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Rosetta 3 - General

Topic / Topic starter Replies Viewssort ascending Last post
Normal topic what is the relationship and difference between Rosetta 3.0 and miniRosetta
by jarod » Thu, 2010-05-06 20:57 		2
 3,002 by jarod
Mon, 2014-04-21 06:47
Normal topic filter score by I_sc and keep top 1000
by aaj » Tue, 2016-01-19 07:13 		2
 3,000 by aaj
Mon, 2016-02-22 07:43
Normal topic Does RNA parses checkpoint matrix as well as protein
by qlj » Wed, 2014-03-05 06:03 		2
 2,998 by qlj
Thu, 2014-03-06 22:20
Normal topic RASREC - finding lowest energy structure
by Lati » Fri, 2015-11-20 03:08 		2
 2,997 by Lati
Tue, 2016-01-12 13:28
Normal topic Selecting Top Scoring Decoys
by kalabharath » Thu, 2011-10-20 22:08 		2
 2,996 by rmoretti
Mon, 2014-04-21 06:47
Normal topic model protein at low pH
by ytao » Mon, 2012-11-05 07:52 		1
 2,995 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to specify residue numbers in a resfile for a batch of pdbs, while some of them have missing residue numbers?
by johnnytam100 » Wed, 2019-05-08 02:30 		2
 2,992 by johnnytam100
Wed, 2019-05-15 18:45
Normal topic de novo RNA loop
by c.ocasion » Sun, 2021-02-14 18:34 		5
 2,988 by everyday847
Mon, 2021-03-29 20:19
Normal topic Add a ligand with only one atom (i.e. Zn) to the RosettaCM
by lanselibai » Tue, 2021-06-22 10:28 		6
 2,988 by rmoretti
Thu, 2021-06-24 12:23
Normal topic Scoring when the protein is a different length
by gw » Wed, 2012-08-01 08:53 		1
 2,984 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to prevent rotamers from being pruned from the interaction graph?
by msun » Wed, 2013-04-17 14:19 		2
 2,981 by smlewis
Mon, 2014-04-21 06:47
Normal topic Can't read constraint type
by allan.ferrari » Fri, 2015-08-28 12:33 		2
 2,979 by allan.ferrari
Mon, 2015-09-21 21:54
Normal topic Run PackRotamersMover on specified rotamer set
by pachecoj » Mon, 2014-11-10 06:51 		2
 2,978 by pachecoj
Tue, 2014-11-11 19:30
Normal topic Modelling Sheets
by monteirotorres » Thu, 2009-07-02 11:41 		2
 2,977 by monteirotorres
Mon, 2014-04-21 06:47
Normal topic fixbb design use
by Lindsay » Fri, 2012-03-23 09:05 		2
 2,972 by Lindsay
Mon, 2014-04-21 06:47
Normal topic Refinement of a PDB structure containing multiple models
by ahmadkhalifa » Wed, 2018-04-18 07:44 		3
 2,972 by smlewis
Wed, 2018-04-18 19:03
Normal topic Calibur-linux binary or source code availability?
by jasnyderjr » Sat, 2016-12-10 23:36 		2
 2,967 by jadolfbr
Sun, 2016-12-11 10:53
Normal topic Rosetta lack of necessary application
by ylwang » Wed, 2018-11-07 01:13 		3
 2,963 by rmoretti
Wed, 2018-11-21 13:50
Normal topic ​​B​3​-protein design using rosettaScript movers
by straore » Mon, 2015-03-16 05:05 		2
 2,953 by straore
Fri, 2015-04-17 01:54
Normal topic relax with restraints
by jtmacd » Mon, 2010-11-08 09:11 		2
 2,953 by jtmacd
Mon, 2014-04-21 06:47
Normal topic Problem with outputing decoys in the process of AbinitioRelax
by MA » Thu, 2017-07-13 23:27 		3
 2,951 by rmoretti
Thu, 2017-08-03 08:50
Normal topic Loop modelling,
by berk » Sat, 2013-06-08 08:29 		2
 2,945 by berk
Mon, 2014-04-21 06:48
Normal topic How to modify disulfide bonds constrain in homology modeling
by eunwook » Mon, 2013-05-13 04:56 		1
 2,936 by smlewis
Mon, 2014-04-21 06:47
Normal topic The -symmetry:perturb_rigid_body_dofs flag
by doranhen » Sat, 2012-04-28 13:01 		2
 2,932 by doranhen
Mon, 2014-04-21 06:47
Normal topic Generating Fragment Libraries for Metal Binding Proteins
by buzb » Wed, 2011-01-26 12:43 		1
 2,928 by kaue
Mon, 2014-04-21 06:47
Normal topic Residue not found in pose
by lzx32 » Fri, 2011-09-09 03:42 		1
 2,926 by rmoretti
Mon, 2014-04-21 06:47
Normal topic RosettaRemodel
by berk » Wed, 2013-07-10 11:21 		2
 2,926 by jadolfbr
Mon, 2014-04-21 06:48
Normal topic is there a preferred way to enforce an hydrogen bond ?
by logandonaldson » Wed, 2013-03-20 13:14 		2
 2,925 by rmoretti
Mon, 2014-04-21 06:47
Normal topic DesignByCavityProximity: element not expected
by karenjgonzalez » Tue, 2020-01-28 05:16 		4
 2,924 by karenjgonzalez
Tue, 2020-02-11 08:44
Normal topic Can't find the source code of FlexPepDock protocol in Rosetta3.1
by SunH » Thu, 2010-09-16 06:28 		2
 2,919 by barak
Mon, 2014-04-21 06:47
Normal topic [dev] determine which score_type's enabled in create_energy_method?
by ipetrik_ambry » Fri, 2017-10-27 15:37 		3
 2,918 by rmoretti
Mon, 2017-10-30 12:02
Normal topic weird prolines with hydroxyls from fixbb.linuxgccrelease
by louisclark » Wed, 2010-08-25 15:01 		2
 2,918 by louisclark
Mon, 2014-04-21 06:47
Normal topic InterfaceAnalyzer atom subset
by Parker.deWaal » Sun, 2016-03-13 13:41 		2
 2,916 by rmoretti
Mon, 2016-03-14 07:58
Normal topic Bug in Loop Modeling
by dseelig » Thu, 2010-09-23 05:55 		2
 2,916 by smlewis
Mon, 2014-04-21 06:47
Normal topic Installing rosetta 3.0
by dalemu » Thu, 2009-09-24 13:28 		1
 2,913 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to prepare the pdblist file for docking_ensmble in Rosetta3.4
by sunlufinal » Mon, 2015-06-01 19:27 		1
 2,913 by rmoretti
Fri, 2015-07-03 12:58
Normal topic make fragments for a loop
by jarod » Mon, 2010-03-15 07:31 		2
 2,911 by jarod
Mon, 2014-04-21 06:47
Normal topic build local user guide
by coomteng@gmail.com » Wed, 2018-03-28 13:55 		3
 2,910 by coomteng@gmail.com
Wed, 2018-03-28 14:58
Normal topic activation of filters in rosetta3.0 or later
by exchhattu » Thu, 2009-12-03 17:52 		2
 2,897 by exchhattu
Mon, 2014-04-21 06:47
Normal topic Number of conformations needed
by JadAbbass » Sun, 2014-02-16 13:21 		2
 2,894 by JadAbbass
Tue, 2014-02-18 07:27
Normal topic Cannot create cst files from upl files
by road runner » Wed, 2015-11-11 22:07 		2
 2,883 by road runner
Tue, 2015-12-01 10:08
Normal topic loop file
by banshee » Tue, 2013-06-04 13:26 		2
 2,880 by banshee
Mon, 2014-04-21 06:48
Normal topic possible idealize app bug - residues being deleted
by jtmacd » Mon, 2009-06-08 06:27 		2
 2,880 by jtmacd
Mon, 2014-04-21 06:47
Normal topic Fragment file viewers
by MajorID » Fri, 2012-02-24 20:57 		2
 2,876 by smlewis
Mon, 2014-04-21 06:47
Normal topic Using NCAAs in protocols with native heme proteins
by htorres » Wed, 2018-01-24 08:32 		2
 2,872 by htorres
Mon, 2018-02-05 06:53
Normal topic adding NCAA to the N-terminal of RCSB pdb
by ate » Tue, 2021-06-08 08:24 		4
 2,866 by Subhrodeep Saha
Sat, 2021-06-19 07:17
Normal topic how same random seeds can be used in rosetta for mpi run.
by exchhattu » Wed, 2009-10-28 22:09 		1
 2,866 by smlewis
Mon, 2014-04-21 06:47
Normal topic SnugDock equivalent in newer Rosetta code
by SenyorDrew » Tue, 2016-03-29 09:16 		2
 2,862 by SenyorDrew
Wed, 2016-04-06 10:52
Normal topic RosettaMatch in Rosetta3.2?
by SenyorDrew » Fri, 2010-08-13 07:47 		1
 2,848 by smlewis
Mon, 2014-04-21 06:47
Normal topic Comparative modelling of dimer
by rt1108 » Fri, 2012-06-15 07:31 		1
 2,846 by smlewis
Mon, 2014-04-21 06:47
Normal topic Problem with ClashCountCalculator
by masterofpuppets » Wed, 2015-01-07 04:47 		2
 2,846 by rmoretti
Fri, 2015-01-09 10:59
Normal topic Questions on energy oddities
by pachecoj » Wed, 2014-10-15 13:26 		2
 2,838 by pachecoj
Wed, 2014-10-15 15:12
Normal topic General Forum Suggestion
by jadolfbr » Thu, 2011-09-29 08:11 		0
 2,837 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic restricting space in a design
by ast » Tue, 2012-01-17 06:31 		2
 2,836 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Running time of Rosetta/FlexPepDock
by gerdos » Thu, 2015-10-15 02:14 		2
 2,835 by gerdos
Fri, 2015-10-16 03:01
Normal topic constrain files tutorial
by knutjbj » Fri, 2011-02-18 23:57 		2
 2,829 by smlewis
Mon, 2014-04-21 06:47
Normal topic jd2 time out error
by ytao » Mon, 2013-03-04 20:47 		2
 2,828 by ytao
Mon, 2014-04-21 06:47
Normal topic Propagating the same mutation over "different" chains
by mdeklotz » Thu, 2018-07-26 09:27 		3
 2,828 by rmoretti
Fri, 2018-08-03 08:42
Normal topic Intermediate file insertion
by exchhattu » Wed, 2009-09-02 18:44 		2
 2,828 by exchhattu
Mon, 2014-04-21 06:47
Normal topic docking mover(s) in rosetta
by aaj » Mon, 2016-01-25 02:38 		2
 2,825 by aaj
Mon, 2016-02-22 07:50
Normal topic decoy vs pose
by Anonymous » Fri, 2012-06-15 02:46 		1
 2,818 by smlewis
Mon, 2014-04-21 06:47
Normal topic error running rosetta3.0
by aschoenr » Wed, 2009-06-10 13:57 		1
 2,815 by jtmacd
Mon, 2014-04-21 06:47
Normal topic Different weights in the constraints for each stage of AbinitioRelax
by allan.ferrari » Sun, 2017-01-15 04:35 		2
 2,815 by smlewis
Sun, 2017-01-15 18:10
Normal topic Chi values for side chains when switching from centroid mode
by MarkW » Fri, 2015-07-03 04:43 		2
 2,809 by MarkW
Fri, 2015-07-03 15:36
Normal topic scoring with omega energy term
by SergeyP » Thu, 2017-03-09 12:03 		2
 2,803 by SergeyP
Fri, 2017-03-10 11:16
Normal topic params file for beta-amino acids
by phonez » Mon, 2021-03-29 18:30 		4
 2,803 by everyday847
Thu, 2021-04-01 11:59
Normal topic can not find a residue type that matches the residue HIS_P:NtermProteinFull
by tarsis » Wed, 2017-04-05 08:51 		1
 2,803 by rmoretti
Fri, 2017-04-14 08:37
Normal topic How to judge docking success for two proteins without knowledge of native structure
by jasnyderjr » Fri, 2015-07-10 14:27 		1
 2,799 by rmoretti
Tue, 2015-07-14 15:27
Normal topic Rosetta (antibody_designer) performance
by Kihang _Youn » Wed, 2022-03-02 00:48 		7
 2,789 by Kihang _Youn
Thu, 2022-03-10 16:30
Normal topic 3D Structure Prediction
by anirbanzz » Sat, 2010-04-17 02:47 		1
 2,786 by smlewis
Mon, 2014-04-21 06:47
Normal topic Error in RMSD calculation when native sequence deviates
by abdullah » Tue, 2009-11-10 08:56 		1
 2,784 by smlewis
Mon, 2014-04-21 06:47
Normal topic Using a broker file with relax
by Al52 » Mon, 2015-11-30 20:24 		2
 2,782 by Al52
Tue, 2015-12-01 18:22
Normal topic Energy updates in Rosetta 3.3
by gipsonb » Tue, 2011-10-11 09:58 		2
 2,777 by gipsonb
Mon, 2014-04-21 06:47
Normal topic how to relax structure constraining CA in Rosetta3.2?
by albumns » Tue, 2011-02-15 06:15 		2
 2,776 by smlewis
Mon, 2014-04-21 06:47
Normal topic Score Differences between Ab Initio Scoring and Rescore
by mmarlett » Wed, 2016-06-15 09:14 		2
 2,770 by mmarlett
Thu, 2016-06-16 07:06
Normal topic could ab initio support running mpi?
by albumns » Mon, 2010-07-05 01:13 		1
 2,770 by smlewis
Mon, 2014-04-21 06:47
Normal topic Abinitio isolated
by ac.research » Wed, 2018-04-04 07:36 		3
 2,768 by smlewis
Wed, 2018-04-04 10:42
Normal topic CS-Rosetta fragments
by isengupta13 » Sun, 2010-05-16 08:08 		1
 2,768 by AndrewBworth
Mon, 2014-04-21 06:47
Normal topic Constraining a docking study
by jos » Tue, 2011-10-18 05:26 		2
 2,767 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Pair potential
by jadolfbr » Thu, 2011-12-08 08:06 		1
 2,762 by smlewis
Mon, 2014-04-21 06:47
Normal topic -RBSegmentRelax:cst_wt not present in ca_to_allatom.linuxgccrelease application?
by Karol » Thu, 2016-05-12 06:30 		2
 2,750 by Karol
Thu, 2016-05-12 07:58
Normal topic Jump::random_trans strange behavior
by SergeyP » Tue, 2015-11-03 07:56 		2
 2,742 by SergeyP
Sat, 2015-12-19 05:20
Normal topic protein-protien docking with uniform trans
by lkingsle » Thu, 2012-02-09 07:19 		1
 2,740 by mpacella
Mon, 2014-04-21 06:47
Normal topic DockingProtocol mover ensemble error
by dfcoelho » Tue, 2018-10-16 08:32 		2
 2,738 by brspurri
Thu, 2020-08-20 13:22
Normal topic abintio clustering - funnel plot
by vamsi » Fri, 2011-03-25 09:18 		1
 2,738 by smlewis
Mon, 2014-04-21 06:47
Normal topic input secondary structure prediction to AbinitioRelax
by biofisikx » Mon, 2010-08-09 12:36 		2
 2,736 by biofisikx
Mon, 2014-04-21 06:47
Normal topic Protein-Protein Docking
by hwillis » Fri, 2009-08-07 01:31 		1
 2,735 by smlewis
Mon, 2014-04-21 06:47
Normal topic Adding centroid .params files for non-canonical residues based on all-atom .params files
by jcminerlanl » Thu, 2017-04-27 09:28 		2
 2,734 by vmulligan
Thu, 2017-04-27 16:41
Normal topic how to docking including HETATM
by tricia » Tue, 2009-05-05 22:03 		1
 2,727 by smlewis
Mon, 2014-04-21 06:47
Normal topic AtomTree::torsion_angle() can't find dof! in match and enzdes
by petrikigor » Fri, 2012-10-19 09:49 		1
 2,720 by rmoretti
Mon, 2014-04-21 06:47
Normal topic De novo density assembly weights don't add up to a 100
by ahmadkhalifa » Fri, 2018-08-03 12:07 		3
 2,720 by rmoretti
Tue, 2019-10-22 07:05
Normal topic no template pdb provided for alignment
by HZHANG020 » Sat, 2014-06-14 06:27 		1
 2,713 by rmoretti
Mon, 2014-06-16 08:23
Normal topic backbone-independent density
by SergeyP » Sun, 2016-03-20 04:57 		2
 2,710 by SergeyP
Thu, 2016-05-05 02:07
Normal topic Is it better to have smaller nstruct but many runs?
by Loki01 » Mon, 2018-11-19 11:50 		3
 2,706 by smlewis
Mon, 2018-11-19 13:20
Normal topic Performace Benchmarking
by Tushar Kush » Wed, 2019-12-04 02:50 		2
 2,704 by smlewis
Wed, 2019-12-04 13:07
Normal topic How to transform a pose from symmetric into non-symmetric?
by msardejani » Tue, 2016-10-04 16:55 		2
 2,699 by msardejani
Wed, 2016-10-05 10:53
Normal topic Can rosetta model cyclic peptide?
by Apiwat » Fri, 2014-02-07 02:08 		1
 2,698 by rmoretti
Tue, 2014-02-11 06:24
Normal topic Predict the N-terminal of a protein
by aliaselin » Mon, 2010-11-08 03:23 		2
 2,691 by smlewis
Mon, 2014-04-21 06:47
Normal topic RestrictToRepackingRLT and PreventRepackingRLT
by coomteng@gmail.com » Mon, 2018-03-05 11:19 		2
 2,685 by coomteng@gmail.com
Tue, 2018-03-06 02:31
Normal topic Getting started with Rosetta
by myang » Tue, 2009-04-07 16:25 		1
 2,672 by smlewis
Mon, 2014-04-21 06:47