, select the decoy to do the further docking, questions
by michael_luntan » Fri, 2011-04-22 04:43
2
3,136 by michael_luntan
Mon, 2014-04-21 06:47
Normal topic Enzdes scorefile lost, can I recreate it
by eyong123 » Wed, 2015-04-15 05:55
2
2,325 by eyong123
Wed, 2015-04-22 11:33
Normal topic How to restart RASREC run
by aep » Fri, 2016-07-01 04:39
2
2,016 by aep
Fri, 2016-07-01 06:54
Normal topic RosettaCM hybridize mover error after fragment picking
by amorin » Thu, 2018-09-06 11:03
2
1,909 by dnamkr
Thu, 2019-12-26 10:22
Normal topic How to run partial_thread in RosettaCM when residure are more than 9999?
by lanselibai » Mon, 2020-05-11 22:43
2
1,554 by lanselibai
Tue, 2020-05-12 20:25
Normal topic hbond_sr_bb and hbond_lr_bb for different chains
by tylerborrman » Tue, 2020-10-13 13:41
2
1,247 by tylerborrman
Tue, 2021-02-09 16:33
Normal topic How to add a residue to one chain of an existing structure?
by sn » Mon, 2017-04-17 09:34
2
2,583 by sn
Thu, 2017-04-20 21:43
Normal topic protein interface design
by Negarsardar » Tue, 2019-05-28 07:04
2
1,677 by Negarsardar
Thu, 2019-05-30 23:46
Normal topic Successful RosettaCM?
by jlawrie » Wed, 2020-08-19 06:53
2
1,249 by jlawrie
Thu, 2020-08-20 11:00
Normal topic Filling the missing loops
by code_Monkey » Tue, 2021-04-27 07:44
2
983 by code_Monkey
Tue, 2021-04-27 12:11
Normal topic ddG filter gives deltaG calculation number?
by jarod » Tue, 2013-05-28 23:43
2
3,514 by jarod
Mon, 2014-04-21 06:47
Normal topic Pepspec - random runtime segfaults (rosetta 3.3 database replaced) [solved]
by loreseeker » Wed, 2011-09-14 08:13
2
3,253 by loreseeker
Mon, 2014-04-21 06:47
Normal topic Disulfide prediction from primary sequence
by zcrook » Wed, 2014-11-12 14:44
2
4,455 by zcrook
Tue, 2014-11-25 10:27
Normal topic Use NMR ensemble in protein-protein docking?
by cossio » Sun, 2015-09-13 07:57
2
2,731 by cossio
Tue, 2015-09-15 12:48
Normal topic Reproducing the exact result using information from previos run
by nawsad » Thu, 2013-03-14 12:05
2
2,255 by nawsad
Mon, 2014-04-21 06:47
Normal topic clean_pdb.py of Rosetta VS cleanATOM of PyRosetta
by lanselibai » Wed, 2014-09-24 03:02
2
4,512 by lanselibai
Wed, 2014-09-24 13:21
Normal topic Trouble enforcing a disulfide in loop building
by chelsell » Sun, 2015-05-10 16:31
2
3,195 by chelsell
Wed, 2015-05-27 14:36
Normal topic Trouble running Enzyme Design application
by danaitop » Thu, 2016-08-11 13:34
2
2,325 by rmoretti
Mon, 2016-09-05 11:10
Normal topic Rosetta fragment tools installation error
by Danielsebas » Thu, 2019-08-29 02:17
2
1,540 by Danielsebas
Sun, 2019-09-01 02:38
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