You are here

Rosetta 3 - General

Topic / Topic starter Replies Viewssort ascending Last post
Normal topic enzyme design implementation
by rohi » Wed, 2020-12-16 09:54
1
798 by rmoretti
Tue, 2021-02-09 11:30
Normal topic location of define_interface.py
by rohi » Mon, 2020-10-26 19:42
1
797 by rmoretti
Mon, 2020-10-26 19:52
Normal topic Error using ddg_monomer application (Assertion `pose.residue(resnum).name1() == wt` failed)
by sgaray » Thu, 2021-06-24 14:47
2
795 by sgaray
Fri, 2021-06-25 11:26
Normal topic Disulfidize mover
by karenjgonzalez » Wed, 2019-07-31 12:35
0
791 by karenjgonzalez
Wed, 2019-07-31 12:35
Normal topic Method to keep ATP in the certain position in the prepack step
by ziqi1234 » Tue, 2017-11-21 05:55
0
789 by ziqi1234
Tue, 2017-11-21 05:55
Normal topic Fragment Picker score type weights
by wellsm10 » Mon, 2020-12-14 13:05
1
788 by dgront
Thu, 2021-02-11 08:30
Normal topic clustering ligand binding mood by ligand RMSD
by rohi » Tue, 2021-01-26 21:11
1
787 by brownbp1
Tue, 2021-02-09 12:12
Normal topic [dev] examples for implementing setup_for_packing, prepare_rotamers_for_packing?
by ipetrik_ambry » Mon, 2017-10-30 17:03
0
776 by ipetrik_ambry
Mon, 2017-10-30 17:03
Normal topic What is the expected behaviour when minimizing a jump edge?
by bio_james » Wed, 2017-12-13 09:13
0
774 by bio_james
Wed, 2017-12-13 09:13
Normal topic RosettaDesign improvements
by ac.research » Mon, 2018-05-14 08:27
0
772 by ac.research
Mon, 2018-05-14 08:27
Normal topic keep ATP in the kinase-peptide structure while docking
by ziqi1234 » Fri, 2017-11-10 04:04
0
770 by ziqi1234
Fri, 2017-11-10 04:04
Normal topic alignblast.pl truncated file
by rlwoltz » Mon, 2019-03-11 18:32
0
766 by rlwoltz
Mon, 2019-03-11 18:32
Normal topic Errors in Interface_design_demo
by zhoubin » Fri, 2019-01-04 13:14
0
760 by zhoubin
Fri, 2019-01-04 13:14
Normal topic protein design for increasing its affinity towards ligand
by rohi » Fri, 2020-10-30 11:33
1
759 by rmoretti
Tue, 2021-02-09 12:25
Normal topic FARFAR and RNA_Tools: problem executing the command helix_preassemble_setup.py
by obdulia » Wed, 2018-04-18 00:45
0
756 by obdulia
Wed, 2018-04-18 00:45
Normal topic Mutate multidomain protein
by frankfurter1 » Wed, 2018-05-09 04:40
0
754 by frankfurter1
Wed, 2018-05-09 04:40
Normal topic env energy term
by bazzoli » Wed, 2018-10-10 01:59
0
752 by bazzoli
Wed, 2018-10-10 01:59
Normal topic error when using script best_ifaceE.py
by windmill » Thu, 2020-06-18 21:30
1
750 by windmill
Thu, 2020-06-18 21:32
Normal topic Segfault with docking protocol
by almeida85 » Mon, 2021-02-08 06:39
2
739 by almeida85
Mon, 2021-02-08 09:50
Normal topic pmut and scoring
by ldlamini » Tue, 2021-09-14 00:46
3
736 by matteoferla
Mon, 2021-09-20 06:05
Normal topic crashed when loading RDC data
by yangshen12 » Fri, 2018-10-26 12:34
0
731 by yangshen12
Fri, 2018-10-26 12:34
Normal topic Rosetta Double changing mmCIF chain ID
by Victor Tobiasson » Thu, 2021-05-13 07:57
2
729 by Victor Tobiasson
Thu, 2021-05-13 08:33
Normal topic Recommendations for CoupledMoves enzyme redesign
by dgm3 » Thu, 2021-03-04 10:53
1
721 by aloshbau
Tue, 2021-03-09 02:47
Normal topic How to set start coordinates for ligand when doing protein_ligand docking
by Huanhuan » Wed, 2021-08-18 21:09
3
720 by matteoferla
Fri, 2021-08-20 08:37
Normal topic problem plotting results from docking_analyser with provided Rscript
by madammolecular » Mon, 2021-02-01 14:44
2
717 by amystevens
Thu, 2021-09-30 14:18
Normal topic Chain name being read as residue
by MarkusAurelius » Mon, 2021-03-22 11:19
2
715 by MarkusAurelius
Mon, 2021-03-29 09:06
Normal topic How to use the <CavityVolume> filter in the released version of Rosetta
by BioPython » Sun, 2019-05-12 20:07
0
714 by BioPython
Sun, 2019-05-12 20:07
Normal topic Difference between interface_delta_X and dG_separated?
by Nicole Deng » Sat, 2020-06-06 06:31
0
712 by Nicole Deng
Sat, 2020-06-06 06:40
Normal topic Correct way to force a specific histidine tautomer
by matteoferla » Fri, 2020-04-10 02:40
0
706 by matteoferla
Fri, 2020-04-10 02:40
Normal topic I Need Help on Validation for a Ligand Docking Experiment.
by tbelec » Sat, 2021-03-20 13:27
1
705 by matteoferla
Mon, 2021-03-22 08:29
Normal topic Denovo density excess map input and segmentation
by ahmadkhalifa » Mon, 2018-04-30 07:28
0
704 by ahmadkhalifa
Fri, 2018-05-04 07:50
Normal topic restrict PackRotamersMover
by pmit » Thu, 2018-05-03 01:48
0
696 by pmit
Thu, 2018-05-03 01:48
Normal topic How to define the surface (???.surf) for surface_docking?
by Anpu » Thu, 2018-09-27 07:34
0
695 by Anpu
Thu, 2018-09-27 23:36
Normal topic Docking Metalloprotein-Protein
by fgomes » Fri, 2019-11-22 19:12
0
687 by fgomes
Fri, 2019-11-22 19:12
Normal topic There is a problem executing “rosetta_scripts.static.linuxgccrelease ”
by zjya » Tue, 2021-02-02 23:44
1
686 by rmoretti
Wed, 2021-02-03 14:45
Normal topic Speeding up FastDesign
by ebetica0 » Wed, 2021-04-28 13:08
1
686 by vmulligan
Wed, 2021-04-28 14:20
Normal topic Sequence Profile/Checkpoint file
by ojmel » Fri, 2021-04-02 17:29
1
684 by taylorjones
Mon, 2021-04-05 13:17
Normal topic FastRelax Mover with symmetry, ligand and membrane
by Michele.Bonus » Wed, 2021-05-26 04:43
1
676 by matteoferla
Thu, 2021-06-03 08:24
Normal topic opencl support programs
by x_wuxi » Mon, 2021-04-12 18:17
1
676 by rmoretti
Tue, 2021-04-13 06:42
Normal topic dealing with Large ligand in Ligand docking and enzyme design
by rohi » Mon, 2021-01-04 09:58
1
675 by rmoretti
Tue, 2021-02-09 10:48
Normal topic contribution of interface residues in binding energy
by rohi » Wed, 2021-01-20 07:33
1
654 by rmoretti
Wed, 2021-01-20 07:39
Normal topic what factors determine the lowest (best) LigInterfaceEnergy score?
by jmaly » Wed, 2020-08-26 13:07
0
642 by jmaly
Wed, 2020-09-02 16:16
Normal topic pyrosetta.rosetta.core.pose.rna
by chenjief » Tue, 2021-11-23 07:03
3
641 by matteoferla
Mon, 2022-01-10 06:44
Normal topic SARS-CoV-2: call for compound predictions against protease
by matteoferla » Sun, 2020-03-22 05:29
0
640 by matteoferla
Sun, 2020-03-22 05:29
Normal topic MakeRotLib
by yinasun » Fri, 2019-07-26 02:17
0
633 by yinasun
Fri, 2019-07-26 02:17
Normal topic how to perform model quality assessment of rosetta generated models?
by Danielsebas » Tue, 2019-09-24 05:03
0
632 by Danielsebas
Tue, 2019-09-24 05:03
Normal topic Error on rna_denovo_setup.py
by zahra_AZ » Mon, 2020-11-09 02:23
0
630 by zahra_AZ
Mon, 2020-11-09 02:23
Normal topic using full atom constraint in docking
by rohi » Thu, 2020-10-15 10:28
0
629 by rohi
Thu, 2020-10-15 10:28
Normal topic Clustering problem
by Suuo » Tue, 2021-04-20 01:40
1
624 by rmoretti
Tue, 2021-04-20 13:06
Normal topic Why does the sum of the per-residue total energy not match the whole score?
by matteoferla » Fri, 2021-07-09 08:36
2
615 by matteoferla
Mon, 2021-07-12 02:23
Normal topic Side-chain grafting in fixed scaffold
by Kazu » Wed, 2020-05-20 08:45
0
614 by Kazu
Wed, 2020-05-20 11:58
Normal topic RosettaCM: help to generate similar models as those from Robetta Server
by haom » Wed, 2020-09-09 09:19
0
609 by haom
Wed, 2020-09-09 09:19
Normal topic partial charge of params file in ligand docking
by rohi » Fri, 2021-05-28 08:43
1
605 by rmoretti
Fri, 2021-05-28 08:54
Normal topic Better minimization with Rosetta
by Elijah_Hix » Wed, 2021-07-28 13:53
1
604 by matteoferla
Mon, 2021-08-09 01:53
Normal topic Help - Protein-Protein interface design
by Dinesh Kumar » Thu, 2021-01-28 00:47
1
603 by rmoretti
Tue, 2021-02-09 10:29
Normal topic Searching density map using real space correlation
by ahmadkhalifa » Fri, 2018-12-28 00:28
0
602 by ahmadkhalifa
Fri, 2018-12-28 00:28
Normal topic PIPER-FlexPepDock protocol file apply_ftresult.py missing
by diasmarieli » Thu, 2021-11-04 06:33
2
592 by diasmarieli
Fri, 2021-11-26 05:11
Normal topic Structure refinement for helical assembles using Rosetta
by xiaoyanzi » Thu, 2020-06-18 00:34
0
591 by xiaoyanzi
Thu, 2020-06-18 00:36
Normal topic Error: Element 'RandomizeBBByRamaPrePro': This element is not expected.
by nferruz » Fri, 2020-08-28 06:04
0
587 by nferruz
Fri, 2020-08-28 06:05
Normal topic Explicit water
by tsztain » Wed, 2021-08-25 05:54
1
580 by matteoferla
Thu, 2021-09-02 03:50
Normal topic ligand docking error
by YuFei » Wed, 2020-04-22 17:27
0
575 by YuFei
Wed, 2020-04-22 17:27
Normal topic Show I be using beta_nov16 scorefxn?
by matteoferla » Thu, 2021-04-01 04:06
0
575 by matteoferla
Thu, 2021-04-01 04:06
Normal topic Unrecognized atom parameter with denovo_density
by kalabharath » Mon, 2020-06-29 06:59
0
573 by kalabharath
Mon, 2020-06-29 06:59
Normal topic how does rosetta handle hydrogens?
by patcD » Tue, 2021-08-31 00:48
2
571 by patcD
Wed, 2021-09-01 06:54
Normal topic Problem with match on enzdes
by ahuls1 » Thu, 2021-07-29 13:21
1
571 by ahuls1
Thu, 2021-07-29 13:23
Normal topic Does it make sense to perform Docking on a complex?
by chrisHKL » Mon, 2020-02-17 09:12
0
567 by chrisHKL
Mon, 2020-02-17 09:12
Normal topic Questions about alanine scanning in Rosetta
by LTJ » Mon, 2020-07-06 14:13
0
566 by LTJ
Mon, 2020-07-06 14:13
Normal topic Extracting a part of a silent file as another silent file
by almeida85 » Wed, 2021-07-28 23:53
1
564 by zivben
Sat, 2021-07-31 08:16
Normal topic How RosettaCM can perform part of C terminal domain (CTD) structure prediction without proper template structures (coordinates)
by haom » Tue, 2020-09-01 13:21
0
562 by haom
Tue, 2020-09-01 18:50
Normal topic Using NCAA
by ate » Sat, 2021-05-01 02:52
0
560 by ate
Sat, 2021-05-01 02:52
Normal topic Scoring in Rosetta
by Elijah_Hix » Wed, 2021-07-14 06:48
1
558 by rmoretti
Wed, 2021-07-14 07:07
Normal topic "Rosetta predictions of density, heat of vaporization (∆Hvap) and heat capacity (Cp(l))"
by matteoferla » Tue, 2020-07-14 01:51
0
556 by matteoferla
Tue, 2020-07-14 01:51
Normal topic RosettaCM: threading okay, but hybridize loses many secondary structure
by lanselibai » Wed, 2021-06-23 13:51
2
553 by lanselibai
Thu, 2021-06-24 10:16
Normal topic Error with filter in rosseta_scripts
by Osmany Guirola » Mon, 2020-05-11 04:52
0
552 by Osmany Guirola
Mon, 2020-05-11 04:52
Normal topic Differences between energy values reported in the tutorials and the ones obtained by running the code, what is normal?
by ericlang » Mon, 2021-07-05 05:43
2
551 by ericlang
Mon, 2021-07-05 06:59
Normal topic ref2015: approx. kcal/mol or actually kJ/mol?
by matteoferla » Thu, 2021-10-07 04:04
2
549 by matteoferla
Thu, 2021-10-07 09:31
Normal topic RosettaCM: "Ligands must be added to all templates"
by lanselibai » Tue, 2021-06-22 10:42
2
545 by lanselibai
Wed, 2021-06-23 13:21
Normal topic I made a params file generation webpage
by matteoferla » Wed, 2020-07-22 03:08
0
543 by matteoferla
Wed, 2020-07-22 03:08
Normal topic Compile C++ Rosetta to Pyrosetta ERROR
by michelleqyh » Fri, 2020-08-21 09:00
0
534 by michelleqyh
Fri, 2020-08-21 09:00
Normal topic Remodel and the depracated EMPTY NC
by matteoferla » Fri, 2021-02-26 07:12
0
531 by matteoferla
Fri, 2021-02-26 07:12
Normal topic Clustering error - Help, please
by karolcia1010 » Wed, 2020-06-17 11:19
0
531 by karolcia1010
Wed, 2020-06-17 11:19
Normal topic BUG REPORT: MySql column protocol.protocol_id must have the AUTO_INCREMENT flag set
by pedro.guillem » Wed, 2020-05-13 18:31
0
530 by pedro.guillem
Wed, 2020-06-24 04:42
Normal topic the question about ddg of disulfide bond mutants
by asbelx » Sun, 2021-08-29 06:40
1
530 by asbelx
Wed, 2021-09-08 23:19
Normal topic Internal error while running AbinitioRelax
by Subhrodeep Saha » Sun, 2021-06-13 03:44
1
527 by rmoretti
Wed, 2021-06-23 02:17
Normal topic Finding affinity-reducing mutants towards a ligand in Ligand-based interface design protocol
by adityapadhi » Wed, 2020-06-24 01:29
0
526 by adityapadhi
Wed, 2020-06-24 01:29
Normal topic ligand docking
by hong wei » Thu, 2021-11-18 05:01
2
523 by hong wei
Thu, 2021-11-25 02:46
Normal topic Comparatively modelled chains are far apart in final structure while the template pdb has all chains in a close-knit complex
by Sunidhi » Sun, 2020-11-01 11:00
0
519 by Sunidhi
Sun, 2020-11-01 11:01
Normal topic Rosetta (antibody_designer) performance
by Kihang _Youn » Wed, 2022-03-02 00:48
7
516 by Kihang _Youn
Thu, 2022-03-10 16:30
Normal topic Using NCAA
by ate » Sat, 2021-05-01 02:22
0
515 by ate
Sat, 2021-05-01 02:22
Normal topic Make fragments
by jeanramos » Mon, 2020-07-13 00:56
0
509 by jeanramos
Mon, 2020-07-13 00:56
Normal topic Output "per-residue" energy score to database
by pedro.guillem » Thu, 2020-05-14 04:22
0
507 by pedro.guillem
Thu, 2020-05-14 04:22
Normal topic How to create a native file for Protein-Protein docking
by Kotimedidhi » Mon, 2020-06-22 08:10
0
506 by Kotimedidhi
Mon, 2020-06-22 08:10
Normal topic Rosetta and design of ligand binding site
by rohi » Mon, 2021-03-15 06:00
0
503 by rohi
Mon, 2021-03-15 06:31
Normal topic Help deciphering an input
by Elijah_Hix » Wed, 2021-09-22 11:12
2
501 by Elijah_Hix
Thu, 2021-09-23 10:13
Normal topic ab initio structure modeling
by pci112 » Mon, 2021-04-12 08:07
0
500 by pci112
Mon, 2021-04-12 08:12
Normal topic calcium metal nomenclature: Rosetta_cm confusing HETATM CA (calcium) with ATOM CA (alpha-carbon)
by rlwoltz » Tue, 2021-08-03 23:26
0
497 by rlwoltz
Tue, 2021-08-03 23:26
Normal topic Blast error for rosetta antibody: No argument value given for Query file
by dngusdnr1 » Tue, 2021-06-08 17:32
1
489 by taylorjones
Wed, 2021-06-09 16:30
Normal topic Quick mysql output question
by pedro.guillem » Thu, 2020-07-23 03:45
0
470 by pedro.guillem
Thu, 2020-07-23 03:45
Normal topic rna_denovo secstruct_general function
by rvandamme » Mon, 2021-02-01 13:39
0
464 by rvandamme
Mon, 2021-02-01 13:39
Normal topic Meaning of Metalbinding_constraint
by Corvin » Wed, 2021-05-19 07:54
0
463 by Corvin
Wed, 2021-05-19 07:54
New posts
No new posts
Hot topic with new posts
Hot topic without new posts
Sticky topic
Locked topic
Subscribe to RSS - Rosetta 3 - General