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Rosetta 3 - Applications

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Normal topic how to find help informations on rosetta_scripts in rosetta3.10
by xinmiaohe » Mon, 2019-08-26 14:48
5
3,276 by xinmiaohe
Tue, 2019-08-27 08:37
Normal topic How to find cluster core structure?
by assignfit » Thu, 2012-03-29 20:35
7
7,520 by attesor
Wed, 2017-06-14 07:32
Normal topic How to estimate the effect of a mutation on the binding energy?
by ltrabuco » Tue, 2011-02-15 08:02
4
5,596 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic How to eliminate "NUL"s when scoring PDBs?
by lanselibai » Tue, 2014-10-14 10:04
2
3,084 by lanselibai
Fri, 2014-10-17 03:36
Normal topic how to do alanine scanning
by xinmiaohe » Mon, 2019-08-26 17:40
5
5,326 by xinmiaohe
Fri, 2019-10-04 08:54
Normal topic How to design the anitgen-antibody interface
by Sunyp_IM » Tue, 2017-12-12 18:44
0
1,254 by Sunyp_IM
Tue, 2017-12-12 18:44
Normal topic How to define pi-pi stacking in cst file?
by lzx32 » Mon, 2011-07-04 23:47
6
8,305 by lzx32
Mon, 2014-04-21 06:47
Normal topic How to debug the XML script file?
by intomybioverse » Wed, 2024-03-06 06:32
2
283 by rmoretti
Wed, 2024-03-06 06:51
Normal topic How to create a native file for Protein-Protein docking
by Kotimedidhi » Fri, 2020-06-19 08:58
2
1,793 by Kotimedidhi
Mon, 2020-06-22 16:19
Normal topic How to correctly incorporate constraint information into ab initio structure prediction?
by johnnytam100 » Tue, 2019-02-19 03:13
2
2,326 by johnnytam100
Fri, 2019-03-01 01:36
Normal topic how to control alignment for energy_based_clustering
by xfradera » Tue, 2023-02-28 10:13
0
1,880 by xfradera
Tue, 2023-02-28 10:13
Normal topic How to concatenate the 3-mer and 9-mer files for RosettaCM?
by lanselibai » Fri, 2020-05-08 05:38
5
3,433 by danpf
Tue, 2020-05-12 10:58
Normal topic How to choose designed antibody
by Sunyp_IM » Wed, 2020-06-24 10:06
6
4,334 by chandana
Tue, 2022-08-09 20:27
Normal topic How to change the axes of "-spin" in docking_protocol
by Zehui Zhou » Mon, 2023-02-13 22:06
0
2,206 by Zehui Zhou
Mon, 2023-02-13 22:06
Normal topic How to calculate dG?
by yperez » Mon, 2012-10-22 07:28
1
3,168 by smlewis
Mon, 2014-04-21 06:47
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
3,212 by lanselibai
Wed, 2015-01-21 02:40
Normal topic How to apply cartesian_ddg to multi-metric enzyme?
by Wang Zhe » Wed, 2021-12-08 10:07
0
977 by Wang Zhe
Wed, 2021-12-08 10:07
Normal topic How to analyse multiple silent files from "Abinitiorelax" output to find best models?
by Danielsebas » Tue, 2019-09-10 10:01
1
1,502 by smlewis
Mon, 2019-09-16 12:22
Normal topic How to add constrains to FlexPepDocking?
by MajorID » Thu, 2011-06-02 11:00
2
3,355 by MajorID
Mon, 2014-04-21 06:47
Normal topic How to add additional rounds of design and optimization in Rosetta scripts?
by Nicole Deng » Tue, 2020-11-03 19:05
2
1,601 by Nicole Deng
Thu, 2020-11-05 03:04
Normal topic How to add a residue to one chain of an existing structure?
by sn » Mon, 2017-04-17 09:34
2
3,405 by sn
Thu, 2017-04-20 21:43
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
1,658 by smlewis
Tue, 2019-09-24 12:43
Normal topic how to generate Fragments using up to 2001 structures only
by oppopomoz » Sat, 2015-07-25 00:43
1
2,170 by rmoretti
Thu, 2015-08-06 08:57
Normal topic How many iterations of remodel is enough?
by daniloboskovic » Thu, 2020-07-16 08:07
0
861 by daniloboskovic
Thu, 2020-07-16 08:14
Normal topic How does the label in pdb files looks like when using ResiduePDBInfoHasLabel?
by johnnytam100 » Fri, 2019-08-16 00:25
1
1,782 by JackMaguire
Fri, 2019-08-16 07:41
Normal topic How do you use two patches simulataneously with ab initio folding?
by smiruthi » Wed, 2011-12-21 15:24
5
5,515 by wangyr
Mon, 2014-04-21 06:47
Normal topic How do I explicitly add residues for design in the interface optimization script?
by ahonegger » Mon, 2014-05-12 07:40
2
3,541 by ahonegger
Mon, 2014-05-12 09:08
Normal topic How do I compare the results of InterfaceAnalyzer using different trimers as input?
by franz72 » Sun, 2023-08-06 10:10
0
347 by franz72
Sun, 2023-08-06 10:10
Normal topic How do I change the default Compiler for Rosetta?
by pagumaaaaa » Wed, 2022-03-16 00:23
2
1,603 by pagumaaaaa
Thu, 2022-03-24 22:40
Normal topic How can I set ref2015 and ligand.wts(-restore_pre_talaris_2013_behavior )
by asbelx » Sat, 2019-06-08 00:07
3
2,731 by happycaapi
Tue, 2021-06-29 15:35
Normal topic How can I prevent coordinates shift when using "loopmodel.linuxgccrelease"?
by lanselibai » Tue, 2014-11-04 14:56
7
7,927 by lanselibai
Wed, 2014-11-12 11:17
Normal topic How can I model ligands in comparative modeling
by Morrian_Lynn » Thu, 2020-02-20 09:57
1
1,312 by danpf
Fri, 2020-02-21 17:05
Normal topic homology modelling with DNA
by zadie1118 » Fri, 2012-09-28 06:35
4
5,877 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Homology Modelling with cofactors
by Derek Smith » Thu, 2015-07-09 08:24
3
4,666 by Derek Smith
Wed, 2016-02-03 05:47
Normal topic Homology modelling applies alignment wrong
by bernhardcl » Thu, 2015-08-06 09:39
1
2,127 by bernhardcl
Tue, 2015-08-11 09:11
Normal topic Homology Modeling-no PDB output
by jlawrie » Wed, 2020-08-12 06:30
2
1,915 by jlawrie
Wed, 2020-08-12 08:56
Normal topic homology modeling- Error: length mismatch between sequence and alignment.
by pdbb » Mon, 2012-10-01 07:57
2
4,513 by pdbb
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
2,969 by jharamesh
Sat, 2015-08-08 19:51
Hot topic homology modeling with end extension
by fred » Mon, 2012-10-08 14:19
19
18,065 by xpzhang
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
2,931 by smlewis
Mon, 2014-04-21 06:48
Normal topic Homodimer interface design
by petrikigor » Fri, 2012-11-16 10:57
3
5,090 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Holes output interpretation
by lah435 » Mon, 2012-06-04 15:02
1
2,538 by smlewis
Mon, 2014-04-21 06:47
Normal topic Highly negative total score
by Ruchi_P_Jain » Wed, 2019-04-24 19:55
1
1,809 by nannemdp
Thu, 2019-04-25 07:58
Normal topic high-res docking
by tfliu » Mon, 2013-07-15 02:49
2
3,387 by tfliu
Mon, 2014-04-21 06:48
Normal topic High energies after loopmodel run
by michki » Thu, 2014-05-08 05:14
3
4,036 by rmoretti
Mon, 2014-05-12 15:16
Normal topic Help with enzyme design files
by Wenithor » Thu, 2021-04-29 10:33
1
1,077 by rmoretti
Thu, 2021-04-29 10:44
Normal topic Help with enzyme design
by lzx32 » Fri, 2011-04-08 22:29
6
6,704 by lzx32
Mon, 2014-04-21 06:47
Normal topic Help to understand docking results
by rtorquato » Fri, 2022-11-25 12:05
0
1,546 by rtorquato
Fri, 2022-11-25 12:05
Normal topic help surface_docking peptide on ice
by engand93 » Wed, 2019-03-27 02:43
0
1,034 by engand93
Wed, 2019-03-27 02:43
Normal topic Helical Symmetry Axis
by Sandy » Tue, 2016-05-31 18:48
0
1,777 by Sandy
Tue, 2016-05-31 18:48
Normal topic heads up for constraints using GAUSSIANFUNC
by attesor » Thu, 2015-10-22 07:30
1
2,015 by smlewis
Thu, 2015-10-22 08:04
Normal topic hbond_sr_bb and hbond_lr_bb for different chains
by tylerborrman » Tue, 2020-10-13 13:41
2
1,910 by tylerborrman
Tue, 2021-02-09 16:33
Normal topic HBNet and RosettaScripts
by protos_heis » Tue, 2014-08-05 06:05
3
4,324 by protos_heis
Tue, 2014-08-05 12:47
Normal topic Hamiltonian Exchange
by JSK » Mon, 2024-03-18 12:48
0
147 by JSK
Tue, 2024-03-19 09:21
Normal topic H3 modeling takes 10 days more?
by jessye » Fri, 2017-10-27 03:11
7
5,499 by jessye
Fri, 2017-11-03 20:15
Normal topic GrowLigand
by allan.ferrari » Sat, 2019-10-19 05:32
2
2,115 by allan.ferrari
Tue, 2019-11-05 16:52
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
991 by SubhaK
Wed, 2023-01-18 23:33
Normal topic Got error when running minirosetta.linuxgccrelease on cluster but fine on Ubuntu
by lanselibai » Mon, 2014-11-10 08:12
2
2,990 by lanselibai
Tue, 2014-11-11 04:42
Normal topic Global Docking with carbohydrates
by ChiauShu » Sat, 2020-08-22 20:16
0
990 by ChiauShu
Sat, 2020-08-22 20:16
Normal topic Getting error with Rosetta "antibody.linuxgccrelease" command
by Sunyp_IM » Mon, 2017-08-07 19:40
1
2,589 by smlewis
Tue, 2017-08-15 23:19
Normal topic getting a3m files
by alonwenger » Wed, 2021-12-15 02:38
2
2,884 by alonwenger
Sat, 2021-12-18 12:32
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
1,446 by xinmiaohe
Fri, 2020-02-07 13:52
Normal topic Generating the 3-mer and 9-mer fragments
by Prasoon » Wed, 2022-02-09 09:04
0
1,243 by Prasoon
Wed, 2022-02-09 09:04
Normal topic Generating non-redundat dataset for loop models
by dario.corrada » Wed, 2016-03-09 03:00
1
1,959 by smlewis
Wed, 2016-03-09 04:11
Normal topic Generating a new Vall database
by vijay.anand » Tue, 2023-06-20 12:08
0
440 by vijay.anand
Tue, 2023-06-20 12:08
Normal topic Generate fragment locally
by deltag » Wed, 2012-02-01 06:26
2
3,545 by deltag
Mon, 2014-04-21 06:47
Normal topic Generate fragment file on my computer
by jrcf » Mon, 2015-09-21 15:41
2
4,202 by jrcf
Mon, 2015-10-05 21:32
Normal topic GeneralizedKIC loop closure error
by chenna » Sat, 2021-04-10 00:21
2
1,611 by chenna
Mon, 2021-04-12 22:08
Normal topic Generalized KIC loop closure affects downstream residues without perturbations
by chenna » Mon, 2021-04-26 02:16
2
1,503 by chenna
Wed, 2021-04-28 07:18
Normal topic General question regarding ligand-docking
by Alison_Yajie » Thu, 2020-05-07 09:48
0
837 by Alison_Yajie
Thu, 2020-05-07 09:48
Hot topic Garbled Ligands from docking_protocol
by skovacs » Tue, 2011-12-20 07:55
21
19,714 by skovacs
Mon, 2014-04-21 06:47
Normal topic Fusing C-terminal or N-terminal segments onto proteins using Remodel
by achambe » Mon, 2016-01-04 11:26
0
1,563 by achambe
Mon, 2016-01-04 11:26
Normal topic Full Protocol
by shekhar » Fri, 2013-10-04 01:07
1
3,092 by rmoretti
Mon, 2014-04-21 06:48
Normal topic fragment_picker:[ ERROR ] UtilityExitException ERROR: can't open file: $ROSETTA/tools/fragment_tools/vall.jul19.2011.gz
by yueyuedake » Wed, 2023-07-12 03:36
6
1,184 by yueyuedake
Sun, 2023-07-16 19:17
Normal topic fragment_picker.mpi.linuxgccrelease can't find : libsqlite3.so
by starone » Mon, 2016-06-20 19:22
11
13,844 by starone
Fri, 2016-06-24 18:29
Normal topic fragment_picker with fasta only
by gw » Tue, 2011-11-15 13:20
3
4,522 by gw
Mon, 2014-04-21 06:47
Normal topic fragment_picker bug
by David Hoover » Wed, 2012-02-29 11:43
0
1,810 by David Hoover
Mon, 2014-04-21 06:47
Normal topic Fragments for long sequence
by exchhattu » Tue, 2011-10-04 01:51
2
3,310 by exchhattu
Mon, 2014-04-21 06:47
Normal topic fragment picker does not follow dihedral constraints
by attesor » Tue, 2016-05-24 23:22
12
11,143 by smlewis
Wed, 2016-08-17 07:56
Normal topic Fragment library (vall file) from Robetta?
by alex » Sun, 2017-02-19 08:12
0
1,680 by alex
Sun, 2017-02-19 08:12
Normal topic Fragment files for membrane_abinitio application
by sumukh21 » Sun, 2011-02-13 20:34
7
7,059 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
3,581 by sumukh21
Mon, 2014-04-21 06:47
Normal topic Fragment Files
by nkemjika » Fri, 2011-07-22 15:11
1
3,138 by dgront
Mon, 2014-04-21 06:47
Hot topic Folppy Tail and Constraints
by sfulad2 » Fri, 2017-05-12 12:23
15
10,507 by smlewis
Fri, 2017-09-08 09:16
Normal topic folding ectodomain in membrane ab initio
by freedman » Mon, 2015-05-25 21:09
3
4,051 by rmoretti
Fri, 2015-06-19 13:53
Normal topic Folding and Docking using Symmetry
by danielles » Wed, 2012-09-12 11:32
0
1,913 by danielles
Mon, 2014-04-21 06:47
Normal topic Fold tree C->N: RosettaScripts
by aroop » Wed, 2013-02-13 10:31
8
8,304 by smlewis
Mon, 2014-04-21 06:47
Normal topic fold and dock protocol not working
by ytao » Mon, 2012-11-26 15:33
1
2,487 by smlewis
Mon, 2014-04-21 06:47
Normal topic Fold and Dock - chains not in contact
by arthuc01 » Wed, 2012-06-13 01:45
2
3,109 by smlewis
Mon, 2014-04-21 06:47
Normal topic Fnat and Irms are nan in score.sc from docking_protocol?
by cossio » Sun, 2015-09-13 07:34
2
3,816 by rmoretti
Thu, 2015-09-17 12:47
Normal topic FloppyTail vs. Remodel for linkers
by attesor » Mon, 2014-07-07 08:36
1
2,366 by smlewis
Mon, 2014-07-07 11:58
Normal topic FloppyTail options error
by DmitriiN » Fri, 2016-11-11 02:54
1
1,901 by smlewis
Fri, 2016-11-11 08:33
Normal topic Floppytail modelling
by felipet » Fri, 2011-06-24 09:23
2
3,835 by felipet
Mon, 2014-04-21 06:47
Hot topic FloppyTail bugs for N-terminal tails
by Dave C » Thu, 2012-03-01 13:06
18
16,253 by bbarryabc
Mon, 2014-04-21 06:47
Normal topic FloppyTail as a rosettascripts file
by tiagogomes89 » Mon, 2015-01-19 02:45
0
1,444 by tiagogomes89
Mon, 2015-01-19 02:45
Normal topic FloppyTail :How to specify range of design(mutation)
by syoifczeri » Mon, 2015-11-02 04:14
6
6,627 by syoifczeri
Sat, 2015-11-07 21:42
Normal topic Floppy tail: sidechain mutation during calculation
by syoifczeri » Mon, 2015-03-09 19:01
2
3,200 by syoifczeri
Tue, 2015-03-10 23:08
Normal topic Flex_ddG突变设计
by wangtao » Thu, 2022-05-05 02:46
0
1,041 by wangtao
Thu, 2022-05-05 02:46
Normal topic Flex_ddG crashes when attempting to move 2 chains (e.g. chains_to_move = A,C)
by jcampecino » Wed, 2020-05-13 12:22
0
1,116 by jcampecino
Wed, 2020-05-13 12:22
Normal topic flexpepdock_score_only
by ays » Sun, 2014-09-21 06:17
2
2,753 by ays
Tue, 2014-09-30 08:31
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