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Rosetta 3 - Applications
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| Topic / Topic starter | Replies |
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Limit on backbone movement in relax? by SWM » Fri, 2020-01-24 07:35 |
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938 |
by SWM Fri, 2020-01-24 07:35 |
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FlexPepDocking by jlawrie » Tue, 2020-09-15 12:52 |
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935 |
by jlawrie Tue, 2020-09-15 12:52 |
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AbinitioRelax detect_disulf_tolerance by aarono » Tue, 2020-06-02 00:13 |
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932 |
by aarono Tue, 2020-06-02 00:13 |
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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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932 |
by chemotaxis_123 Sun, 2022-01-02 16:01 |
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Segment File Gen - no ouput by CATarr » Wed, 2019-10-09 19:05 |
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927 |
by CATarr Wed, 2019-10-09 19:05 |
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Local docking- should I use KIC? by seayoung lee » Fri, 2022-05-27 02:45 |
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923 |
by seayoung lee Fri, 2022-05-27 02:45 |
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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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ligand_docking: ligand preparation by Alison_Yajie » Thu, 2020-07-02 07:05 |
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919 |
by Alison_Yajie Thu, 2020-07-02 07:10 |
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RemodelMover and Input Pose by ozyo » Tue, 2020-12-29 09:41 |
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916 |
by ozyo Tue, 2020-12-29 09:41 |
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Design of multimeric protein by ldlamini » Mon, 2021-01-11 07:23 |
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916 |
by ldlamini Mon, 2021-01-11 07:23 |
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protein relax by Alison_Yajie » Tue, 2020-05-19 08:29 |
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915 |
by Alison_Yajie Tue, 2020-05-19 08:29 |
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Problems with waters in CoupledMoves application by Corvin » Tue, 2021-11-16 07:16 |
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914 |
by Corvin Tue, 2021-11-16 07:22 |
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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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913 |
by eyaaaan Tue, 2022-08-09 21:59 |
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Enzyme Design Not Editing Structure by liuwenxi » Wed, 2022-05-18 10:12 |
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910 |
by liuwenxi Wed, 2022-05-18 10:12 |
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Can remodel really handle multiple insertions in one simulation? by lanselibai » Sat, 2019-12-28 12:51 |
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910 |
by lanselibai Sat, 2019-12-28 12:51 |
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Trehalose by jpfuenzalidawx » Thu, 2022-09-08 00:49 |
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909 |
by jpfuenzalidawx Thu, 2022-09-08 00:49 |
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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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Params for a stapled helix peptide by e3lm » Thu, 2022-05-26 12:55 |
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904 |
by e3lm Thu, 2022-05-26 12:55 |
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Modelling humanized camelid like antibody by terabithia2011 » Tue, 2021-01-26 10:12 |
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902 |
by terabithia2011 Tue, 2021-01-26 10:12 |
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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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901 |
by Sunyp_IM Thu, 2020-06-04 05:54 |
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Comparative Modeling Templates for Protein with Multiple Domains by Morrian_Lynn » Wed, 2020-03-04 10:42 |
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900 |
by Morrian_Lynn Wed, 2020-03-04 10:42 |
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Docking one protein into interface between two other proteins by Cheems » Sat, 2023-05-06 09:49 |
3 |
900 |
by rmoretti Mon, 2023-05-08 13:14 |
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Metal Ion in symmetric design by tschiex » Wed, 2020-07-08 05:28 |
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895 |
by tschiex Wed, 2020-07-08 05:28 |
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Residue selector by Alison_Yajie » Wed, 2020-06-17 19:57 |
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886 |
by Alison_Yajie Thu, 2020-06-18 09:47 |
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Dimeric interface redesign by kjs1728 » Mon, 2022-05-02 21:57 |
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883 |
by kjs1728 Mon, 2022-05-02 21:57 |
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RosettaAntibody3 - How can I model an extended H3? by brspurri » Fri, 2020-08-28 09:11 |
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881 |
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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879 |
by HHL_SIUC Wed, 2020-07-01 10:49 |
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Pepspec - sequence sampling by almeida85 » Thu, 2022-06-23 04:05 |
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877 |
by almeida85 Thu, 2022-06-23 05:50 |
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Creating fragment files for proteins less than 27 aa in length by Poladu » Tue, 2021-01-26 07:50 |
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876 |
by Poladu Tue, 2021-01-26 07:50 |
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Ligand docking with constraint by Alison_Yajie » Wed, 2020-06-24 12:34 |
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876 |
by Alison_Yajie Wed, 2020-06-24 12:34 |
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appropriate sampling for protein docking to a multi chain assembly by SWM » Fri, 2020-01-24 11:22 |
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863 |
by SWM Fri, 2020-01-24 11:22 |
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SecundaryStructure Filter by Soler » Sun, 2021-11-21 22:20 |
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862 |
by Soler Sun, 2021-11-21 22:20 |
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Prepacking a macrocycle for docking / preserving cyclization by almeida85 » Thu, 2022-09-08 06:54 |
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859 |
by almeida85 Thu, 2022-09-08 06:54 |
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Pepspec Anchor Dock by Soler » Wed, 2020-09-16 19:08 |
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858 |
by Soler Wed, 2020-09-16 19:08 |
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Include MHC alpha helices in loop modelling protocol for pMHC complex by Roberto » Thu, 2022-08-04 07:22 |
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854 |
by Roberto Thu, 2022-08-04 07:22 |
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zero standard deviation of I_sc in protein-protein docking by rohi » Fri, 2020-07-03 22:19 |
0 |
850 |
by rohi Fri, 2020-07-03 22:20 |
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How many iterations of remodel is enough? by daniloboskovic » Thu, 2020-07-16 08:07 |
0 |
850 |
by daniloboskovic Thu, 2020-07-16 08:14 |
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constraining different chains together in rosetta_cm by y_atsmonraz » Thu, 2021-11-18 02:59 |
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849 |
by y_atsmonraz Thu, 2021-11-18 03:01 |
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CS-Rosetta cofactor by martongadanecz » Wed, 2022-08-03 01:05 |
0 |
842 |
by martongadanecz Wed, 2022-08-03 01:05 |
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Fewer than expected structures in clustering output by fabiotrovato » Thu, 2020-08-20 00:59 |
0 |
841 |
by fabiotrovato Thu, 2020-08-20 00:59 |
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Question with rosetta AbPredict tutorial by terabithia2011 » Mon, 2021-01-25 09:24 |
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838 |
by terabithia2011 Mon, 2021-01-25 09:24 |
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Error with RNA_denovo by zmfowler » Thu, 2022-07-14 05:34 |
0 |
836 |
by zmfowler Thu, 2022-07-14 05:34 |
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Side-chain grafting at the fixed protein and position by Kazu » Wed, 2020-05-20 08:49 |
0 |
834 |
by Kazu Wed, 2020-05-20 08:49 |
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FastRelax Refinement severe clashes by Victor Tobiasson » Thu, 2021-05-20 06:55 |
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833 |
by Victor Tobiasson Thu, 2021-05-20 06:55 |
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simple_cycpep_predict thioether_lariat option by Ken » Mon, 2022-03-14 15:14 |
0 |
827 |
by Ken Mon, 2022-03-14 15:14 |
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multi ligand docking using rosetta script by syntekabio2019 » Tue, 2021-04-13 19:31 |
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823 |
by syntekabio2019 Tue, 2021-04-13 19:31 |
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General question regarding ligand-docking by Alison_Yajie » Thu, 2020-05-07 09:48 |
0 |
821 |
by Alison_Yajie Thu, 2020-05-07 09:48 |
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pMHC modelling by Roberto » Thu, 2022-08-04 07:11 |
0 |
817 |
by Roberto Thu, 2022-08-04 07:11 |
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Linker Building in scFv by sam_dc » Sat, 2021-10-09 05:38 |
0 |
817 |
by sam_dc Sat, 2021-10-09 05:38 |
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Protein Protein Docking with Linker by mrinal » Mon, 2023-03-20 15:58 |
0 |
815 |
by mrinal Mon, 2023-03-20 15:58 |
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Issues with modifying dock.xml for multiple ligand docking by DGR95 » Fri, 2021-05-14 12:51 |
0 |
797 |
by DGR95 Fri, 2021-05-14 12:51 |
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clashes created with enzdes by listofdina » Mon, 2021-08-02 06:51 |
0 |
796 |
by listofdina Mon, 2021-08-02 06:51 |
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Ab Initio folding with HEM ligand molecule by jseco » Fri, 2021-03-05 06:49 |
0 |
794 |
by jseco Mon, 2021-03-08 03:40 |
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clustering output file has few structures by fabiotrovato » Mon, 2020-08-17 11:37 |
0 |
791 |
by fabiotrovato Mon, 2020-08-17 11:37 |
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flexpepdcok of lipid conjugated peptide with glyco protein. by ravi.thakkkar369 » Fri, 2020-12-18 13:00 |
0 |
789 |
by ravi.thakkkar369 Fri, 2020-12-18 13:00 |
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Symmetry definition file versions by Jeff Qu » Tue, 2021-09-28 09:53 |
0 |
786 |
by Jeff Qu Tue, 2021-09-28 09:53 |
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Per residue total score by johnnytam100 » Wed, 2022-07-13 21:57 |
0 |
784 |
by johnnytam100 Wed, 2022-07-13 21:57 |
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PDB Clustering by code_Monkey » Mon, 2021-04-05 10:40 |
0 |
783 |
by code_Monkey Mon, 2021-04-05 10:40 |
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FlexPepDock bug? Constraints do not appear in total_score? by nrollins » Mon, 2021-07-26 14:29 |
0 |
782 |
by nrollins Mon, 2021-07-26 14:29 |
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Bug Report - Encoding issue by daniloboskovic » Tue, 2020-08-04 07:02 |
0 |
775 |
by daniloboskovic Tue, 2020-08-04 07:02 |
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Patch to impose tetrahedral geometry on backbone O atom by georg » Thu, 2021-04-08 09:30 |
0 |
774 |
by georg Thu, 2021-04-08 09:31 |
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problem in using "zinc_site_redesign" tool by Isomerase » Mon, 2022-03-28 01:19 |
0 |
773 |
by Isomerase Mon, 2022-03-28 01:19 |
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Is Biopython required to run pdb_renumber.py? by ljjjxay » Wed, 2023-11-22 20:00 |
6 |
768 |
by ljjjxay Wed, 2023-12-06 19:24 |
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Writing down properties for new atom types by Corvin » Tue, 2021-01-12 04:30 |
0 |
748 |
by Corvin Wed, 2021-01-13 04:00 |
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What is an SS0 predictor? by ojmel » Fri, 2021-04-02 14:25 |
0 |
746 |
by ojmel Mon, 2021-04-12 07:50 |
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metalloprotein ab initio with glutamic acid by inorgchem » Tue, 2020-06-16 20:45 |
0 |
740 |
by inorgchem Tue, 2020-06-16 20:45 |
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FlexPepDock ab initio: behavior without fragment files by nrollins » Mon, 2021-07-26 14:16 |
0 |
736 |
by nrollins Mon, 2021-07-26 14:16 |
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Rosetta DARc suboptimal dockings by ddhoyo » Mon, 2021-10-11 06:18 |
0 |
734 |
by ddhoyo Mon, 2021-10-11 06:18 |
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CC (or similar) calculation for cryoEM fitting by almeida85 » Tue, 2023-05-16 01:32 |
2 |
728 |
by almeida85 Tue, 2023-05-23 08:23 |
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Segfault with Pepspec by almeida85 » Thu, 2021-02-11 02:56 |
0 |
727 |
by almeida85 Thu, 2021-02-11 02:56 |
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Repacker vs minimization by Elijah_Hix » Fri, 2021-07-02 07:25 |
0 |
687 |
by Elijah_Hix Fri, 2021-07-02 07:25 |
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Are catalytic residues mutatable? by uka147 » Thu, 2023-10-26 03:49 |
3 |
646 |
by uka147 Mon, 2023-10-30 01:53 |
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Cannot install DAlphaBall by gerdos » Fri, 2023-10-13 07:55 |
1 |
624 |
by Seongsung Fri, 2023-11-24 04:52 |
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Rosetta Design: Non-canonical amino acid substrate not accepted by Friedrich Ehinger » Fri, 2023-08-04 00:09 |
2 |
616 |
by Friedrich Ehinger Fri, 2023-08-04 08:38 |
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Error with xml script by almeida85 » Tue, 2023-03-28 01:53 |
0 |
613 |
by almeida85 Tue, 2023-05-16 01:00 |
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cluster docked pdbs by kwu030 » Wed, 2023-06-14 22:48 |
1 |
602 |
by rmoretti Wed, 2023-06-28 12:36 |
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ValueError("Path %s does not exist!" % path_name) for rna_helix.py by kameisel » Wed, 2023-08-16 00:39 |
2 |
577 |
by kameisel Wed, 2023-09-13 02:16 |
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Dock cyclic peptide with non-canonical amino acids to protein target using rosetta flexpepdock? by lei » Mon, 2023-09-11 23:34 |
2 |
575 |
by lei Wed, 2023-09-13 19:35 |
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Memory Leak: Relax Density MPI RAM overusage kills process by mmfarrugia » Sun, 2023-12-31 12:02 |
5 |
564 |
by mmfarrugia Fri, 2024-01-12 10:35 |
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dG_separated values comparison by almeida85 » Mon, 2023-04-24 03:34 |
0 |
554 |
by almeida85 Tue, 2023-05-16 01:02 |
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rosetta_cm - ERROR: Assertion `tlen < slen` failed on File: src/core/fragment/util.cc:177 by ramon-arg » Thu, 2023-07-13 18:41 |
2 |
550 |
by ramon-arg Fri, 2023-07-14 07:47 |
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remove membrane for RosettaMPdock by lluoto » Wed, 2023-12-06 06:22 |
2 |
534 |
by lluoto Wed, 2024-02-21 17:39 |
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Missing atoms, unable to fill in missing atoms by kwu030 » Fri, 2023-05-05 13:41 |
1 |
532 |
by rmoretti Fri, 2023-05-05 13:44 |
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PyIgClassify cannot renumber and label CDRs my Nanobody-Antigen complex for RabD by WBNeT » Fri, 2023-07-07 10:58 |
1 |
491 |
by jadolfbr Mon, 2023-07-10 09:05 |
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Simple_cycpep_predict with crosslinker BBMB by Ken » Tue, 2023-05-09 08:52 |
0 |
480 |
by Ken Tue, 2023-05-09 08:52 |
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Error about rifdocking step 12 by ng98 » Mon, 2024-01-08 16:27 |
3 |
478 |
by ng98 Tue, 2024-01-09 23:42 |
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error in loop remodeling by syntekabio2019 » Wed, 2023-04-05 01:00 |
0 |
472 |
by syntekabio2019 Wed, 2023-04-05 01:01 |
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RECCESS-Rosetta Segmentation Fault with nonnatural residues by skorro » Tue, 2023-07-25 17:13 |
1 |
463 |
by skorro Fri, 2023-07-28 12:20 |
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Error about rifdocking step 15 by ng98 » Sun, 2024-01-21 16:30 |
4 |
456 |
by ng98 Tue, 2024-01-23 17:01 |
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ERROR: ResidueType::add_ring: Requested atoms don't exist in this ResidueType! by walidabualafia » Thu, 2023-07-20 09:44 |
1 |
438 |
by rmoretti Thu, 2023-07-20 10:08 |
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FixedBB design output no beta strands by tkoh » Fri, 2023-08-25 01:02 |
1 |
436 |
by rmoretti Tue, 2023-08-29 20:13 |
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non-zero ddG of binding even without mutations by top-gun98 » Wed, 2023-06-07 17:19 |
0 |
429 |
by top-gun98 Wed, 2023-06-07 17:19 |
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Generating a new Vall database by vijay.anand » Tue, 2023-06-20 12:08 |
0 |
403 |
by vijay.anand Tue, 2023-06-20 12:08 |
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Silent File Scores Missing: RNA Protein Complex Predition by axio23 » Fri, 2023-06-16 05:45 |
0 |
396 |
by axio23 Fri, 2023-06-16 05:45 |
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analyze_flex_ddG.py by valebut » Tue, 2023-11-28 04:30 |
1 |
381 |
by Aleksandra Panfilova Tue, 2023-11-28 05:34 |
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I want to refine my pdb file,but it has multiple breaks or has multiple loops missing resi by Edward » Sat, 2023-11-25 04:58 |
1 |
375 |
by Edward Sat, 2023-11-25 05:17 |
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nomenclature question in molfile_to_params_polymer.py in ncaa design by lei » Tue, 2023-11-21 09:47 |
2 |
351 |
by lei Wed, 2023-11-22 06:23 |
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PIPER-FlexPepDock [commercial user] by Skelly » Tue, 2024-01-23 16:14 |
0 |
325 |
by Skelly Tue, 2024-01-30 14:08 |
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Memory Leak in FragmentPicker.cxx11thread application by Corvin » Tue, 2023-07-11 06:04 |
0 |
324 |
by Corvin Thu, 2023-07-13 05:30 |
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How do I compare the results of InterfaceAnalyzer using different trimers as input? by franz72 » Sun, 2023-08-06 10:10 |
0 |
324 |
by franz72 Sun, 2023-08-06 10:10 |
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