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Rosetta 3 - Applications

Topic / Topic startersort descending Replies Views Last post
Normal topic Generating non-redundat dataset for loop models
by dario.corrada » Wed, 2016-03-09 03:00
1
1,176 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
513 by xinmiaohe
Fri, 2020-02-07 13:52
Normal topic Getting error with Rosetta "antibody.linuxgccrelease" command
by Sunyp_IM » Mon, 2017-08-07 19:40
1
1,471 by smlewis
Tue, 2017-08-15 23:19
Normal topic Global Docking with carbohydrates
by ChiauShu » Sat, 2020-08-22 20:16
0
255 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
1,947 by lanselibai
Tue, 2014-11-11 04:42
Normal topic GrowLigand
by allan.ferrari » Sat, 2019-10-19 05:32
2
939 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
2,775 by jessye
Fri, 2017-11-03 20:15
Normal topic HBNet and RosettaScripts
by protos_heis » Tue, 2014-08-05 06:05
3
2,953 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
377 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
1,182 by smlewis
Thu, 2015-10-22 08:04
Normal topic Helical Symmetry Axis
by Sandy » Tue, 2016-05-31 18:48
0
1,148 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
450 by engand93
Wed, 2019-03-27 02:43
Normal topic Help with enzyme design
by lzx32 » Fri, 2011-04-08 22:29
6
4,344 by lzx32
Mon, 2014-04-21 06:47
Normal topic Help with enzyme design files
by Wenithor » Thu, 2021-04-29 10:33
1
63 by rmoretti
Thu, 2021-04-29 10:44
Normal topic High energies after loopmodel run
by michki » Thu, 2014-05-08 05:14
3
2,710 by rmoretti
Mon, 2014-05-12 15:16
Normal topic high-res docking
by tfliu » Mon, 2013-07-15 02:49
2
2,312 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
783 by nannemdp
Thu, 2019-04-25 07:58
Normal topic Holes output interpretation
by lah435 » Mon, 2012-06-04 15:02
1
1,751 by smlewis
Mon, 2014-04-21 06:47
Normal topic Homodimer interface design
by petrikigor » Fri, 2012-11-16 10:57
3
3,588 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
2,212 by smlewis
Mon, 2014-04-21 06:48
Hot topic homology modeling with end extension
by fred » Mon, 2012-10-08 14:19
19
12,293 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
1,949 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
3,373 by pdbb
Mon, 2014-04-21 06:47
Normal topic Homology Modeling-no PDB output
by jlawrie » Wed, 2020-08-12 06:30
2
516 by jlawrie
Wed, 2020-08-12 08:56
Normal topic Homology modelling applies alignment wrong
by bernhardcl » Thu, 2015-08-06 09:39
1
1,358 by bernhardcl
Tue, 2015-08-11 09:11
Normal topic Homology Modelling with cofactors
by Derek Smith » Thu, 2015-07-09 08:24
3
3,027 by Derek Smith
Wed, 2016-02-03 05:47
Normal topic homology modelling with DNA
by zadie1118 » Fri, 2012-09-28 06:35
4
4,123 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
466 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
5,147 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
2
913 by asbelx
Sat, 2019-06-08 17:03
Normal topic How do I explicitly add residues for design in the interface optimization script?
by ahonegger » Mon, 2014-05-12 07:40
2
2,431 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
3,545 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
707 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
263 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
1,338 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
588 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
1,747 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
389 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
2,243 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
520 by smlewis
Mon, 2019-09-16 12:22
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
2,217 by lanselibai
Wed, 2015-01-21 02:40
Normal topic How to calculate dG?
by yperez » Mon, 2012-10-22 07:28
1
2,091 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
948 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
1,065 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
1,096 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
577 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
5,772 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
662 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
1,807 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
1,980 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
3,789 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
4,784 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
1,205 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
3,557 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
629 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
701 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
469 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
1,057 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
1,093 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
2,341 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
9,269 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
3,735 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
3,238 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
2,009 by rmoretti
Tue, 2017-10-10 09:58
Normal topic how to pick fragments for a transmembrane protein
by tevang » Mon, 2012-05-28 06:52
1
1,589 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
1,785 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
2,290 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
6,071 by jfhuang
Mon, 2014-04-21 06:47
Normal topic How to restart RASREC run
by aep » Fri, 2016-07-01 04:39
2
1,457 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
414 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
1,747 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
681 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
1,500 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
358 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
2,505 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
1,287 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
7,232 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
122 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
680 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
2,209 by rmoretti
Sat, 2015-07-11 13:38
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
473 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
1,909 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
69 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
690 by rmoretti
Fri, 2019-03-29 09:45
Normal topic I need some help for using pHDock applications(histidine protonation / pH-dependent binding)
by leygkn » Tue, 2020-09-22 18:40
1
320 by leygkn
Tue, 2020-09-22 22:46
Normal topic Idealize in Rosetta 3.3
by jadolfbr » Tue, 2011-12-06 11:59
2
2,249 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
4,589 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
685 by chenna
Wed, 2020-03-04 03:24
Normal topic in silico affinity maturation design
by jarod » Mon, 2013-05-20 02:07
11
8,838 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
1,433 by ashu4487
Sun, 2016-12-11 19:03
Normal topic Including waters in RosettaCM
by ajkal » Thu, 2017-04-27 11:59
9
4,485 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
1,808 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
5,573 by rmoretti
Mon, 2014-04-21 06:47
Normal topic input file for loop modeling
by Negarsardar » Tue, 2019-04-16 10:21
1
689 by rmoretti
Tue, 2019-04-16 11:07
Normal topic Input structure
by Soler » Mon, 2020-09-28 13:18
1
323 by ssrb
Tue, 2020-09-29 12:37
Normal topic Inserting residues using RosettaRemodel
by eleishaj » Tue, 2015-11-24 08:54
7
5,452 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
1,370 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
606 by ziqi1234
Fri, 2017-12-08 07:52
Normal topic Interface Analyzer Segmentation Fault
by h_trasatti » Tue, 2017-02-21 12:48
1
1,408 by smlewis
Tue, 2017-02-21 14:10
Normal topic InterfaceAnalyzer -resfile
by gw » Wed, 2011-11-02 16:01
1
2,094 by smlewis
Mon, 2014-04-21 06:47
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