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Rosetta 3 - Applications
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constraints in Rosetta ligand docking (AddorRemoveMatchCsts, Addconstraints Mover, and ConstraintSetMover) by rohi » Mon, 2021-01-11 13:32 |
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1,036 |
by rohi Mon, 2021-01-11 13:58 |
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Can anybody suggests some flags to run Rifdock? by Hyunmi Song » Sun, 2022-01-23 16:45 |
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1,307 |
by Hyunmi Song Sun, 2022-01-23 16:45 |
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FlexPepDock bug? Constraints do not appear in total_score? by nrollins » Mon, 2021-07-26 14:29 |
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786 |
by nrollins Mon, 2021-07-26 14:29 |
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Ligand Rotamer Control in Macther by Hirbond » Tue, 2022-10-25 13:01 |
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1,756 |
by Hirbond Wed, 2022-10-26 12:57 |
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Secondary Matching build_sets Error by enmirts » Wed, 2018-03-28 10:33 |
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1,141 |
by enmirts Wed, 2018-03-28 10:34 |
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multi ligand docking using rosetta script by syntekabio2019 » Tue, 2021-04-13 19:31 |
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826 |
by syntekabio2019 Tue, 2021-04-13 19:31 |
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Per residue total score by johnnytam100 » Wed, 2022-07-13 21:57 |
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787 |
by johnnytam100 Wed, 2022-07-13 21:57 |
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Fewer than expected structures in clustering output by fabiotrovato » Thu, 2020-08-20 00:59 |
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842 |
by fabiotrovato Thu, 2020-08-20 00:59 |
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Benchmarking Rosetta DDG Methods by sareeves96 » Fri, 2022-07-29 09:55 |
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957 |
by sareeves96 Fri, 2022-07-29 09:55 |
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Creation of crystal_complex.pdb for docking by HBenson » Mon, 2024-03-11 08:57 |
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167 |
by HBenson Mon, 2024-03-11 08:57 |
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Ligand docking with constraint by Alison_Yajie » Wed, 2020-06-24 12:34 |
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877 |
by Alison_Yajie Wed, 2020-06-24 12:34 |
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Question with rosetta AbPredict tutorial by terabithia2011 » Mon, 2021-01-25 09:24 |
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842 |
by terabithia2011 Mon, 2021-01-25 09:24 |
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Rosetta Matcher not recognizing protonation forms of CST files like CYZ, HIS_D, etc by Hirbond » Tue, 2022-03-01 13:16 |
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1,091 |
by Hirbond Tue, 2022-03-01 13:16 |
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Folding and Docking using Symmetry by danielles » Wed, 2012-09-12 11:32 |
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1,902 |
by danielles Mon, 2014-04-21 06:47 |
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Symmetry definition file versions by Jeff Qu » Tue, 2021-09-28 09:53 |
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791 |
by Jeff Qu Tue, 2021-09-28 09:53 |
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RosettaCM Ignoring Ligand by Delfosse57 » Sun, 2022-12-04 12:05 |
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3,972 |
by Delfosse57 Sun, 2022-12-04 12:05 |
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FloppyTail as a rosettascripts file by tiagogomes89 » Mon, 2015-01-19 02:45 |
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1,438 |
by tiagogomes89 Mon, 2015-01-19 02:45 |
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application for affinity optimization by wentlewi » Fri, 2020-03-13 03:24 |
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1,011 |
by wentlewi Fri, 2020-03-13 03:24 |
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FastRelax Refinement severe clashes by Victor Tobiasson » Thu, 2021-05-20 06:55 |
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836 |
by Victor Tobiasson Thu, 2021-05-20 06:55 |
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Does antibody_numbering_converter support camelid antibody? by mxp » Tue, 2020-07-07 01:21 |
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908 |
by mxp Tue, 2020-07-07 01:21 |
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problem in using "zinc_site_redesign" tool by Isomerase » Mon, 2022-03-28 01:19 |
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775 |
by Isomerase Mon, 2022-03-28 01:19 |
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The problems on pdb renumbering by Sunyp_IM » Sun, 2017-08-20 06:39 |
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2,246 |
by Sunyp_IM Sun, 2017-08-20 06:39 |
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Comparing a prediction to the native structure and calculate RMSD for RNA by danwolf_33 » Thu, 2023-02-09 09:32 |
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1,943 |
by danwolf_33 Thu, 2023-02-09 09:34 |
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Urgent issue: Error with submitting a new Rosetta-Vienna RNP-ddG job by eyaaaan » Sun, 2022-08-07 22:03 |
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914 |
by eyaaaan Tue, 2022-08-09 21:59 |
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Model GFP chromophore(cro) using NCAA or NC backbone method? by lei » Thu, 2024-04-04 06:23 |
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88 |
by lei Thu, 2024-04-04 06:23 |
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How many iterations of remodel is enough? by daniloboskovic » Thu, 2020-07-16 08:07 |
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851 |
by daniloboskovic Thu, 2020-07-16 08:14 |
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extract docking pose from ligand docking silent file by Ruska322 » Sat, 2019-09-07 05:21 |
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1,034 |
by Ruska322 Sat, 2019-09-07 05:21 |
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How to apply cartesian_ddg to multi-metric enzyme? by Wang Zhe » Wed, 2021-12-08 10:07 |
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968 |
by Wang Zhe Wed, 2021-12-08 10:07 |
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Protein Protein Docking with Linker by mrinal » Mon, 2023-03-20 15:58 |
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819 |
by mrinal Mon, 2023-03-20 15:58 |
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backrub application, resfile, and pivot_residues by tylerborrman » Tue, 2016-12-06 14:46 |
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1,310 |
by tylerborrman Tue, 2016-12-06 14:46 |
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Dock two domains using topology broker by sn » Thu, 2017-10-05 17:07 |
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1,157 |
by sn Thu, 2017-10-05 17:07 |
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"Residue 7 was disulfide bonded but had no partner" with antibody.linuxgccrelease by Sunyp_IM » Thu, 2020-06-04 05:53 |
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902 |
by Sunyp_IM Thu, 2020-06-04 05:54 |
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Protein design: Ligand binding between two units of a homodimer by chemotaxis_123 » Sun, 2022-01-02 16:01 |
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935 |
by chemotaxis_123 Sun, 2022-01-02 16:01 |
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PDB Clustering by code_Monkey » Mon, 2021-04-05 10:40 |
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788 |
by code_Monkey Mon, 2021-04-05 10:40 |
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RNP structure prediction flags by daniloboskovic » Fri, 2019-08-16 11:10 |
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986 |
by daniloboskovic Fri, 2019-08-16 11:17 |
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Robetta ab initio - TrRosetta for membrane proteins by benhardy » Wed, 2020-09-30 08:42 |
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1,377 |
by benhardy Wed, 2020-09-30 08:42 |
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Topobuilder segmentation fault by tatsiana.bylund » Mon, 2021-08-09 07:10 |
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1,252 |
by tatsiana.bylund Mon, 2021-08-09 07:10 |
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Help to understand docking results by rtorquato » Fri, 2022-11-25 12:05 |
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1,516 |
by rtorquato Fri, 2022-11-25 12:05 |
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FlexPepDock Multi chain receptor by evo_umich » Mon, 2018-04-02 12:13 |
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1,253 |
by evo_umich Mon, 2018-04-02 12:13 |
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Error with RNA_denovo by zmfowler » Thu, 2022-07-14 05:34 |
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840 |
by zmfowler Thu, 2022-07-14 05:34 |
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RosettaAntibody3 - How can I model an extended H3? by brspurri » Fri, 2020-08-28 09:11 |
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882 |
by brspurri Fri, 2020-08-28 09:11 |
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Scoring after HBNet by HHL_SIUC » Wed, 2020-07-01 10:49 |
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882 |
by HHL_SIUC Wed, 2020-07-01 10:49 |
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Pepspec options by shaunmk » Mon, 2015-04-27 02:33 |
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1,684 |
by shaunmk Mon, 2015-04-27 02:33 |
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Linker Building in scFv by sam_dc » Sat, 2021-10-09 05:38 |
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821 |
by sam_dc Sat, 2021-10-09 05:38 |
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Finding lowest energy structure among generated structures by Marius1987 » Sun, 2016-04-10 11:38 |
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1,587 |
by Marius1987 Sun, 2016-04-10 12:09 |
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What means "[ ERROR ] TIME_STAMP: AbrelaxMover: finished ...NO_BATCH S_0001." by Corvin » Thu, 2020-04-02 00:16 |
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1,006 |
by Corvin Thu, 2020-04-02 00:16 |
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help surface_docking peptide on ice by engand93 » Wed, 2019-03-27 02:43 |
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1,019 |
by engand93 Wed, 2019-03-27 02:43 |
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Error with docking_prepack_protocol while executing the tutorial "Docking Flexible Proteins" by vitoralmeida1808 » Mon, 2023-11-06 09:43 |
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257 |
by vitoralmeida1808 Mon, 2023-11-06 09:43 |
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pmut_scan_parallel by G Mustafa » Wed, 2018-10-17 05:41 |
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1,475 |
by G Mustafa Wed, 2018-10-17 05:41 |
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ligand_docking: ligand preparation by Alison_Yajie » Thu, 2020-05-21 09:42 |
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980 |
by Alison_Yajie Thu, 2020-05-21 09:42 |
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constraining different chains together in rosetta_cm by y_atsmonraz » Thu, 2021-11-18 02:59 |
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853 |
by y_atsmonraz Thu, 2021-11-18 03:01 |
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Docking HeparinSulfate to proteins using GlycanDock by GebauerJ » Tue, 2022-08-16 07:44 |
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978 |
by GebauerJ Tue, 2022-08-16 07:44 |
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Helical Symmetry Axis by Sandy » Tue, 2016-05-31 18:48 |
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1,772 |
by Sandy Tue, 2016-05-31 18:48 |
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RosettaAntibody3 core.pose.util error by linhhoang157 » Tue, 2020-07-28 12:40 |
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1,016 |
by linhhoang157 Tue, 2020-07-28 12:40 |
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IL-2 gets better binding with beta / gamma by tonycheng1688 » Wed, 2022-05-25 10:23 |
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920 |
by tonycheng1688 Wed, 2022-05-25 10:23 |
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Problems with mpi version of antibody.linuxgccrelease by Sunyp_IM » Thu, 2020-05-28 23:06 |
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1,118 |
by Sunyp_IM Thu, 2020-05-28 23:07 |
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Protonating all possible sites: the problem in MOL2 file format or the innate Rosetta feature(bug)? by Corvin » Wed, 2020-12-16 04:58 |
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1,095 |
by Corvin Wed, 2020-12-30 09:21 |
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Segfault error while running MR Rosetta in Phenix by memilton » Thu, 2021-12-16 09:09 |
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1,053 |
by memilton Thu, 2021-12-16 09:09 |
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Design of multimeric protein by ldlamini » Mon, 2021-01-11 07:23 |
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917 |
by ldlamini Mon, 2021-01-11 07:23 |
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ligand dock into HEM containg pdb by syntekabio2019 » Thu, 2022-01-20 03:05 |
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1,049 |
by syntekabio2019 Thu, 2022-01-20 03:05 |
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non-zero ddG of binding even without mutations by top-gun98 » Wed, 2023-06-07 17:19 |
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434 |
by top-gun98 Wed, 2023-06-07 17:19 |
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new BUNS for FunFolDes run by tatsiana.bylund » Wed, 2019-08-14 20:57 |
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1,004 |
by tatsiana.bylund Wed, 2019-08-14 20:57 |
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FlexPepDock ab initio: behavior without fragment files by nrollins » Mon, 2021-07-26 14:16 |
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737 |
by nrollins Mon, 2021-07-26 14:16 |
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Setting pivots points for GenKIC by almeida85 » Tue, 2022-10-25 02:32 |
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1,705 |
by almeida85 Tue, 2022-10-25 02:32 |
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Molecular Replacement with multiple chains by brspurri » Fri, 2011-06-10 08:25 |
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2,188 |
by brspurri Mon, 2014-04-21 06:47 |
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PIPER-FlexPepDock [commercial user] by Skelly » Tue, 2024-01-23 16:14 |
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332 |
by Skelly Tue, 2024-01-30 14:08 |
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Stub Libraries for DockWithHotspotMover by ayush_patel » Sat, 2024-03-09 22:43 |
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136 |
by ayush_patel Sat, 2024-03-09 22:43 |
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Using GlycanDock and the Antibody Affinity Maturation protocol. by tbelec » Mon, 2022-02-28 12:37 |
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1,256 |
by tbelec Mon, 2022-02-28 12:37 |
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DNA Interface design by zadie1118 » Wed, 2011-06-22 07:05 |
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2,196 |
by zadie1118 Mon, 2014-04-21 06:47 |
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Docking protein complexes when constrained by oligomer symmetry by msk » Tue, 2014-06-03 11:09 |
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1,544 |
by msk Tue, 2014-06-03 11:09 |
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Extracting top score PIPER models by almeida85 » Mon, 2020-08-31 07:17 |
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1,040 |
by almeida85 Mon, 2020-08-31 07:17 |
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How to design the anitgen-antibody interface by Sunyp_IM » Tue, 2017-12-12 18:44 |
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1,243 |
by Sunyp_IM Tue, 2017-12-12 18:44 |
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Symmetry mode in Remodel for N-terminal extension by yvonne.chan2 » Mon, 2019-11-04 13:41 |
0 |
1,269 |
by yvonne.chan2 Mon, 2019-11-04 13:41 |
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zero standard deviation of I_sc in protein-protein docking by rohi » Fri, 2020-07-03 22:19 |
0 |
853 |
by rohi Fri, 2020-07-03 22:20 |
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Segfault with Pepspec by almeida85 » Thu, 2021-02-11 02:56 |
0 |
729 |
by almeida85 Thu, 2021-02-11 02:56 |
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snugdock run error: Sequence for partner1 does not match first member of ensemble1 by pagumaaaaa » Fri, 2022-03-25 01:21 |
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955 |
by pagumaaaaa Fri, 2022-03-25 01:21 |
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Side-chain grafting at the fixed protein and position by Kazu » Wed, 2020-05-20 08:49 |
0 |
837 |
by Kazu Wed, 2020-05-20 08:49 |
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core.pose.util: [ ERROR ] Can't find residue type 'UNK' in type set of mode fa_standard by AlfredoKCL » Sat, 2020-11-07 18:21 |
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1,339 |
by AlfredoKCL Sat, 2020-11-07 18:21 |
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prepack - residue count fails by xfradera » Fri, 2023-01-27 06:36 |
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1,223 |
by xfradera Fri, 2023-01-27 06:36 |
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Symmetric assembly and output reconstruction by felipet » Wed, 2014-07-02 10:23 |
0 |
1,492 |
by felipet Wed, 2014-07-02 10:23 |
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Error Implementing Match Style Constraints by pwging13 » Thu, 2019-12-19 09:53 |
0 |
1,024 |
by pwging13 Thu, 2019-12-19 09:53 |
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Can't find RosettaRemodel in Rosetta 3.4 by petrikigor » Mon, 2012-12-03 13:56 |
0 |
1,797 |
by petrikigor Mon, 2014-04-21 06:47 |
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cartesian_ddg crashes when the mutfile contains multiple mutations to non-canonical residues by ValentinaSora » Sun, 2020-05-24 12:32 |
0 |
1,465 |
by ValentinaSora Sun, 2020-05-24 12:32 |
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core.pose.util: (0) {0} [ ERROR ] Can't find residue type 'UNK' in type set of mode fa_standard by ldx022 » Thu, 2023-03-16 04:13 |
0 |
1,163 |
by ldx022 Thu, 2023-03-16 04:13 |
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Weighted scores?? by sizhang » Wed, 2018-12-05 15:22 |
0 |
1,017 |
by sizhang Wed, 2018-12-05 15:22 |
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flexpepdcok of lipid conjugated peptide with glyco protein. by ravi.thakkkar369 » Fri, 2020-12-18 13:00 |
0 |
791 |
by ravi.thakkkar369 Fri, 2020-12-18 13:00 |
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DNA-protein docking by ksteczk » Sat, 2020-04-11 11:23 |
0 |
1,430 |
by ksteczk Sat, 2020-04-11 11:23 |
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Pepspec Anchor Dock by Soler » Wed, 2020-09-16 19:08 |
0 |
859 |
by Soler Wed, 2020-09-16 19:08 |
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Repacker vs minimization by Elijah_Hix » Fri, 2021-07-02 07:25 |
0 |
688 |
by Elijah_Hix Fri, 2021-07-02 07:25 |
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Prepacking a macrocycle for docking / preserving cyclization by almeida85 » Thu, 2022-09-08 06:54 |
0 |
862 |
by almeida85 Thu, 2022-09-08 06:54 |
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algebric library for rosetta by yigallah » Mon, 2014-12-15 08:46 |
0 |
1,438 |
by yigallah Mon, 2014-12-15 08:46 |
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appropriate sampling for protein docking to a multi chain assembly by SWM » Fri, 2020-01-24 11:22 |
0 |
865 |
by SWM Fri, 2020-01-24 11:22 |
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Bug Report - Encoding issue by daniloboskovic » Tue, 2020-08-04 07:02 |
0 |
776 |
by daniloboskovic Tue, 2020-08-04 07:02 |
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PlaceStub filter by a-eatemadi@razi... » Wed, 2017-11-15 04:19 |
0 |
1,469 |
by a-eatemadi@razi... Mon, 2017-12-04 23:52 |
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Residue selector by Alison_Yajie » Wed, 2020-06-17 19:57 |
0 |
888 |
by Alison_Yajie Thu, 2020-06-18 09:47 |
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FastRelaxMover parameters for antibody-antigen interaction analysis by samuel_k » Thu, 2022-01-27 01:08 |
0 |
1,032 |
by samuel_k Thu, 2022-01-27 01:08 |
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Generating a new Vall database by vijay.anand » Tue, 2023-06-20 12:08 |
0 |
411 |
by vijay.anand Tue, 2023-06-20 12:08 |
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behind threading protocol by fred » Tue, 2011-10-25 05:37 |
0 |
2,258 |
by fred Mon, 2014-04-21 06:47 |
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NCAA Rotamers for Cyclosporin by marinok » Mon, 2020-09-28 14:11 |
0 |
1,228 |
by marinok Mon, 2020-09-28 14:11 |
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ddg_monomer: if MPI executable is reproducible and efficient? by lanselibai » Sun, 2015-01-11 09:48 |
0 |
1,675 |
by lanselibai Sun, 2015-01-11 10:50 |
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