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Rosetta 3 - Applications

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Normal topic Fragment Files
by nkemjika » Fri, 2011-07-22 15:11
1
2,411 by dgront
Mon, 2014-04-21 06:47
Normal topic Fragment files for membrane_abinitio application
by sumukh21 » Sun, 2011-02-13 20:34
7
5,031 by yarovoy
Mon, 2014-04-21 06:47
Normal topic Fragment files for membrane_abinitio application
by sumukh21 » Tue, 2011-02-15 17:23
2
2,651 by sumukh21
Mon, 2014-04-21 06:47
Normal topic Fragment library (vall file) from Robetta?
by alex » Sun, 2017-02-19 08:12
0
1,174 by alex
Sun, 2017-02-19 08:12
Normal topic fragment picker does not follow dihedral constraints
by attesor » Tue, 2016-05-24 23:22
12
7,891 by smlewis
Wed, 2016-08-17 07:56
Normal topic Fragments for long sequence
by exchhattu » Tue, 2011-10-04 01:51
2
2,456 by exchhattu
Mon, 2014-04-21 06:47
Normal topic fragment_picker bug
by David Hoover » Wed, 2012-02-29 11:43
0
1,390 by David Hoover
Mon, 2014-04-21 06:47
Normal topic fragment_picker with fasta only
by gw » Tue, 2011-11-15 13:20
3
3,412 by gw
Mon, 2014-04-21 06:47
Normal topic fragment_picker.mpi.linuxgccrelease can't find : libsqlite3.so
by starone » Mon, 2016-06-20 19:22
11
9,404 by starone
Fri, 2016-06-24 18:29
Normal topic Full Protocol
by shekhar » Fri, 2013-10-04 01:07
1
2,472 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Fusing C-terminal or N-terminal segments onto proteins using Remodel
by achambe » Mon, 2016-01-04 11:26
0
1,108 by achambe
Mon, 2016-01-04 11:26
Hot topic Garbled Ligands from docking_protocol
by skovacs » Tue, 2011-12-20 07:55
21
14,233 by skovacs
Mon, 2014-04-21 06:47
Normal topic General question regarding ligand-docking
by Alison_Yajie » Thu, 2020-05-07 09:48
0
389 by Alison_Yajie
Thu, 2020-05-07 09:48
Normal topic Generalized KIC loop closure affects downstream residues without perturbations
by chenna » Mon, 2021-04-26 02:16
2
437 by chenna
Wed, 2021-04-28 07:18
Normal topic GeneralizedKIC loop closure error
by chenna » Sat, 2021-04-10 00:21
2
472 by chenna
Mon, 2021-04-12 22:08
Normal topic Generate fragment file on my computer
by jrcf » Mon, 2015-09-21 15:41
2
3,147 by jrcf
Mon, 2015-10-05 21:32
Normal topic Generate fragment locally
by deltag » Wed, 2012-02-01 06:26
2
2,796 by deltag
Mon, 2014-04-21 06:47
Normal topic Generating non-redundat dataset for loop models
by dario.corrada » Wed, 2016-03-09 03:00
1
1,345 by smlewis
Wed, 2016-03-09 04:11
Normal topic get an increased energy after energy minimization when using different score functions for repacking and energy minimization
by xinmiaohe » Fri, 2020-02-07 11:59
1
724 by xinmiaohe
Fri, 2020-02-07 13:52
Normal topic getting a3m files
by alonwenger » Wed, 2021-12-15 02:38
2
153 by alonwenger
Sat, 2021-12-18 12:32
Normal topic Getting error with Rosetta "antibody.linuxgccrelease" command
by Sunyp_IM » Mon, 2017-08-07 19:40
1
1,768 by smlewis
Tue, 2017-08-15 23:19
Normal topic Global Docking with carbohydrates
by ChiauShu » Sat, 2020-08-22 20:16
0
384 by ChiauShu
Sat, 2020-08-22 20:16
Normal topic Got error when running minirosetta.linuxgccrelease on cluster but fine on Ubuntu
by lanselibai » Mon, 2014-11-10 08:12
2
2,179 by lanselibai
Tue, 2014-11-11 04:42
Normal topic GrowLigand
by allan.ferrari » Sat, 2019-10-19 05:32
2
1,218 by allan.ferrari
Tue, 2019-11-05 16:52
Normal topic H3 modeling takes 10 days more?
by jessye » Fri, 2017-10-27 03:11
7
3,392 by jessye
Fri, 2017-11-03 20:15
Normal topic HBNet and RosettaScripts
by protos_heis » Tue, 2014-08-05 06:05
3
3,239 by protos_heis
Tue, 2014-08-05 12:47
Normal topic hbond_sr_bb and hbond_lr_bb for different chains
by tylerborrman » Tue, 2020-10-13 13:41
2
734 by tylerborrman
Tue, 2021-02-09 16:33
Normal topic heads up for constraints using GAUSSIANFUNC
by attesor » Thu, 2015-10-22 07:30
1
1,361 by smlewis
Thu, 2015-10-22 08:04
Normal topic Helical Symmetry Axis
by Sandy » Tue, 2016-05-31 18:48
0
1,286 by Sandy
Tue, 2016-05-31 18:48
Normal topic help surface_docking peptide on ice
by engand93 » Wed, 2019-03-27 02:43
0
567 by engand93
Wed, 2019-03-27 02:43
Normal topic Help with enzyme design
by lzx32 » Fri, 2011-04-08 22:29
6
4,838 by lzx32
Mon, 2014-04-21 06:47
Normal topic Help with enzyme design files
by Wenithor » Thu, 2021-04-29 10:33
1
339 by rmoretti
Thu, 2021-04-29 10:44
Normal topic High energies after loopmodel run
by michki » Thu, 2014-05-08 05:14
3
3,005 by rmoretti
Mon, 2014-05-12 15:16
Normal topic high-res docking
by tfliu » Mon, 2013-07-15 02:49
2
2,572 by tfliu
Mon, 2014-04-21 06:48
Normal topic Highly negative total score
by Ruchi_P_Jain » Wed, 2019-04-24 19:55
1
1,007 by nannemdp
Thu, 2019-04-25 07:58
Normal topic Holes output interpretation
by lah435 » Mon, 2012-06-04 15:02
1
1,918 by smlewis
Mon, 2014-04-21 06:47
Normal topic Homodimer interface design
by petrikigor » Fri, 2012-11-16 10:57
3
3,923 by rmoretti
Mon, 2014-04-21 06:47
Normal topic homology membrane modeling demo in rosetta 3.5
by rlwoltz » Mon, 2013-09-09 10:26
1
2,367 by smlewis
Mon, 2014-04-21 06:48
Hot topic homology modeling with end extension
by fred » Mon, 2012-10-08 14:19
19
13,721 by xpzhang
Mon, 2014-04-21 06:47
Normal topic homology modeling with threading says length mismatch between sequence and alignment
by rqliang » Thu, 2015-08-06 11:46
2
2,175 by jharamesh
Sat, 2015-08-08 19:51
Normal topic homology modeling- Error: length mismatch between sequence and alignment.
by pdbb » Mon, 2012-10-01 07:57
2
3,639 by pdbb
Mon, 2014-04-21 06:47
Normal topic Homology Modeling-no PDB output
by jlawrie » Wed, 2020-08-12 06:30
2
840 by jlawrie
Wed, 2020-08-12 08:56
Normal topic Homology modelling applies alignment wrong
by bernhardcl » Thu, 2015-08-06 09:39
1
1,517 by bernhardcl
Tue, 2015-08-11 09:11
Normal topic Homology Modelling with cofactors
by Derek Smith » Thu, 2015-07-09 08:24
3
3,380 by Derek Smith
Wed, 2016-02-03 05:47
Normal topic homology modelling with DNA
by zadie1118 » Fri, 2012-09-28 06:35
4
4,581 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How can I model ligands in comparative modeling
by Morrian_Lynn » Thu, 2020-02-20 09:57
1
638 by danpf
Fri, 2020-02-21 17:05
Normal topic How can I prevent coordinates shift when using "loopmodel.linuxgccrelease"?
by lanselibai » Tue, 2014-11-04 14:56
7
5,766 by lanselibai
Wed, 2014-11-12 11:17
Normal topic How can I set ref2015 and ligand.wts(-restore_pre_talaris_2013_behavior )
by asbelx » Sat, 2019-06-08 00:07
3
1,363 by happycaapi
Tue, 2021-06-29 15:35
Normal topic How do I explicitly add residues for design in the interface optimization script?
by ahonegger » Mon, 2014-05-12 07:40
2
2,669 by ahonegger
Mon, 2014-05-12 09:08
Normal topic How do you use two patches simulataneously with ab initio folding?
by smiruthi » Wed, 2011-12-21 15:24
5
4,016 by wangyr
Mon, 2014-04-21 06:47
Normal topic How does the label in pdb files looks like when using ResiduePDBInfoHasLabel?
by johnnytam100 » Fri, 2019-08-16 00:25
1
978 by JackMaguire
Fri, 2019-08-16 07:41
Normal topic How many iterations of remodel is enough?
by daniloboskovic » Thu, 2020-07-16 08:07
0
379 by daniloboskovic
Thu, 2020-07-16 08:14
Normal topic how to generate Fragments using up to 2001 structures only
by oppopomoz » Sat, 2015-07-25 00:43
1
1,501 by rmoretti
Thu, 2015-08-06 08:57
Normal topic how to "rescore" the models using lowest energy model from rosetta run as native, for RMSD vs Score plot?
by Danielsebas » Tue, 2019-09-24 03:51
1
829 by smlewis
Tue, 2019-09-24 12:43
Normal topic How to add a residue to one chain of an existing structure?
by sn » Mon, 2017-04-17 09:34
2
2,059 by sn
Thu, 2017-04-20 21:43
Normal topic How to add additional rounds of design and optimization in Rosetta scripts?
by Nicole Deng » Tue, 2020-11-03 19:05
2
658 by Nicole Deng
Thu, 2020-11-05 03:04
Normal topic How to add constrains to FlexPepDocking?
by MajorID » Thu, 2011-06-02 11:00
2
2,491 by MajorID
Mon, 2014-04-21 06:47
Normal topic How to analyse multiple silent files from "Abinitiorelax" output to find best models?
by Danielsebas » Tue, 2019-09-10 10:01
1
754 by smlewis
Mon, 2019-09-16 12:22
Normal topic How to apply cartesian_ddg to multi-metric enzyme?
by Wang Zhe » Wed, 2021-12-08 10:07
0
94 by Wang Zhe
Wed, 2021-12-08 10:07
Normal topic How to build disulfide bond between two cysteine, i.e. change two "-SH" (sulfydryl) into "-S-S-"?
by lanselibai » Sat, 2015-01-17 11:19
1
2,456 by lanselibai
Wed, 2015-01-21 02:40
Normal topic How to calculate dG?
by yperez » Mon, 2012-10-22 07:28
1
2,282 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to choose designed antibody
by Sunyp_IM » Wed, 2020-06-24 10:06
5
1,526 by jadolfbr
Fri, 2020-07-24 07:24
Normal topic How to concatenate the 3-mer and 9-mer files for RosettaCM?
by lanselibai » Fri, 2020-05-08 05:38
5
1,671 by danpf
Tue, 2020-05-12 10:58
Normal topic How to correctly incorporate constraint information into ab initio structure prediction?
by johnnytam100 » Tue, 2019-02-19 03:13
2
1,379 by johnnytam100
Fri, 2019-03-01 01:36
Normal topic How to create a native file for Protein-Protein docking
by Kotimedidhi » Fri, 2020-06-19 08:58
2
844 by Kotimedidhi
Mon, 2020-06-22 16:19
Normal topic How to define pi-pi stacking in cst file?
by lzx32 » Mon, 2011-07-04 23:47
6
6,386 by lzx32
Mon, 2014-04-21 06:47
Normal topic How to design the anitgen-antibody interface
by Sunyp_IM » Tue, 2017-12-12 18:44
0
814 by Sunyp_IM
Tue, 2017-12-12 18:44
Normal topic how to do alanine scanning
by xinmiaohe » Mon, 2019-08-26 17:40
5
2,639 by xinmiaohe
Fri, 2019-10-04 08:54
Normal topic How to eliminate "NUL"s when scoring PDBs?
by lanselibai » Tue, 2014-10-14 10:04
2
2,219 by lanselibai
Fri, 2014-10-17 03:36
Normal topic How to estimate the effect of a mutation on the binding energy?
by ltrabuco » Tue, 2011-02-15 08:02
4
4,156 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic How to find cluster core structure?
by assignfit » Thu, 2012-03-29 20:35
7
5,402 by attesor
Wed, 2017-06-14 07:32
Normal topic how to find help informations on rosetta_scripts in rosetta3.10
by xinmiaohe » Mon, 2019-08-26 14:48
5
1,621 by xinmiaohe
Tue, 2019-08-27 08:37
Normal topic how to fix the ATP HETATM by using movemap or constraint file?
by ziqi1234 » Mon, 2017-11-20 06:43
9
4,296 by ziqi1234
Wed, 2017-11-22 06:21
Normal topic How to freeze ligand during FastRelax?
by dnamkr » Thu, 2020-01-02 14:53
1
890 by aloshbau
Fri, 2020-01-10 16:48
Normal topic how to generate the whole molecule that contains all the symmetric chains
by Sunyp_IM » Sun, 2017-12-10 19:43
0
813 by Sunyp_IM
Sun, 2017-12-10 19:43
Normal topic how to know the precedure of solving a actural bio problem? like interface design?
by qq7678500549 » Thu, 2020-08-06 18:45
2
716 by qq7678500549
Sun, 2020-08-09 18:59
Normal topic how to make "static" built binaries use multiple cpus like "mpi"?
by Danielsebas » Wed, 2019-09-18 06:41
3
1,407 by rmoretti
Wed, 2019-09-18 10:21
Normal topic How to make new VALL database?
by Danielsebas » Sun, 2019-09-08 02:16
2
1,480 by Danielsebas
Wed, 2019-09-11 00:44
Normal topic How to minimize the decoys obtained from backrub?
by Vedasheersh » Wed, 2017-06-14 10:26
5
2,751 by SenyorDrew
Fri, 2017-06-30 09:47
Normal topic How to model missing residues on a protein from multiple PDB files?
by cossio » Fri, 2015-08-21 07:18
6
10,346 by rmoretti
Fri, 2015-09-11 13:27
Normal topic How to only constructure the tail conformation when using "FloppyTail.linuxgccrelease"?
by lanselibai » Mon, 2014-10-13 10:26
5
4,145 by lanselibai
Wed, 2014-10-15 03:52
Normal topic How to output all iteration structures from ddg_monomer?
by cossio » Fri, 2014-12-26 13:40
4
3,615 by cossio
Mon, 2015-01-19 07:10
Normal topic How to perform abinitiorelax.mpi.linuxgccrelease in parallel mode with MPI
by kingljy » Sun, 2017-09-24 18:37
3
2,395 by rmoretti
Tue, 2017-10-10 09:58
Normal topic How to Perform point mutations with NCAA
by Subhrodeep Saha » Tue, 2021-06-22 02:05
1
273 by vmulligan
Thu, 2021-06-24 13:23
Normal topic how to pick fragments for a transmembrane protein
by tevang » Mon, 2012-05-28 06:52
1
1,757 by tevang
Mon, 2014-04-21 06:47
Normal topic How to preserve ACE/NME termini?
by nitroamos » Tue, 2018-05-22 13:07
3
2,332 by rmoretti
Thu, 2018-06-28 12:44
Normal topic how to reconstruct the whole complex after symmetric docking
by Anonymous » Tue, 2012-07-03 02:44
2
2,521 by felipet
Wed, 2014-07-02 07:26
Normal topic how to repacking loop while freezing other residues?
by jfhuang » Wed, 2012-07-25 06:59
10
6,757 by jfhuang
Mon, 2014-04-21 06:47
Normal topic How to restart RASREC run
by aep » Fri, 2016-07-01 04:39
2
1,671 by aep
Fri, 2016-07-01 06:54
Normal topic how to run ala_scan.xml
by xinmiaohe » Mon, 2019-08-26 09:38
0
554 by xinmiaohe
Mon, 2019-08-26 09:38
Normal topic how to run my openmp programe in rosetta3.3?
by lihowe » Mon, 2012-02-27 23:43
1
1,901 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to run partial_thread in RosettaCM when residure are more than 9999?
by lanselibai » Mon, 2020-05-11 22:43
2
1,074 by lanselibai
Tue, 2020-05-12 20:25
Normal topic How to scan double mutations in RosettaScripts?
by msardejani » Mon, 2016-12-12 16:52
2
1,703 by msardejani
Mon, 2016-12-12 17:48
Normal topic How to select docked models
by Sunyp_IM » Mon, 2020-06-22 00:50
1
547 by ssrb
Mon, 2020-06-22 13:12
Normal topic How to sort a Silent File based on RMSD
by JadAbbass » Sun, 2013-08-04 14:40
2
2,733 by lanselibai
Mon, 2014-10-06 15:30
Normal topic How to specify only design surface residues and loops by RosettaScripts?
by johnnytam100 » Sun, 2019-04-07 21:47
4
1,702 by johnnytam100
Wed, 2019-04-10 02:48
Normal topic How to use -cst_fa_file and -relax:constrain_relax_to_native_coords at the same time
by Anatol » Thu, 2012-11-29 14:12
11
8,200 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to use base_pair_constraint for RNA as a constraint term?
by yels » Sat, 2021-04-03 01:19
1
388 by everyday847
Sun, 2021-04-04 12:48
Normal topic How to use MHC Epitope energy (mhc_epitope) to deimmunize a protein structure?
by Sunyp_IM » Sun, 2020-11-08 08:07
5
1,294 by Brahm Yachnin
Wed, 2020-11-18 17:21
Normal topic How to use Rosetta to DISCARD a protein-protein docking interface?
by cossio » Tue, 2015-05-26 06:24
2
2,441 by rmoretti
Sat, 2015-07-11 13:38
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