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Rosetta 3 - Applications

Topic / Topic startersort descending Replies Views Last post
Normal topic How to write down a connection between ligand's atom and metal ion from enzyme?
by Corvin » Mon, 2021-02-15 06:54
7
1,276 by aloshbau
Mon, 2021-03-01 20:06
Normal topic How tu use Delta filter's relax_mover
by pocin » Sun, 2017-02-19 05:21
3
2,199 by rmoretti
Wed, 2017-03-01 13:10
Normal topic hpatch commands and how to identify patches
by Bianca Oliva » Thu, 2021-04-29 04:02
0
284 by Bianca Oliva
Thu, 2021-04-29 04:02
Normal topic hybrid approach - comparative and ab initio modelling
by eprates » Wed, 2019-03-20 11:58
1
863 by rmoretti
Fri, 2019-03-29 09:45
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
87 by Wenithor
Thu, 2022-01-06 12:20
Normal topic I need some help for using pHDock applications(histidine protonation / pH-dependent binding)
by leygkn » Tue, 2020-09-22 18:40
1
531 by leygkn
Tue, 2020-09-22 22:46
Normal topic Idealize in Rosetta 3.3
by jadolfbr » Tue, 2011-12-06 11:59
2
2,472 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic If "clustering.py" can be used for PDBs contain two chains?
by lanselibai » Wed, 2014-11-05 06:05
7
5,227 by lanselibai
Tue, 2014-12-02 09:43
Normal topic Imitating induced fit protocol in SymDock2 without any symmetry constraints
by chenna » Fri, 2020-02-14 01:35
2
1,030 by chenna
Wed, 2020-03-04 03:24
Normal topic in silico affinity maturation design
by jarod » Mon, 2013-05-20 02:07
11
9,724 by jarod
Mon, 2014-04-21 06:47
Normal topic Including ab-initio predicted model in fragment library generation
by ashu4487 » Thu, 2016-12-08 17:49
2
1,637 by ashu4487
Sun, 2016-12-11 19:03
Normal topic Including waters in RosettaCM
by ajkal » Thu, 2017-04-27 11:59
9
5,311 by rpavlov
Tue, 2017-06-06 11:45
Normal topic Incorporating iron-sulfur cluster into ROSETTA applications
by Derek Smith » Thu, 2014-08-14 23:12
1
1,996 by rmoretti
Fri, 2014-08-15 08:06
Normal topic Incorrect Jump being set in RosettaScripts docking mover
by weehee » Fri, 2012-06-08 10:23
6
6,089 by rmoretti
Mon, 2014-04-21 06:47
Normal topic input file for loop modeling
by Negarsardar » Tue, 2019-04-16 10:21
1
870 by rmoretti
Tue, 2019-04-16 11:07
Normal topic Input structure
by Soler » Mon, 2020-09-28 13:18
1
513 by ssrb
Tue, 2020-09-29 12:37
Normal topic Inserting residues using RosettaRemodel
by eleishaj » Tue, 2015-11-24 08:54
7
6,189 by eyong123
Wed, 2015-12-09 07:17
Normal topic Instructing design scripts to use noncanonical AA instead of canonical
by zcrook » Tue, 2014-11-25 10:43
1
1,544 by rmoretti
Wed, 2014-11-26 07:51
Normal topic Interesting scoring performance in flexpepdock against random peptides
by ziqi1234 » Fri, 2017-12-08 07:52
0
709 by ziqi1234
Fri, 2017-12-08 07:52
Normal topic Interface Analyzer Segmentation Fault
by h_trasatti » Tue, 2017-02-21 12:48
1
1,628 by smlewis
Tue, 2017-02-21 14:10
Normal topic InterfaceAnalyzer -resfile
by gw » Wed, 2011-11-02 16:01
1
2,290 by smlewis
Mon, 2014-04-21 06:47
Normal topic InterfaceAnalyzer dSasa calculation
by mintseris » Wed, 2015-09-02 09:43
2
3,324 by jadolfbr
Thu, 2015-09-03 16:18
Normal topic InterfaceAnalyzer problem
by almeida » Mon, 2014-03-03 14:56
3
3,798 by smlewis
Fri, 2014-03-07 14:09
Normal topic InterfaceAnalyzer:“too many tries in fill_missing_atoms!”
by mxp » Tue, 2019-08-06 00:41
8
3,256 by mxp
Mon, 2019-08-12 18:42
Normal topic interface_delta ligand_docking
by Prasanth Kumar » Tue, 2013-06-18 08:37
1
2,056 by rmoretti
Mon, 2014-04-21 06:48
Normal topic is it necessary to always run relax before any Rosetta
by mainzer » Fri, 2019-04-12 01:35
1
1,118 by rmoretti
Wed, 2019-07-10 09:47
Normal topic Is it possible to restart the ddg_monomer.linuxgccrelease?
by lanselibai » Mon, 2015-09-07 03:46
1
1,507 by rmoretti
Wed, 2015-09-09 12:01
Normal topic Is native.pdb necess for fragment_picker?
by ylwang » Thu, 2020-03-12 00:57
2
990 by ylwang
Thu, 2020-03-12 20:42
Normal topic Is there a way to restrict memory usage of ddg_monomer?
by cossio » Fri, 2015-01-30 14:35
5
3,791 by rmoretti
Mon, 2015-02-09 12:04
Normal topic Issue with Rosetta LinkResidues Script
by adityapadhi » Wed, 2019-11-20 22:00
1
743 by JackMaguire
Fri, 2019-11-22 13:45
Normal topic issues about cstfile in RosettaMatch
by Nicole Deng » Fri, 2020-12-18 05:44
3
985 by He Xiao
Sun, 2021-04-11 19:29
Normal topic Issues with modifying dock.xml for multiple ligand docking
by DGR95 » Fri, 2021-05-14 12:51
0
245 by DGR95
Fri, 2021-05-14 12:51
Normal topic JD2 MPI
by jrcf » Wed, 2015-10-28 14:45
1
1,651 by rmoretti
Sat, 2015-10-31 08:57
Normal topic jd2 quits before reaching -nstruct # in roseta_scripts.mpi.linuxgccrelease
by fradom » Mon, 2017-11-27 02:55
6
3,165 by fradom
Tue, 2017-12-05 01:52
Normal topic JobDistributor problem in antibody modeling
by Wizard » Wed, 2015-04-22 00:35
2
2,509 by Wizard
Sun, 2015-04-26 22:36
Normal topic kcenters_clustering_of_fragments
by bjharris » Mon, 2019-07-01 16:16
1
838 by bjharris
Wed, 2020-07-01 23:25
Normal topic KeyError: 'subject-id' in antibody modelling
by bogac » Mon, 2017-03-06 02:00
2
2,106 by bogac
Tue, 2017-03-07 02:11
Normal topic KIC with fragments versus Next generation KIC
by Loki01 » Fri, 2018-09-07 05:06
3
1,901 by smlewis
Mon, 2018-09-10 11:48
Normal topic kinematic loop modeling multiple input: possible?
by a_s_a » Thu, 2011-05-12 09:33
2
2,588 by a_s_a
Mon, 2014-04-21 06:47
Normal topic Lammps or RosettaSurface
by StevPChem » Fri, 2016-06-10 10:13
3
2,894 by Anpu
Tue, 2018-09-25 18:53
Normal topic latest version of rosetta unable to build models
by pramod » Mon, 2014-11-03 11:31
1
2,006 by rmoretti
Tue, 2014-11-04 10:33
Normal topic Ligand atom RMSD calculation
by lkrathn » Wed, 2013-08-14 21:25
2
3,910 by lkrathn
Mon, 2014-04-21 06:48
Normal topic ligand conformer generation for enzyme design
by bo » Mon, 2013-02-11 16:51
1
1,897 by smlewis
Mon, 2014-04-21 06:47
Normal topic Ligand creation
by Prasanth Kumar » Fri, 2013-08-02 09:48
1
1,953 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Ligand dock analysis
by sacch » Tue, 2012-05-22 01:20
3
3,013 by glemmon
Mon, 2014-04-21 06:47
Normal topic ligand dock into HEM containg pdb
by syntekabio2019 » Thu, 2022-01-20 03:05
0
46 by syntekabio2019
Thu, 2022-01-20 03:05
Normal topic ligand dock question
by sacch » Sun, 2012-05-20 19:49
4
3,427 by sacch
Mon, 2014-04-21 06:47
Normal topic Ligand docking and protein design of an internal pocket in a protein with a cofactor
by oerbilgin » Mon, 2011-06-20 13:55
2
3,888 by frichter
Mon, 2014-04-21 06:47
Normal topic Ligand docking at specific orientation
by ShiranBZ » Mon, 2020-04-13 20:46
1
609 by matteoferla
Mon, 2020-05-04 02:02
Normal topic Ligand docking cannot open the protein file
by swarekwood » Tue, 2017-10-17 08:17
1
981 by rmoretti
Tue, 2017-10-17 09:03
Normal topic Ligand Docking with ARLS
by cam11 » Thu, 2016-06-23 09:34
1
1,546 by rmoretti
Thu, 2016-06-23 10:55
Normal topic Ligand docking with constraint
by Alison_Yajie » Wed, 2020-06-24 12:34
0
402 by Alison_Yajie
Wed, 2020-06-24 12:34
Normal topic ligand docking with MPI
by Ruska322 » Wed, 2019-09-04 03:47
2
996 by Ruska322
Fri, 2019-09-06 07:13
Normal topic Ligand Docking with Rosetta Scripts memory problem
by Swillard » Thu, 2017-08-17 14:59
5
3,278 by rmoretti
Mon, 2018-11-12 14:31
Normal topic Ligand Docking with RosettaScripts gives a ParsedProtocol exception
by brspurri » Sun, 2017-05-14 17:51
2
2,087 by brspurri
Mon, 2017-05-15 11:48
Normal topic ligand docking, how to combine some silent.out files into a silent_all.out file
by Ryhon Wang » Fri, 2013-12-06 01:53
6
5,624 by rmoretti
Wed, 2017-01-11 12:53
Normal topic Ligand docking: ERROR: set_atom_base: atoms must be bonded!
by mengzhang » Mon, 2014-05-12 12:36
1
2,057 by rmoretti
Mon, 2014-05-12 15:08
Normal topic Ligand docking: ERROR: set_atom_base: atoms must be bonded!
by mengzhang » Mon, 2014-05-12 12:36
1
2,431 by jharamesh
Mon, 2014-11-03 12:50
Normal topic Ligand params file proton_chi parameters
by staciekim » Thu, 2017-08-17 14:50
2
1,987 by staciekim
Thu, 2017-08-17 17:06
Normal topic ligand_docking ligand preparation
by Alison_Yajie » Thu, 2020-05-21 10:21
2
839 by Alison_Yajie
Wed, 2020-06-24 12:38
Normal topic ligand_docking tutorial help: do crystal_complex.pdb files need to be prepped before using with <InterfaceScoreCalculator>
by DGR95 » Fri, 2021-04-16 19:26
4
702 by DGR95
Wed, 2021-04-28 16:13
Normal topic ligand_docking: ligand preparation
by Alison_Yajie » Thu, 2020-05-21 09:42
0
431 by Alison_Yajie
Thu, 2020-05-21 09:42
Normal topic ligand_docking: ligand preparation
by Alison_Yajie » Thu, 2020-07-02 07:05
0
418 by Alison_Yajie
Thu, 2020-07-02 07:10
Normal topic ligand_docking_analysis
by Prasanth Kumar » Thu, 2013-05-09 23:51
4
3,993 by rmoretti
Mon, 2014-04-21 06:47
Normal topic ligand_docking_error
by Alison_Yajie » Mon, 2020-04-20 12:27
3
1,201 by YuFei
Sat, 2020-05-30 00:12
Normal topic Limit on backbone movement in relax?
by SWM » Fri, 2020-01-24 07:35
0
504 by SWM
Fri, 2020-01-24 07:35
Normal topic limit_cluster_size default value
by sacch » Thu, 2011-11-24 17:57
2
2,148 by sacch
Mon, 2014-04-21 06:47
Normal topic Line search failed even after resetting Hessian
by Loki01 » Wed, 2017-12-13 16:52
6
3,932 by Loki01
Thu, 2018-02-15 13:54
Normal topic Linker Building in scFv
by sam_dc » Sat, 2021-10-09 05:38
0
144 by sam_dc
Sat, 2021-10-09 05:38
Normal topic Local docking: "manually place the two proteins facing each other" ?
by mdeklotz » Fri, 2018-07-20 10:24
5
2,632 by dfcoelho
Tue, 2018-10-16 09:05
Normal topic loop design for Conformational bias
by dhirajks » Thu, 2019-05-09 21:22
1
926 by jadolfbr
Fri, 2019-05-10 07:53
Normal topic Loop design with length variation
by jarod » Thu, 2016-06-16 19:54
3
2,848 by rmoretti
Tue, 2016-07-12 09:41
Normal topic Loop modeling - the appropriate way to model a peptide insertion?
by xding » Thu, 2018-08-02 15:30
6
2,947 by smlewis
Wed, 2018-08-08 15:48
Normal topic loop modeling during enzyme design?
by lzx32 » Wed, 2011-11-16 00:30
6
4,381 by lzx32
Mon, 2014-04-21 06:47
Normal topic loop modeling scoring
by Nicky_Learning_... » Wed, 2015-05-13 20:00
1
2,073 by rmoretti
Mon, 2015-05-25 11:30
Normal topic Loop modeling with constraints
by agctomer » Sat, 2021-03-20 03:53
3
734 by agctomer
Thu, 2021-04-08 07:37
Normal topic Loop modeling/closure for many structures
by sn » Mon, 2017-03-06 11:25
1
1,114 by rmoretti
Mon, 2017-03-06 12:39
Normal topic Loop modeling: KIC with fragments producing unusual models
by kamau » Mon, 2015-06-01 12:06
1
1,654 by rmoretti
Sat, 2015-06-20 20:07
Normal topic Loop modelling before peptide docking
by wsgosal » Tue, 2013-10-01 07:24
4
4,172 by wsgosal
Mon, 2014-04-21 06:48
Normal topic Loop prediction
by yzhou » Thu, 2013-07-18 14:24
3
3,390 by jadolfbr
Mon, 2014-04-21 06:48
Normal topic loop re-modeling std::out_of_range
by rlwoltz » Tue, 2013-03-12 18:11
9
6,548 by smlewis
Mon, 2014-04-21 06:47
Normal topic loopmodel issue
by chiendarret » Fri, 2012-01-27 00:51
1
2,502 by smlewis
Mon, 2014-04-21 06:47
Normal topic loopmodel thinks there are no residues in the pose
by lah435 » Wed, 2013-03-27 02:46
3
3,358 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Loopmodel with DNA has no energy score
by Nicky_Learning_... » Sun, 2015-05-10 19:31
1
1,687 by rmoretti
Mon, 2015-05-25 12:30
Normal topic LoopModeler mover unable to determine cut point
by gszwabowski » Mon, 2020-06-01 13:12
1
794 by matteoferla
Thu, 2020-07-02 07:27
Normal topic loop_length_changing
by lanselibai » Tue, 2014-10-14 04:10
14
10,235 by lanselibai
Fri, 2014-11-07 02:06
Normal topic Make error during installation of updated ncbi-blast-2.9.0+-src plus error with nr-database
by Corvin » Tue, 2019-10-01 02:04
6
3,573 by Corvin
Tue, 2019-10-15 01:12
Normal topic make fragment
by zadie1118 » Thu, 2012-08-30 07:45
3
4,083 by smlewis
Mon, 2014-04-21 06:47
Normal topic Make Fragments
by Run » Mon, 2013-11-11 05:31
1
2,118 by smlewis
Mon, 2014-04-21 06:48
Normal topic make_fragments.pl error
by almeida85 » Mon, 2020-08-31 04:39
2
906 by almeida85
Tue, 2020-09-01 01:29
Normal topic make_rot_lib issue
by jarek » Thu, 2013-04-11 08:21
4
3,851 by smlewis
Mon, 2014-04-21 06:47
Normal topic manually defining CDRs in antibody modelling
by gard.nelson » Fri, 2020-07-10 13:31
1
617 by brspurri
Wed, 2021-01-20 08:11
Normal topic matdes_design: ERROR]EXCN_utility_exit has been thrown from: src/core/io/silent/SilentFileData.cc line: 302
by siciliu » Fri, 2014-03-21 17:51
5
4,762 by siciliu
Thu, 2014-04-10 09:50
Normal topic MaxSub and MaxSub2.0
by JadAbbass » Tue, 2013-10-15 13:36
2
2,785 by JadAbbass
Mon, 2014-04-21 06:48
Normal topic membrane ab initio modeling application with constraints
by ytao » Thu, 2012-11-08 11:56
2
3,529 by ytao
Mon, 2014-04-21 06:47
Normal topic membrane ab-initio modeling, is the quality comparable to comparative modeling of 20% id template?
by fglaser » Thu, 2011-04-07 07:57
0
1,814 by fglaser
Mon, 2014-04-21 06:47
Normal topic Membrane ab-initio modelling of a beta-strand
by hzhekova » Mon, 2019-06-10 14:22
1
894 by rmoretti
Mon, 2019-06-24 14:39
Normal topic Membrane Abinitio modeling
by bharat_46010 » Mon, 2017-03-13 22:39
1
1,168 by benhardy
Wed, 2020-09-30 04:24
Normal topic Membrane Abinitio modeling error
by jkyan007 » Thu, 2020-10-29 03:30
1
516 by noahC_noahDo
Tue, 2020-11-17 10:35
Normal topic Membrane homology modeling loop building gives very strange outputs
by chelsell » Tue, 2014-09-30 14:46
2
2,411 by chelsell
Wed, 2014-10-08 12:25
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