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Rosetta 3 - Applications

Topic / Topic starter Repliessort descending Views Last post
Normal topic deltaG calculations
by Prasanth Kumar » Wed, 2013-05-15 07:06 		3
 6,637 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Different scoring applications (score vs score_aln vs score_jd2, etc.)?
by cossio » Fri, 2014-12-26 07:19 		3
 5,012 by Patrícia Antunes
Fri, 2023-01-20 11:55
Normal topic sam.predict-2nd for make_fragments.pl script
by sumukh21 » Thu, 2011-02-17 12:29 		3
 4,971 by fukamitka
Mon, 2014-04-21 06:47
Normal topic Problems incorporating nucleotides (GTP/GDP) into the modeling process for RosettaCM
by ajkal » Fri, 2017-04-14 08:44 		3
 3,743 by rmoretti
Thu, 2017-04-20 13:59
Normal topic Unable to locate the "compute_ddg.py" file and running the RosettaMP protocol
by Sajjad » Mon, 2022-11-28 14:09 		3
 5,217 by Sajjad
Wed, 2022-11-30 11:50
Normal topic Missing common atom definitions in constraints
by ic3reyes » Sat, 2011-06-11 13:09 		3
 5,281 by smlewis
Mon, 2014-04-21 06:47
Normal topic ab initio
by malkeet.singh » Thu, 2018-05-10 05:34 		3
 3,508 by malkeet.singh
Mon, 2018-05-21 04:26
Normal topic fragment_picker with fasta only
by gw » Tue, 2011-11-15 13:20 		3
 4,604 by gw
Mon, 2014-04-21 06:47
Normal topic Modeling of side-chains onto membrane ab initio cluster?
by akfried » Thu, 2011-06-23 04:03 		3
 4,205 by nkemjika
Mon, 2014-04-21 06:47
Normal topic comparative modeling of protein-ligand complex
by tevang » Mon, 2013-09-09 09:06 		3
 4,519 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
 4,116 by rmoretti
Fri, 2015-06-19 13:53
Normal topic Residue_energy_breakdown utility
by cn » Sat, 2012-03-17 06:11 		3
 3,801 by cn
Mon, 2014-04-21 06:47
Normal topic Up to date Vall database
by JadAbbass » Sat, 2013-06-29 10:35 		3
 6,094 by rmoretti
Tue, 2017-06-20 09:02
Normal topic  The error of InterfaceAnalyzer
by asbelx » Thu, 2017-12-21 19:04 		3
 4,273 by smlewis
Sat, 2017-12-23 15:56
Normal topic How to perform abinitiorelax.mpi.linuxgccrelease in parallel mode with MPI
by kingljy » Sun, 2017-09-24 18:37 		3
 4,058 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
 2,438 by danpf
Mon, 2019-09-16 09:51
Normal topic Using Rosetta Docking for nucleic acids
by Adrien Guilhot » Thu, 2011-04-28 06:16 		3
 5,314 by Adrien Guilhot
Mon, 2014-04-21 06:47
Normal topic Lammps or RosettaSurface
by StevPChem » Fri, 2016-06-10 10:13 		3
 4,118 by Anpu
Tue, 2018-09-25 18:53
Normal topic Extract PDB structures from database
by cossio » Mon, 2018-01-29 09:30 		3
 4,093 by rmoretti
Fri, 2018-11-23 11:23
Normal topic Syntax for the alignment file in "minirosetta comparative modeling"
by lanselibai » Thu, 2014-10-16 15:29 		3
 4,725 by lanselibai
Thu, 2014-10-23 03:26
Normal topic Constraints in RosettaCM
by kbuhr » Fri, 2015-07-31 06:55 		3
 4,341 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
 2,319 by benhardy
Fri, 2020-06-19 07:55
Normal topic Does it make sense if I do backrub after sequence design?
by johnnytam100 » Thu, 2019-08-15 05:15 		3
 2,466 by johnnytam100
Fri, 2019-08-16 00:20
Normal topic RosettaCM or FastRelax?
by Tianyang89 » Wed, 2020-09-23 07:46 		3
 2,309 by danpf
Thu, 2020-09-24 13:44
Normal topic Missing CS-HM-Rosetta Binary files
by Marius1987 » Wed, 2016-02-10 05:52 		3
 4,052 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
 3,821 by ahmadkhalifa
Sun, 2019-03-31 23:27
Normal topic ddg_monomer.mpi
by gw » Thu, 2011-10-27 16:45 		3
 4,394 by smlewis
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
 3,836 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
 3,089 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
 2,477 by jkleman
Tue, 2020-05-19 15:02
Normal topic De novo model-building guided by exprimental density data
by dee2711453 » Thu, 2016-03-10 17:28 		3
 3,773 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
 3,377 by rmoretti
Thu, 2018-06-28 12:58
Normal topic Rosetta make_fragments.pl error?
by Danielsebas » Mon, 2019-09-02 07:51 		3
 2,578 by Danielsebas
Thu, 2019-09-05 03:35
Normal topic partial ab initio modeling
by fred » Wed, 2011-08-17 14:14 		3
 4,361 by smlewis
Mon, 2014-04-21 06:47
Normal topic what does initialize_rigid_body_dofs do?
by attesor » Mon, 2015-10-26 05:12 		3
 4,103 by rmoretti
Tue, 2015-11-10 11:35
Normal topic assymetric dymer modelling with comparative and ab initio
by marcia » Mon, 2013-10-14 08:33 		3
 5,043 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Docking one protein into interface between two other proteins
by Cheems » Sat, 2023-05-06 09:49 		3
 1,100 by rmoretti
Mon, 2023-05-08 13:14
Normal topic Enzdes constraint file not defined correctly
by eyong123 » Fri, 2015-03-27 07:16 		3
 3,998 by rmoretti
Thu, 2015-04-16 10:38
Normal topic clustering in RosettaRemodel
by cheyuk » Wed, 2014-04-23 03:09 		3
 4,185 by rmoretti
Mon, 2014-05-12 08:45
Normal topic Allow region of protein to move in a certain direction
by sn » Wed, 2017-08-23 17:07 		3
 3,453 by rmoretti
Thu, 2017-08-24 11:00
Normal topic Why there are two outputs using pmut_scan_parallel.linuxgccrelease with a mutant list file?
by lanselibai » Sun, 2014-11-16 10:26 		3
 4,021 by G Mustafa
Thu, 2018-10-18 05:31
Normal topic How tu use Delta filter's relax_mover
by pocin » Sun, 2017-02-19 05:21 		3
 3,467 by rmoretti
Wed, 2017-03-01 13:10
Normal topic Can only relax one structure at a time
by lah435 » Wed, 2012-12-12 01:55 		3
 4,098 by smlewis
Mon, 2014-04-21 06:47
Normal topic NCAA attached at two points
by tsztain » Wed, 2021-06-16 15:20 		3
 1,993 by matteoferla
Sat, 2021-06-19 03:07
Normal topic Rosetta 3.4 "Relax pdb with allatom constraints" does not work with structures containing multiple chains
by ahonegger » Tue, 2012-04-24 01:34 		3
 4,320 by ahonegger
Mon, 2014-04-21 06:47
Normal topic ddg monomer vs pmut scan
by dave » Tue, 2014-03-04 10:18 		3
 4,641 by smlewis
Fri, 2014-03-07 13:02
Normal topic Simple comparative modeling (threading) example is failing with "unknown atom name: CA CB"
by brspurri » Fri, 2017-03-24 10:52 		3
 3,952 by brspurri
Fri, 2017-03-24 11:35
Normal topic protein protein interaction design
by Negarsardar » Wed, 2019-05-15 06:13 		3
 3,786 by ajasja
Wed, 2019-05-15 15:40
Normal topic pmut_scan does not produce log file
by fglaser » Wed, 2013-10-16 07:25 		3
 4,569 by matteoferla
Tue, 2018-10-30 02:54
Normal topic Ligand dock analysis
by sacch » Tue, 2012-05-22 01:20 		3
 4,033 by glemmon
Mon, 2014-04-21 06:47
Normal topic No Space
by jrcf » Mon, 2016-01-11 16:18 		3
 3,641 by jrcf
Fri, 2016-02-12 16:42
Normal topic score to use for picking top docking solutions?
by sudhar » Tue, 2011-06-14 06:47 		3
 6,112 by weitzner
Mon, 2014-04-21 06:47
Normal topic RosettaAntibody
by mpendleton » Mon, 2011-04-04 10:27 		3
 5,175 by jianqing
Mon, 2014-04-21 06:47
Normal topic How to preserve ACE/NME termini?
by nitroamos » Tue, 2018-05-22 13:07 		3
 3,955 by rmoretti
Thu, 2018-06-28 12:44
Normal topic loopmodel thinks there are no residues in the pose
by lah435 » Wed, 2013-03-27 02:46 		3
 4,348 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Negative Design
by rbjacob » Thu, 2018-10-11 09:18 		3
 3,082 by smlewis
Mon, 2018-10-15 08:42
Normal topic ERROR: no fragment to compute secondary structure
by byin » Sun, 2011-08-07 23:55 		3
 4,691 by smlewis
Mon, 2014-04-21 06:47
Normal topic Discrepancy between the total pose energy and sum of per residue energies
by vijayan » Tue, 2013-07-02 07:24 		3
 4,681 by rmoretti
Mon, 2014-04-21 06:48
Normal topic ddg_monomer: what is the theoretical solution condition for the scoring?
by lanselibai » Sat, 2016-04-30 03:26 		3
 4,026 by smlewis
Mon, 2016-05-02 08:20
Normal topic Error encountered during Rosetta loop modeling
by max » Tue, 2014-11-25 02:17 		3
 4,001 by max
Thu, 2014-11-27 02:56
Normal topic Loop modeling with constraints
by agctomer » Sat, 2021-03-20 03:53 		3
 2,161 by agctomer
Thu, 2021-04-08 07:37
Normal topic Abrelax - Dunbrack02.lib.bin missing
by omirus » Sun, 2011-09-18 06:30 		3
 5,117 by smlewis
Mon, 2014-04-21 06:47
Normal topic make fragment
by zadie1118 » Thu, 2012-08-30 07:45 		3
 5,373 by smlewis
Mon, 2014-04-21 06:47
Normal topic Loop prediction
by yzhou » Thu, 2013-07-18 14:24 		3
 4,456 by jadolfbr
Mon, 2014-04-21 06:48
Normal topic relax a protein with phosphorylated serine residue
by zruan » Thu, 2018-02-01 09:18 		3
 3,131 by rmoretti
Tue, 2018-02-06 09:47
Normal topic proline patching problem
by xun » Tue, 2012-01-03 11:15 		3
 4,137 by xun
Mon, 2014-04-21 06:47
Normal topic strange effect in: SymDock.linuxgccrelease
by ast » Tue, 2013-06-11 11:05 		3
 3,982 by ast
Mon, 2014-04-21 06:48
Normal topic New CSRosetta toolbox
by sn » Mon, 2017-04-24 12:42 		3
 3,040 by rmoretti
Tue, 2017-04-25 06:41
Normal topic How can I set ref2015 and ligand.wts(-restore_pre_talaris_2013_behavior )
by asbelx » Sat, 2019-06-08 00:07 		3
 2,814 by happycaapi
Tue, 2021-06-29 15:35
Normal topic Relax both peptide and ligands
by matteoferla » Thu, 2018-09-13 03:11 		3
 2,844 by smlewis
Fri, 2018-09-14 10:34
Normal topic using Rosetta to compute pH dependent binding?
by JuliusSu » Sun, 2014-06-15 20:28 		3
 5,767 by rmoretti
Tue, 2014-06-17 08:51
Normal topic Are catalytic residues mutatable?
by uka147 » Thu, 2023-10-26 03:49 		3
 834 by uka147
Mon, 2023-10-30 01:53
Normal topic auto_setup_metals flag with loop modeling application fails
by beowulfey » Wed, 2015-06-10 07:44 		3
 4,428 by beowulfey
Tue, 2015-06-23 16:10
Normal topic RosettaScripts filter BuriedUnsatHbonds2 missing still
by zdaw » Fri, 2020-12-11 12:39 		3
 1,969 by zdaw
Tue, 2020-12-15 15:38
Normal topic analysis of clustering
by loris.moretti » Thu, 2012-04-19 02:52 		3
 7,284 by rmoretti
Mon, 2014-04-21 06:47
Normal topic InterfaceAnalyzer problem
by almeida » Mon, 2014-03-03 14:56 		3
 5,138 by smlewis
Fri, 2014-03-07 14:09
Normal topic remodel gives no output
by coomteng@gmail.com » Tue, 2018-03-06 07:40 		3
 3,475 by rmoretti
Wed, 2018-03-07 08:44
Normal topic problem with fixed_membrane option of membrane abinitio
by yescalona » Thu, 2013-01-17 15:42 		3
 3,690 by smlewis
Mon, 2014-04-21 06:47
Normal topic Model truncated proteins
by BuddySphinx » Wed, 2018-12-12 10:32 		3
 3,080 by smlewis
Wed, 2018-12-12 16:51
Normal topic ligand_docking_error
by Alison_Yajie » Mon, 2020-04-20 12:27 		3
 2,402 by YuFei
Sat, 2020-05-30 00:12
Normal topic parameterizing new residues
by chiendarret » Fri, 2012-02-03 22:59 		3
 7,910 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Problems with always_constrained_relax_script
by wsgosal » Wed, 2013-05-29 04:39 		3
 4,900 by rmoretti
Mon, 2014-04-21 06:47
Normal topic High energies after loopmodel run
by michki » Thu, 2014-05-08 05:14 		3
 4,093 by rmoretti
Mon, 2014-05-12 15:16
Normal topic xyzVector error in Enzyme design
by ajmbarbosa » Tue, 2016-01-05 09:46 		3
 4,499 by rmoretti
Fri, 2016-06-17 10:36
Normal topic Deciding -nstruct for RNA FARFAR2
by mandar » Thu, 2024-03-07 22:16 		3
 525 by mandar
Thu, 2024-03-14 22:25
Normal topic Running RosettaHoles2
by weehee » Wed, 2013-02-13 09:35 		3
 3,901 by weehee
Mon, 2014-04-21 06:47
Normal topic Per residue scoring
by chelsell » Mon, 2015-08-17 14:43 		3
 4,359 by rmoretti
Wed, 2015-09-02 12:33
Normal topic RosettaCM input file for running on Stampede
by smathersc » Wed, 2017-01-18 16:12 		3
 3,365 by rmoretti
Thu, 2017-02-02 09:02
Normal topic Rosetta_CM error unrecognized atom 'CS' this atom is not in PDB
by rlwoltz » Thu, 2019-01-24 19:43 		3
 4,509 by bjharris
Sun, 2020-08-23 14:03
Normal topic DockingProtocol
by Soler » Fri, 2022-02-11 00:12 		3
 2,247 by gezmi
Tue, 2022-02-15 21:47
Normal topic revert_design_to_native app comparison to FavorNativeResidue mover
by nwhoppe » Wed, 2016-06-29 14:35 		3
 4,349 by rmoretti
Tue, 2016-07-12 09:30
Normal topic The confussion about an example in tutorial in Rosetta Virtual Workshop 2020
by ldx022 » Tue, 2022-11-29 04:58 		3
 4,582 by ldx022
Tue, 2022-11-29 08:38
Normal topic FlexPepDocking with GDP-bound protein
by LI » Sun, 2011-06-12 20:02 		3
 4,924 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Docking membrane ions and water
by jrcf » Tue, 2017-02-07 15:47 		3
 3,418 by smlewis
Wed, 2017-02-15 07:43
Normal topic RosettaDock 4.0 ambiguous ERROR
by sam_dc » Fri, 2022-03-18 09:36 		3
 2,235 by rmoretti
Tue, 2022-03-22 09:10
Normal topic Relax is resulting in a Segmentation Fault
by brspurri » Thu, 2017-08-24 18:46 		3
 3,975 by brspurri
Sat, 2017-08-26 07:08
Normal topic What is a rational minimal value for the "-nstruct" option
by Sunyp_IM » Fri, 2020-05-22 01:28 		3
 2,339 by nannemdp
Sun, 2020-05-24 14:46
Normal topic relax with resfile
by gw » Fri, 2011-08-05 10:57 		3
 6,399 by nannemdp
Mon, 2014-04-21 06:47
Normal topic Comparative modeling of metalloproteins
by ctqwong » Sun, 2020-07-12 13:51 		3
 2,230 by ctqwong
Mon, 2020-07-27 01:48
Normal topic issues about cstfile in RosettaMatch
by Nicole Deng » Fri, 2020-12-18 05:44 		3
 2,956 by He Xiao
Sun, 2021-04-11 19:29