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Rosetta 3 - Applications

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Sticky topic Sticky: FAQ
by admin » Mon, 2010-08-30 04:18
0
13,443 by admin
Fri, 2015-09-04 16:17
Normal topic prepack - residue count fails
by xfradera » Fri, 2023-01-27 06:36
0
61 by xfradera
Fri, 2023-01-27 06:36
Normal topic Different scoring applications (score vs score_aln vs score_jd2, etc.)?
by cossio » Fri, 2014-12-26 07:19
3
3,469 by Patrícia Antunes
Fri, 2023-01-20 11:55
Normal topic snugdock(sequence position requested was greater than the number of residues in the pose)
by lei » Thu, 2023-01-12 01:40
5
1,171 by lei
Fri, 2023-01-20 08:11
Normal topic Grafting using antibody.mpi.linuxgccrelease and specifying custom template which doesnt have pdb id.
by SubhaK » Wed, 2023-01-18 23:33
0
431 by SubhaK
Wed, 2023-01-18 23:33
Normal topic Snugdock Error: The sequence position requested was greater than the number of residues
by stannowitz » Tue, 2023-01-17 07:37
0
546 by stannowitz
Tue, 2023-01-17 23:48
Normal topic relax protein with multi-conformer bound ligand
by xfradera » Thu, 2023-01-12 09:10
3
927 by xfradera
Fri, 2023-01-13 09:07
Normal topic ReplicaDock 2.0 Native vs Input Structure Flags Confusion
by katherinemccoy » Tue, 2022-12-27 06:42
1
1,972 by Ameya
Tue, 2022-12-27 11:21
Normal topic RosettaCM Ignoring Ligand
by Delfosse57 » Sun, 2022-12-04 12:05
0
3,513 by Delfosse57
Sun, 2022-12-04 12:05
Normal topic Unable to locate the "compute_ddg.py" file and running the RosettaMP protocol
by Sajjad » Mon, 2022-11-28 14:09
3
3,926 by Sajjad
Wed, 2022-11-30 11:50
Normal topic unable to generate the span file with "mp_span_from_pdb.default.linuxgccrelease" from a PDB file
by Sajjad » Wed, 2022-11-30 11:40
0
3,359 by Sajjad
Wed, 2022-11-30 11:40
Normal topic The confussion about an example in tutorial in Rosetta Virtual Workshop 2020
by ldx022 » Tue, 2022-11-29 04:58
3
3,453 by ldx022
Tue, 2022-11-29 08:38
Normal topic Score.sc file showing total score 0 for all protein structures created
by aanshi » Wed, 2022-11-23 11:13
1
2,772 by nannemdp
Mon, 2022-11-28 09:39
Normal topic Help to understand docking results
by rtorquato » Fri, 2022-11-25 12:05
0
1,016 by rtorquato
Fri, 2022-11-25 12:05
Normal topic snugdock: constrained backbone
by mahendra » Mon, 2022-11-14 02:51
0
1,271 by mahendra
Mon, 2022-11-14 02:51
Normal topic Ligand Rotamer Control in Macther
by Hirbond » Tue, 2022-10-25 13:01
0
1,338 by Hirbond
Wed, 2022-10-26 12:57
Normal topic Setting pivots points for GenKIC
by almeida85 » Tue, 2022-10-25 02:32
0
1,217 by almeida85
Tue, 2022-10-25 02:32
Normal topic Small molecule dimer/trimer/etc docking
by lukasz » Tue, 2022-10-04 06:49
1
1,096 by rmoretti
Tue, 2022-10-04 07:57
Normal topic Symmetry definition question
by mrconde96 » Sun, 2022-10-02 05:34
0
877 by mrconde96
Sun, 2022-10-02 05:34
Normal topic Old Knotfind algorithm
by Martin Floor » Thu, 2022-09-22 07:28
1
467 by rmoretti
Fri, 2022-09-23 09:38
Normal topic ReplicaDock2.0 demo fails with MPIFileBufJobDistributor: (1) [ ERROR ]
by erpannec » Tue, 2022-08-09 05:42
4
649 by erpannec
Thu, 2022-09-15 05:17
Normal topic Prepacking a macrocycle for docking / preserving cyclization
by almeida85 » Thu, 2022-09-08 06:54
0
294 by almeida85
Thu, 2022-09-08 06:54
Normal topic Trehalose
by jpfuenzalidawx » Thu, 2022-09-08 00:49
0
259 by jpfuenzalidawx
Thu, 2022-09-08 00:49
Normal topic Macrocycle from a C-terminal amidated peptide
by almeida85 » Thu, 2022-08-18 07:53
0
347 by almeida85
Thu, 2022-08-18 07:53
Normal topic Docking HeparinSulfate to proteins using GlycanDock
by GebauerJ » Tue, 2022-08-16 07:44
0
300 by GebauerJ
Tue, 2022-08-16 07:44
Normal topic RIFdocking:Unable to locate database file chemical/residue_type_sets/fa_standard/residue_types/
by sia » Tue, 2022-08-02 20:06
2
511 by SeongRyeong Go
Mon, 2022-08-15 18:31
Normal topic simple_cycpep_predict - Design mode - The base name "ARG" was added more than once
by almeida85 » Thu, 2022-08-04 02:57
4
607 by almeida85
Thu, 2022-08-11 00:58
Normal topic Urgent issue: Error with submitting a new Rosetta-Vienna RNP-ddG job
by eyaaaan » Sun, 2022-08-07 22:03
0
343 by eyaaaan
Tue, 2022-08-09 21:59
Normal topic Nanobody design
by chandana » Tue, 2022-08-09 20:36
0
356 by chandana
Tue, 2022-08-09 20:36
Normal topic How to choose designed antibody
by Sunyp_IM » Wed, 2020-06-24 10:06
6
2,686 by chandana
Tue, 2022-08-09 20:27
Normal topic Unknown Element "SE" when generating NCAA params file containing selenium
by liuwenxi » Thu, 2022-08-04 16:24
2
479 by liuwenxi
Fri, 2022-08-05 09:50
Normal topic Include MHC alpha helices in loop modelling protocol for pMHC complex
by Roberto » Thu, 2022-08-04 07:22
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305 by Roberto
Thu, 2022-08-04 07:22
Normal topic pMHC modelling
by Roberto » Thu, 2022-08-04 07:11
0
303 by Roberto
Thu, 2022-08-04 07:11
Normal topic CS-Rosetta cofactor
by martongadanecz » Wed, 2022-08-03 01:05
0
316 by martongadanecz
Wed, 2022-08-03 01:05
Normal topic errors about RIFdocking
by sia » Sun, 2022-07-24 20:45
6
856 by sia
Tue, 2022-08-02 20:08
Normal topic Benchmarking Rosetta DDG Methods
by sareeves96 » Fri, 2022-07-29 09:55
0
321 by sareeves96
Fri, 2022-07-29 09:55
Normal topic ERROR: Assertion `static_cast< size_type >( i - l_ ) < super::size()` failed. ERROR:: Exit from: src/utility/vectorL.hh line: 42
by yliang20 » Wed, 2022-06-15 22:22
1
478 by adriancmf25
Thu, 2022-07-28 02:09
Normal topic Expected density
by GabrielDucrocq » Thu, 2022-07-14 06:38
1
430 by matteoferla
Wed, 2022-07-20 10:50
Normal topic shape complementarity
by holdenj » Fri, 2022-07-15 13:24
1
387 by rmoretti
Fri, 2022-07-15 13:50
Normal topic Error with RNA_denovo
by zmfowler » Thu, 2022-07-14 05:34
0
330 by zmfowler
Thu, 2022-07-14 05:34
Normal topic Error with RoseTTAFold
by sc19 » Thu, 2022-07-14 03:40
0
340 by sc19
Thu, 2022-07-14 03:40
Normal topic Ligand Docking with ROSETTA
by sc19 » Thu, 2022-07-14 01:32
0
345 by sc19
Thu, 2022-07-14 01:34
Normal topic Per residue total score
by johnnytam100 » Wed, 2022-07-13 21:57
0
318 by johnnytam100
Wed, 2022-07-13 21:57
Normal topic SnugDock Partners parameter
by tyang39 » Fri, 2022-07-08 10:02
1
383 by rmoretti
Fri, 2022-07-08 10:27
Normal topic Pepspec - sequence sampling
by almeida85 » Thu, 2022-06-23 04:05
0
348 by almeida85
Thu, 2022-06-23 05:50
Normal topic Rosetta Remodel - Error in core::conformation::Conformation::residue(): The sequence position requested was 0.
by daniloboskovic » Fri, 2019-11-08 08:24
1
2,111 by Payne
Tue, 2022-06-21 07:25
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
539 by yliang20
Wed, 2022-06-15 13:46
Normal topic Segmentation Fault in Rosetta CM Hybridize
by yliang20 » Mon, 2022-06-06 17:25
2
567 by yliang20
Tue, 2022-06-07 08:36
Normal topic Local docking- should I use KIC?
by seayoung lee » Fri, 2022-05-27 02:45
0
401 by seayoung lee
Fri, 2022-05-27 02:45
Normal topic Params for a stapled helix peptide
by e3lm » Thu, 2022-05-26 12:55
0
378 by e3lm
Thu, 2022-05-26 12:55
Normal topic Noncanonical amino acids
by wsgosal » Tue, 2014-03-18 05:29
8
5,951 by e3lm
Thu, 2022-05-26 12:51
Normal topic IL-2 gets better binding with beta / gamma
by tonycheng1688 » Wed, 2022-05-25 10:23
0
398 by tonycheng1688
Wed, 2022-05-25 10:23
Normal topic Relax evaluates protein-DNA complexes?
by pablogalazdavison » Thu, 2022-05-12 12:05
2
612 by pablogalazdavison
Fri, 2022-05-20 12:27
Normal topic Enzyme Design Not Editing Structure
by liuwenxi » Wed, 2022-05-18 10:12
0
367 by liuwenxi
Wed, 2022-05-18 10:12
Normal topic minimize_ppi.mpi.linuxgccrelease doesn't use jd2?
by e3lm » Tue, 2022-05-17 11:58
0
393 by e3lm
Tue, 2022-05-17 11:58
Normal topic Disulfidize- "Extra content at the end of the document"
by ldlamini » Tue, 2022-05-17 02:37
1
504 by rmoretti
Tue, 2022-05-17 07:29
Normal topic Flex_ddG突变设计
by wangtao » Thu, 2022-05-05 02:46
0
438 by wangtao
Thu, 2022-05-05 02:46
Normal topic Dimeric interface redesign
by kjs1728 » Mon, 2022-05-02 21:57
0
376 by kjs1728
Mon, 2022-05-02 21:57
Normal topic Pepspec error
by almeida85 » Mon, 2022-05-02 04:07
1
466 by almeida85
Mon, 2022-05-02 05:05
Normal topic about “protein mimic designer”
by sia » Wed, 2022-04-27 19:59
0
381 by sia
Wed, 2022-04-27 19:59
Normal topic How to Perform point mutations with NCAA
by Subhrodeep Saha » Tue, 2021-06-22 02:05
2
1,057 by dnamkr
Fri, 2022-04-22 17:00
Normal topic Ways to improve AbRelax performance?
by Corvin » Tue, 2022-04-19 06:10
2
651 by Corvin
Thu, 2022-04-21 00:50
Normal topic trRosetta - Nan occuring in Hbond calculation
by y_atsmonraz » Mon, 2021-10-04 09:16
1
659 by shivarawat115
Mon, 2022-04-11 16:10
Normal topic problem in using "zinc_site_redesign" tool
by Isomerase » Mon, 2022-03-28 01:19
0
357 by Isomerase
Mon, 2022-03-28 01:19
Normal topic snugdock run error: Sequence for partner1 does not match first member of ensemble1
by pagumaaaaa » Fri, 2022-03-25 01:21
0
417 by pagumaaaaa
Fri, 2022-03-25 01:21
Normal topic How do I change the default Compiler for Rosetta?
by pagumaaaaa » Wed, 2022-03-16 00:23
2
746 by pagumaaaaa
Thu, 2022-03-24 22:40
Normal topic Modelling at defined pH - for pmutscan - pH:mode not working
by cagfa1 » Tue, 2022-03-15 04:05
1
580 by Rituparna_Saman...
Wed, 2022-03-23 11:21
Normal topic RosettaDock 4.0 ambiguous ERROR
by sam_dc » Fri, 2022-03-18 09:36
3
1,004 by rmoretti
Tue, 2022-03-22 09:10
Normal topic Error in a new docking
by jrcf » Wed, 2017-05-17 19:26
2
3,414 by tingting
Tue, 2022-03-15 23:55
Normal topic simple_cycpep_predict thioether_lariat option
by Ken » Mon, 2022-03-14 15:14
0
412 by Ken
Mon, 2022-03-14 15:14
Normal topic small ligand docking in Ubuntu 20.04, please help
by guowuchen » Sun, 2022-03-06 18:12
2
789 by guowuchen
Mon, 2022-03-07 23:34
Normal topic Rosetta Matcher not recognizing protonation forms of CST files like CYZ, HIS_D, etc
by Hirbond » Tue, 2022-03-01 13:16
0
480 by Hirbond
Tue, 2022-03-01 13:16
Normal topic Using GlycanDock and the Antibody Affinity Maturation protocol.
by tbelec » Mon, 2022-02-28 12:37
0
506 by tbelec
Mon, 2022-02-28 12:37
Normal topic DockingProtocol
by Soler » Fri, 2022-02-11 00:12
3
1,016 by gezmi
Tue, 2022-02-15 21:47
Normal topic RAbD with N-term,Proline-like ncaa returns segmentation fault during CCDEndsGraftMover
by CordycepsLin » Sun, 2022-02-06 19:09
9
1,860 by CordycepsLin
Wed, 2022-02-09 19:39
Normal topic Generating the 3-mer and 9-mer fragments
by Prasoon » Wed, 2022-02-09 09:04
0
564 by Prasoon
Wed, 2022-02-09 09:04
Normal topic FastRelaxMover parameters for antibody-antigen interaction analysis
by samuel_k » Thu, 2022-01-27 01:08
0
548 by samuel_k
Thu, 2022-01-27 01:08
Normal topic Relax in membrane pull my protein out of the membrane
by Martin Floor » Wed, 2022-01-26 07:46
0
573 by Martin Floor
Wed, 2022-01-26 07:46
Normal topic Can anybody suggests some flags to run Rifdock?
by Hyunmi Song » Sun, 2022-01-23 16:45
0
677 by Hyunmi Song
Sun, 2022-01-23 16:45
Normal topic ligand dock into HEM containg pdb
by syntekabio2019 » Thu, 2022-01-20 03:05
0
559 by syntekabio2019
Thu, 2022-01-20 03:05
Normal topic charge grid in rosetta ligand docking using rosetta script
by syntekabio2019 » Mon, 2022-01-17 23:53
0
525 by syntekabio2019
Mon, 2022-01-17 23:53
Normal topic I need help with cst file the paper: De Novo Computational Design of Retro-Aldol Enzymes
by Wenithor » Thu, 2022-01-06 12:20
0
528 by Wenithor
Thu, 2022-01-06 12:20
Normal topic Protein design: Ligand binding between two units of a homodimer
by chemotaxis_123 » Sun, 2022-01-02 16:01
0
486 by chemotaxis_123
Sun, 2022-01-02 16:01
Normal topic [LoopModelerMover] ERROR: Can't build a fold tree from a loop with an unspecified cut point.
by dgm3 » Sun, 2021-12-26 18:32
1
681 by dgm3
Fri, 2021-12-31 17:42
Normal topic ERROR: APBS failed to generate the result file.
by bhavranek » Sat, 2021-12-18 11:01
1
641 by bhavranek
Sun, 2021-12-26 21:05
Normal topic Question about running scallo
by danbo » Mon, 2021-11-29 23:25
8
1,951 by danbo
Wed, 2021-12-22 23:51
Normal topic getting a3m files
by alonwenger » Wed, 2021-12-15 02:38
2
1,329 by alonwenger
Sat, 2021-12-18 12:32
Normal topic simple_cycpep_predict with N-term acetylation
by Ken » Fri, 2021-12-17 09:49
0
499 by Ken
Fri, 2021-12-17 09:49
Normal topic Segfault error while running MR Rosetta in Phenix
by memilton » Thu, 2021-12-16 09:09
0
557 by memilton
Thu, 2021-12-16 09:09
Normal topic Remodel's problem in treatment with non-protein residues
by Corvin » Mon, 2021-12-13 09:07
0
493 by Corvin
Mon, 2021-12-13 09:07
Normal topic Relaxed proteins show higher clash score in molprobity results.
by Wang Zhe » Fri, 2021-12-03 04:32
4
1,453 by smlewis
Wed, 2021-12-08 13:02
Normal topic How to apply cartesian_ddg to multi-metric enzyme?
by Wang Zhe » Wed, 2021-12-08 10:07
0
492 by Wang Zhe
Wed, 2021-12-08 10:07
Normal topic SecundaryStructure Filter
by Soler » Sun, 2021-11-21 22:20
0
534 by Soler
Sun, 2021-11-21 22:20
Normal topic ERROR: Unable to fill in missing atoms.
by mieczyslaw » Tue, 2020-10-20 09:43
7
4,362 by rayyoung
Thu, 2021-11-18 10:13
Normal topic constraining different chains together in rosetta_cm
by y_atsmonraz » Thu, 2021-11-18 02:59
0
545 by y_atsmonraz
Thu, 2021-11-18 03:01
Normal topic Problems with waters in CoupledMoves application
by Corvin » Tue, 2021-11-16 07:16
0
563 by Corvin
Tue, 2021-11-16 07:22
Normal topic The energy terms in InterfaceAnalyzer
by Sunyp_IM » Tue, 2021-11-02 18:43
2
905 by zivben
Sat, 2021-11-13 04:49
Normal topic C-termini remodelling of dimeric structure removes second chain
by LeonhardJS » Wed, 2021-10-13 06:23
1
701 by LeonhardJS
Fri, 2021-11-12 01:20
Normal topic connecting rna strands together
by y_atsmonraz » Tue, 2021-11-09 05:42
1
637 by y_atsmonraz
Thu, 2021-11-11 04:51
Normal topic building a protein-dna homology model via cm_rosetta
by y_atsmonraz » Wed, 2021-10-20 23:11
4
1,198 by y_atsmonraz
Tue, 2021-11-02 01:47

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