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Rosetta 3 - Applications

Topic / Topic starter Replies Viewssort ascending Last post
Normal topic Standalone alanine scanning protocol
by exchhattu » Thu, 2011-10-13 19:40
1
5,428 by smlewis
Mon, 2014-04-21 06:47
Normal topic using Rosetta to compute pH dependent binding?
by JuliusSu » Sun, 2014-06-15 20:28
3
5,419 by rmoretti
Tue, 2014-06-17 08:51
Normal topic Unable to run Rosetta LoopModeling application
by BDBorrillo » Tue, 2011-07-19 14:06
2
5,417 by BDBorrillo
Mon, 2014-04-21 06:47
Normal topic domain:domain fusion
by felipet » Thu, 2017-06-15 13:13
5
5,414 by felipet
Fri, 2017-06-16 11:42
Normal topic How to estimate the effect of a mutation on the binding energy?
by ltrabuco » Tue, 2011-02-15 08:02
4
5,390 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic SymDock for docking only the ligand?
by ast » Mon, 2013-06-17 09:53
4
5,381 by rmoretti
Mon, 2014-04-21 06:48
Normal topic score_jd2.mpi.linuxgccrelease failed
by fred » Wed, 2014-03-26 13:54
2
5,381 by fred
Tue, 2014-04-01 08:24
Normal topic Multistate design on Rosetta - no generations produced
by tong » Wed, 2018-06-13 00:36
8
5,374 by smlewis
Thu, 2018-06-14 10:26
Normal topic How do you use two patches simulataneously with ab initio folding?
by smiruthi » Wed, 2011-12-21 15:24
5
5,343 by wangyr
Mon, 2014-04-21 06:47
Normal topic AbinitioRelax with native fragments
by ks » Mon, 2016-09-05 03:03
5
5,303 by ks
Mon, 2016-09-12 03:14
Normal topic Does linker modeling exist?
by aroop » Wed, 2012-02-22 07:34
5
5,299 by smlewis
Mon, 2014-04-21 06:47
Normal topic Docking flags
by AmelieH » Thu, 2014-11-13 08:46
5
5,291 by AmelieH
Wed, 2014-11-19 11:26
Normal topic Multiple ligands in enzyme design application
by yogeshkd » Mon, 2013-02-11 10:13
4
5,280 by yogeshkd
Mon, 2014-04-21 06:47
Normal topic H3 modeling takes 10 days more?
by jessye » Fri, 2017-10-27 03:11
7
5,276 by jessye
Fri, 2017-11-03 20:15
Normal topic Loop modelling before peptide docking
by wsgosal » Tue, 2013-10-01 07:24
4
5,249 by wsgosal
Mon, 2014-04-21 06:48
Normal topic enzyme design and output_matchres_only
by petrikigor » Wed, 2012-10-24 18:45
6
5,232 by petrikigor
Mon, 2014-04-21 06:47
Normal topic fixbb algorithm reference?
by tylerborrman » Wed, 2015-09-23 10:20
4
5,231 by tylerborrman
Mon, 2015-09-28 09:30
Normal topic Why is proline hydroxylated?
by kwonglynn » Tue, 2013-06-25 02:38
3
5,192 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Is there a way to restrict memory usage of ddg_monomer?
by cossio » Fri, 2015-01-30 14:35
5
5,161 by rmoretti
Mon, 2015-02-09 12:04
Normal topic make fragment
by zadie1118 » Thu, 2012-08-30 07:45
3
5,154 by smlewis
Mon, 2014-04-21 06:47
Normal topic Rebuilding the structure from unknown residues
by sushreet » Mon, 2016-06-27 09:32
4
5,149 by rmoretti
Tue, 2016-07-12 09:35
Normal topic Backrub Params Files
by protos_heis » Tue, 2012-09-18 06:15
4
5,142 by protos_heis
Mon, 2014-04-21 06:47
Normal topic Adding bridged water interaction in constraint file
by purvi24 » Thu, 2019-02-28 07:01
8
5,140 by purvi24
Mon, 2019-03-11 06:43
Normal topic Syntax for python-based (.py) command line on cluster
by lanselibai » Fri, 2014-11-14 09:32
2
5,117 by lanselibai
Thu, 2014-11-20 02:15
Normal topic Missing common atom definitions in constraints
by ic3reyes » Sat, 2011-06-11 13:09
3
5,095 by smlewis
Mon, 2014-04-21 06:47
Normal topic "Problem in calculating overlap between atoms" error occurred in Point Mutant Scan application
by xfliu » Thu, 2012-06-21 09:07
4
5,091 by smlewis
Mon, 2014-04-21 06:47
Normal topic Error during single state design
by sujigeorge1979 » Sat, 2020-01-18 00:37
5
5,083 by rmoretti
Thu, 2020-01-30 15:42
Normal topic minirosetta: weird behavior
by fred » Wed, 2014-01-22 05:57
4
5,082 by fred
Mon, 2014-04-21 06:48
Normal topic Using Rosetta Docking for nucleic acids
by Adrien Guilhot » Thu, 2011-04-28 06:16
3
5,078 by Adrien Guilhot
Mon, 2014-04-21 06:47
Normal topic ddG_monomer
by cott1117 » Thu, 2014-06-12 09:53
3
5,068 by rmoretti
Wed, 2014-07-02 16:55
Normal topic running in MPI mode and multiple scores per output PDB file?
by dantimatter » Wed, 2019-10-30 09:42
7
5,064 by dantimatter
Wed, 2019-11-06 09:51
Normal topic Error while running RosettaLigand
by Ryhon Wang » Tue, 2013-07-30 02:51
4
5,058 by Ryhon Wang
Mon, 2014-04-21 06:48
Normal topic how to do alanine scanning
by xinmiaohe » Mon, 2019-08-26 17:40
5
5,036 by xinmiaohe
Fri, 2019-10-04 08:54
Normal topic ligand_docking_analysis
by Prasanth Kumar » Thu, 2013-05-09 23:51
4
5,032 by rmoretti
Mon, 2014-04-21 06:47
Normal topic clean_pdb.py of Rosetta VS cleanATOM of PyRosetta
by lanselibai » Wed, 2014-09-24 03:02
2
4,995 by lanselibai
Wed, 2014-09-24 13:21
Normal topic extract_pdbs fails to open silent file when -auto_setup_metals enabled
by attesor » Thu, 2015-01-15 03:22
4
4,983 by attesor
Tue, 2015-01-27 02:20
Normal topic Disulfide prediction from primary sequence
by zcrook » Wed, 2014-11-12 14:44
2
4,970 by zcrook
Tue, 2014-11-25 10:27
Normal topic Homodimer interface design
by petrikigor » Fri, 2012-11-16 10:57
3
4,964 by rmoretti
Mon, 2014-04-21 06:47
Normal topic pair energies across interface
by irini » Fri, 2012-02-10 09:17
5
4,953 by Anonymous
Mon, 2014-04-21 06:47
Normal topic RosettaAntibody
by mpendleton » Mon, 2011-04-04 10:27
3
4,950 by jianqing
Mon, 2014-04-21 06:47
Normal topic RosettaCM -weights, fragments and relax
by jsv » Tue, 2017-05-09 10:20
5
4,938 by rmoretti
Thu, 2017-06-01 08:52
Normal topic fa_plane enregy term in scoring weights
by ytao » Fri, 2012-11-30 20:25
4
4,937 by smlewis
Mon, 2014-04-21 06:47
Normal topic ddg_monomer conformational search...
by yperez » Wed, 2012-05-09 11:10
5
4,936 by yperez
Mon, 2014-04-21 06:47
Normal topic Antibody modeling
by Maryam_tabasinezhad » Fri, 2015-09-04 11:00
4
4,931 by rmoretti
Wed, 2015-09-09 12:08
Normal topic molfile to params polymer python errors
by tsztain » Sun, 2018-12-02 15:38
5
4,917 by tsztain
Tue, 2018-12-11 13:41
Normal topic InterfaceAnalyzer problem
by almeida » Mon, 2014-03-03 14:56
3
4,915 by smlewis
Fri, 2014-03-07 14:09
Normal topic Abrelax - Dunbrack02.lib.bin missing
by omirus » Sun, 2011-09-18 06:30
3
4,909 by smlewis
Mon, 2014-04-21 06:47
Normal topic make_rot_lib issue
by jarek » Thu, 2013-04-11 08:21
4
4,904 by smlewis
Mon, 2014-04-21 06:47
Normal topic a question about ligand docking
by yzhou » Wed, 2012-05-30 18:57
5
4,882 by yzhou
Mon, 2014-04-21 06:47
Normal topic fixbb and ncaa's
by jarek » Thu, 2012-11-08 04:55
4
4,876 by jcminerlanl
Thu, 2017-12-21 10:13
Normal topic Unable to locate the "compute_ddg.py" file and running the RosettaMP protocol
by Sajjad » Mon, 2022-11-28 14:09
3
4,867 by Sajjad
Wed, 2022-11-30 11:50
Normal topic jd2 quits before reaching -nstruct # in roseta_scripts.mpi.linuxgccrelease
by fradom » Mon, 2017-11-27 02:55
6
4,854 by fradom
Tue, 2017-12-05 01:52
Normal topic assymetric dymer modelling with comparative and ab initio
by marcia » Mon, 2013-10-14 08:33
3
4,847 by rmoretti
Mon, 2014-04-21 06:48
Normal topic How to output all iteration structures from ddg_monomer?
by cossio » Fri, 2014-12-26 13:40
4
4,842 by cossio
Mon, 2015-01-19 07:10
Normal topic [TopologyBroker Exception]: BBTorsion at pos 468unitialized...unclaimed
by tevang » Wed, 2013-04-10 15:07
5
4,808 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Ligand Docking with Rosetta Scripts memory problem
by Swillard » Thu, 2017-08-17 14:59
5
4,799 by rmoretti
Mon, 2018-11-12 14:31
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
4,779 by frichter
Mon, 2014-04-21 06:47
Normal topic RosettaCM Tutorials
by smathersc » Wed, 2017-01-11 15:59
5
4,765 by rmoretti
Thu, 2017-01-19 09:11
Normal topic favor native residue in fixBB design
by ast » Mon, 2012-12-10 06:00
4
4,752 by smlewis
Mon, 2014-04-21 06:47
Normal topic modeling an extracellular loop of a transmembrane protein
by Hothman » Fri, 2016-08-12 06:16
5
4,740 by rmoretti
Mon, 2016-09-05 10:59
Normal topic sam.predict-2nd for make_fragments.pl script
by sumukh21 » Thu, 2011-02-17 12:29
3
4,738 by fukamitka
Mon, 2014-04-21 06:47
Normal topic Re: Glutamic acid protonation
by bharat_46010 » Fri, 2017-02-10 03:08
4
4,733 by rmoretti
Mon, 2017-02-20 08:09
Normal topic Problems with always_constrained_relax_script
by wsgosal » Wed, 2013-05-29 04:39
3
4,728 by rmoretti
Mon, 2014-04-21 06:47
Normal topic FlexPepDocking with GDP-bound protein
by LI » Sun, 2011-06-12 20:02
3
4,713 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Loop modeling - the appropriate way to model a peptide insertion?
by xding » Thu, 2018-08-02 15:30
6
4,693 by smlewis
Wed, 2018-08-08 15:48
Normal topic Can I assume the outputs from different runs are from a same batch?
by lanselibai » Mon, 2014-11-03 06:34
4
4,689 by lanselibai
Mon, 2014-11-03 13:15
Normal topic Rosetta ScriptsFeatures Reporter issue
by David Weis » Sun, 2017-03-12 08:19
5
4,668 by David Weis
Mon, 2017-03-13 10:59
Normal topic Ligand atom RMSD calculation
by lkrathn » Wed, 2013-08-14 21:25
2
4,649 by lkrathn
Mon, 2014-04-21 06:48
Normal topic Different scoring applications (score vs score_aln vs score_jd2, etc.)?
by cossio » Fri, 2014-12-26 07:19
3
4,637 by Patrícia Antunes
Fri, 2023-01-20 11:55
Normal topic Positive scores with SymmDock in helical symmetry
by kxiao » Tue, 2014-02-11 07:37
4
4,630 by kxiao
Thu, 2014-06-05 08:37
Normal topic cyclization_type flag in simple_cycpep_predict
by Florent Langenfeld » Thu, 2018-01-04 09:22
5
4,626 by Florent Langenfeld
Tue, 2018-03-27 11:44
Normal topic Symmetric Minimization
by aroop » Mon, 2012-12-17 11:45
5
4,619 by aroop
Mon, 2014-04-21 06:47
Normal topic Error when running cluster
by aloshbau » Wed, 2013-05-01 20:45
3
4,613 by rmoretti
Mon, 2014-04-21 06:47
Normal topic ReplicaDock 2.0 Native vs Input Structure Flags Confusion
by katherinemccoy » Tue, 2022-12-27 06:42
2
4,612 by katherinemccoy
Tue, 2023-02-28 18:19
Normal topic Docking structures with ligands in cryo-EM maps
by galushin » Wed, 2012-07-11 12:40
1
4,563 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic Rosetta DNA - Protein-DNA scoring function and binding energy
by tanoramb » Tue, 2012-05-08 14:00
1
4,555 by smlewis
Mon, 2014-04-21 06:47
Normal topic Local docking: "manually place the two proteins facing each other" ?
by mdeklotz » Fri, 2018-07-20 10:24
5
4,545 by dfcoelho
Tue, 2018-10-16 09:05
Normal topic Syntax for the alignment file in "minirosetta comparative modeling"
by lanselibai » Thu, 2014-10-16 15:29
3
4,544 by lanselibai
Thu, 2014-10-23 03:26
Normal topic the meaning of total_score in docking
by libai2098 » Mon, 2011-03-21 05:46
2
4,541 by libai2098
Mon, 2014-04-21 06:47
Normal topic ERROR: no fragment to compute secondary structure
by byin » Sun, 2011-08-07 23:55
3
4,503 by smlewis
Mon, 2014-04-21 06:47
Normal topic Warning messages in Interface analyzer output
by Pernille » Wed, 2015-03-25 00:53
4
4,502 by rmoretti
Tue, 2015-03-31 08:20
Normal topic Homology Modelling with cofactors
by Derek Smith » Thu, 2015-07-09 08:24
3
4,495 by Derek Smith
Wed, 2016-02-03 05:47
Normal topic Discrepancy between the total pose energy and sum of per residue energies
by vijayan » Tue, 2013-07-02 07:24
3
4,477 by rmoretti
Mon, 2014-04-21 06:48
Normal topic ligand dock question
by sacch » Sun, 2012-05-20 19:49
4
4,450 by sacch
Mon, 2014-04-21 06:47
Normal topic Protein-DNA Docking using RosettaScripts?
by brspurri » Fri, 2013-06-07 09:06
1
4,446 by rmoretti
Mon, 2014-04-21 06:48
Normal topic ddg monomer vs pmut scan
by dave » Tue, 2014-03-04 10:18
3
4,431 by smlewis
Fri, 2014-03-07 13:02
Normal topic InterfaceAnalyzer dSasa calculation
by mintseris » Wed, 2015-09-02 09:43
2
4,426 by jadolfbr
Thu, 2015-09-03 16:18
Normal topic terminal amino acids of gap has incomplete valency
by malkeet.singh » Wed, 2017-11-29 05:20
6
4,424 by rmoretti
Fri, 2017-12-01 12:05
Normal topic cluster.mpi running in MPI mode?
by sacch » Fri, 2011-11-18 23:30
2
4,416 by sacch
Mon, 2014-04-21 06:47
Normal topic homology modeling- Error: length mismatch between sequence and alignment.
by pdbb » Mon, 2012-10-01 07:57
2
4,414 by pdbb
Mon, 2014-04-21 06:47
Normal topic Error in a new docking
by jrcf » Wed, 2017-05-17 19:26
2
4,405 by tingting
Tue, 2022-03-15 23:55
Normal topic conway2016 correction on beta-nov15?
by attesor » Wed, 2017-03-15 05:26
5
4,394 by attesor
Thu, 2017-03-16 01:21
Normal topic AbinitioRelax Disulfide Bonds are not being retained
by brspurri » Wed, 2011-09-28 13:55
1
4,390 by parmef
Mon, 2014-04-21 06:47
Normal topic fragment_picker with fasta only
by gw » Tue, 2011-11-15 13:20
3
4,383 by gw
Mon, 2014-04-21 06:47
Normal topic pmut_scan does not produce log file
by fglaser » Wed, 2013-10-16 07:25
3
4,363 by matteoferla
Tue, 2018-10-30 02:54
Normal topic protein-protein docking with flexible backbone
by tim » Fri, 2013-12-20 05:52
1
4,363 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Pepspec Errors running 3.4
by rrphenix » Tue, 2013-05-28 12:08
4
4,358 by rmoretti
Mon, 2014-04-21 06:47
Normal topic comparative modeling of protein-ligand complex
by tevang » Mon, 2013-09-09 09:06
3
4,338 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Snugdock_input
by luicui » Wed, 2017-01-18 16:48
5
4,307 by smlewis
Fri, 2017-01-20 08:14
Normal topic Error when running Remodel with EnzDes constraint file to extend c-terminal
by Jeffrey_Chen » Thu, 2017-01-19 06:20
4
4,293 by dfcoelho
Tue, 2017-10-17 11:52
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