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Rosetta 3 - General

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Normal topic How do you implement phosphoserine in ab -initio folding?
by smiruthi » Fri, 2011-12-16 14:45 		10
 10,337 by brspurri
Mon, 2014-04-21 06:47
Normal topic How do the homology sequences exclude from fragment files?
by exchhattu » Mon, 2010-04-05 03:04 		1
 2,140 by smlewis
Mon, 2014-04-21 06:47
Normal topic How do I implement more CPU cores in the execution of FlexPepDock?
by ChoripanSalado » Thu, 2024-05-02 08:55 		1
 207 by rmoretti
Thu, 2024-06-20 13:34
Normal topic How do I add virtual atom to my cofactor (metal ion) in rosettadock?
by monos_morpheus » Sat, 2011-02-05 21:24 		2
 3,458 by monos_morpheus
Mon, 2014-04-21 06:47
Normal topic How do I add hydrogen atoms to my PDB file?
by monos_morpheus » Wed, 2011-03-30 03:30 		6
 14,001 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How did you begin to learn Rosetta?
by mdeklotz » Mon, 2018-07-30 10:08 		1
 2,294 by jkleman
Tue, 2018-07-31 13:19
Normal topic How can move peptide on cleft of enzyme on Flexpepdock?
by phanvy » Thu, 2014-06-05 02:22 		4
 4,723 by zaldini
Fri, 2015-01-02 05:38
Normal topic How can I use InterfaceScore terms in docking as GenericMonteCarlo criterion
by wwwmrzkwww » Sun, 2021-08-15 00:19 		0
 855 by wwwmrzkwww
Sun, 2021-08-15 00:19
Normal topic how build (N-terminal 17 residues) structre /fragment file generation
by venkatazb » Wed, 2016-07-27 23:56 		3
 3,525 by smlewis
Fri, 2016-07-29 07:43
Normal topic Homology modeling starter script
by gobli033 » Thu, 2010-04-01 07:27 		0
 1,574 by gobli033
Mon, 2014-04-21 06:47
Normal topic Homology modeling
by mchldln » Mon, 2009-08-17 13:04 		2
 3,805 by smlewis
Mon, 2014-04-21 06:47
Normal topic Homology Model gives output - but completely wrong!
by Julix » Wed, 2012-10-31 10:10 		1
 3,410 by rmoretti
Mon, 2014-04-21 06:47
Normal topic homo-oligomeric proteins.............folddock+symmetry+abinito
by anusmita_sahoo » Thu, 2010-04-29 02:59 		2
 3,758 by biofisikx
Mon, 2014-04-21 06:47
Normal topic Histidine protonation
by DmitriiN » Mon, 2016-09-26 13:15 		11
 19,108 by rmoretti
Mon, 2018-01-15 15:37
Normal topic Histidine phosphorylation by a patch
by felipet » Sat, 2016-07-09 06:51 		2
 3,183 by felipet
Sat, 2016-07-09 09:50
Hot topic high resolution protein docking doesn't work
by albumns » Thu, 2010-12-02 02:36 		17
 14,595 by albumns
Mon, 2014-04-21 06:47
Normal topic help with perturbation docking please
by einew » Fri, 2011-03-25 16:16 		2
 3,245 by einew
Mon, 2014-04-21 06:47
Normal topic Help with get_pdb.py for PDB file cleaning
by lzx32 » Mon, 2011-03-28 02:11 		7
 9,240 by smlewis
Mon, 2014-04-21 06:47
Normal topic Help with filtering (Rosetta scripts)
by wentlewi » Sat, 2020-10-24 10:12 		1
 1,457 by rmoretti
Tue, 2021-02-09 12:35
Normal topic Help with file in article Kemp elimination catalysts by computational enzyme design
by Wenithor » Sat, 2021-10-09 07:23 		0
 738 by Wenithor
Sat, 2021-10-09 07:23
Normal topic Help deciphering an input
by Elijah_Hix » Wed, 2021-09-22 11:12 		2
 1,434 by Elijah_Hix
Thu, 2021-09-23 10:13
Normal topic Help - Protein-Protein interface design
by Dinesh Kumar » Thu, 2021-01-28 00:47 		1
 1,166 by rmoretti
Tue, 2021-02-09 10:29
Normal topic Helix at loop site
by berk » Fri, 2013-05-31 07:04 		1
 2,345 by smlewis
Mon, 2014-04-21 06:48
Normal topic Helical symmetry for cryo-EM refinement
by fmerino » Mon, 2017-10-16 04:02 		0
 1,446 by fmerino
Mon, 2017-10-16 04:02
Normal topic header pathways not accessable: No such file or directory
by rlwoltz » Tue, 2012-09-18 17:44 		1
 2,423 by smlewis
Mon, 2014-04-21 06:47
Normal topic Hbond tripped
by alejandro » Mon, 2011-11-21 04:17 		3
 3,919 by alejandro
Mon, 2014-04-21 06:47
Normal topic HBNetStapleInterface
by sdh_h » Wed, 2016-08-24 03:30 		1
 1,816 by smlewis
Wed, 2016-08-24 07:23
Normal topic hbnet
by mintseris » Mon, 2018-03-19 09:02 		1
 1,733 by rmoretti
Mon, 2018-03-19 09:08
Normal topic Having trouble producing a .pdb file from a silent output file after running abinitio relax
by burkheadlab » Wed, 2011-03-09 12:48 		2
 3,148 by burkheadlab
Mon, 2014-04-21 06:47
Normal topic have trouble with "relax" models
by wszjzhang » Thu, 2010-01-28 10:02 		1
 2,198 by smlewis
Mon, 2014-04-21 06:47
Normal topic harmonic_Calphas in RosettaLigand flags.txt
by cpkuntz » Wed, 2010-07-14 08:57 		2
 2,668 by smlewis
Mon, 2014-04-21 06:47
Normal topic Handling peptide with noncanonical aminoacids
by tigerous » Sat, 2013-12-28 17:16 		1
 3,635 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Hamiltonian Exchange
by JSK » Mon, 2024-03-18 12:44 		0
 228 by JSK
Tue, 2024-03-19 09:21
Normal topic H3 modelling scoring function
by aneamtu » Wed, 2017-12-27 23:10 		2
 2,369 by aneamtu
Mon, 2018-01-08 23:49
Normal topic Grafting using antibody.mpi.linuxgccrelease , the modelled structure does not have constant region of the antibody.
by SubhaK » Thu, 2023-01-26 21:29 		1
 704 by rmoretti
Mon, 2023-02-06 14:35
Normal topic Good baseline settings for side chain packing
by pachecoj » Tue, 2015-01-13 19:25 		2
 4,433 by rmoretti
Wed, 2015-01-21 10:05
Normal topic Global ligand docking with Rosetta script and PyRosetta
by tisozaki » Tue, 2021-12-14 17:16 		0
 804 by tisozaki
Tue, 2021-12-14 17:16
Normal topic Global Docking with output analysis RMS
by kwu030 » Fri, 2024-02-23 09:17 		1
 377 by rmoretti
Mon, 2024-02-26 08:24
Normal topic Give preference to native residue during fixed backbone designing
by tusharranjanmoharana » Mon, 2016-04-04 12:43 		6
 5,964 by rmoretti
Thu, 2016-04-28 15:19
Normal topic Give diferent chain information for a single sequence (comparative modeling)
by Martin Floor » Tue, 2013-04-02 08:59 		4
 4,876 by Martin Floor
Mon, 2014-04-21 06:47
Normal topic get_distances command in rosetta 3.5
by pramod » Mon, 2014-01-20 11:31 		3
 3,685 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Getting started with Rosetta
by myang » Tue, 2009-04-07 16:25 		1
 2,671 by smlewis
Mon, 2014-04-21 06:47
Normal topic Getting an interface score from RosettaDock without docking
by rosend » Fri, 2015-12-18 14:02 		3
 6,658 by rosend
Fri, 2015-12-18 19:39
Normal topic Get nchi for heavy atoms
by pachecoj » Tue, 2014-11-04 19:04 		1
 2,213 by rmoretti
Tue, 2014-11-11 13:22
Normal topic Get fasta from PDB script correction - Solved
by ialvy » Tue, 2022-08-30 00:00 		0
 604 by ialvy
Tue, 2022-08-30 00:00
Normal topic genkic mover produced an unwanted HN - CA bond
by cttm4a1 » Mon, 2022-06-20 14:25 		2
 1,087 by cttm4a1
Mon, 2022-06-20 16:58
Normal topic Generating Protein/NA decoys
by rbeier1 » Mon, 2016-01-11 03:25 		1
 2,606 by rmoretti
Thu, 2016-04-28 16:25
Normal topic Generating Params File for water molecule
by Ahmed Raslan » Thu, 2023-08-17 13:13 		0
 611 by Ahmed Raslan
Thu, 2023-08-17 13:13
Normal topic Generating Fragment Libraries for Metal Binding Proteins
by buzb » Wed, 2011-01-26 12:43 		1
 2,927 by kaue
Mon, 2014-04-21 06:47
Normal topic generating 10 lowest energy structures from abinitio
by isengupta13 » Fri, 2010-05-07 11:44 		2
 2,666 by ndousis
Mon, 2014-04-21 06:47
Normal topic Generate template parameter file for a polymer
by anarob » Fri, 2022-06-10 11:05 		1
 819 by matteoferla
Fri, 2022-06-17 10:38
Normal topic Generate structural fragments
by kingljy » Tue, 2011-05-10 20:18 		2
 5,236 by pepfolder
Mon, 2014-04-21 06:47
Normal topic Generate full symmetric assembly from subsystem
by lj269 » Thu, 2011-04-28 20:04 		1
 2,483 by IAndre
Mon, 2014-04-21 06:47
Normal topic generate full atom coordinates with abinitio rosetta structure prediction
by anusmita_sahoo » Tue, 2010-03-30 00:11 		2
 3,263 by Trentage
Mon, 2014-04-21 06:47
Normal topic GeneralizedKIC side chain closure.
by almeida85 » Mon, 2022-09-19 06:13 		0
 649 by almeida85
Mon, 2022-09-19 07:22
Normal topic GeneralizedKIC disulfide closure
by Ken » Tue, 2022-08-16 13:32 		2
 1,139 by Ken
Wed, 2022-08-17 08:04
Normal topic general question about protein docking
by albumns » Mon, 2010-12-13 23:26 		1
 2,554 by JeffreyGray
Mon, 2014-04-21 06:47
Normal topic General protein-protein docking when no info. on structure is availble
by jasnyderjr » Fri, 2016-12-09 04:55 		3
 3,350 by smlewis
Tue, 2016-12-20 10:40
Normal topic General Protein Folding Question
by twopint23oz » Sun, 2012-04-01 22:57 		7
 6,693 by smlewis
Mon, 2014-04-21 06:47
Normal topic General Forum Suggestion
by jadolfbr » Thu, 2011-09-29 08:11 		0
 2,836 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic Gaussian Constraint For Dihedrals
by jinli711 » Thu, 2020-07-23 10:47 		1
 1,469 by matteoferla
Fri, 2020-07-24 03:06
Normal topic GALigandDock errors
by Delfosse57 » Mon, 2023-08-07 13:16 		0
 533 by Delfosse57
Mon, 2023-08-07 13:16
Normal topic Fusing C-terminal or N-terminal segments onto proteins using Remodel
by achambe » Tue, 2016-01-05 09:39 		1
 2,554 by achambe
Wed, 2016-01-13 10:46
Normal topic Free FSC score for validating refinement
by ahmadkhalifa » Thu, 2018-05-10 05:53 		2
 2,560 by ahmadkhalifa
Fri, 2018-06-29 07:54
Normal topic fragment_picker problem
by adva » Tue, 2012-12-18 01:15 		13
 13,019 by sabine
Mon, 2014-04-21 06:47
Normal topic fragment_picker error secondarysimilarity.cc line:132
by leanawen » Mon, 2013-04-15 14:33 		1
 2,219 by smlewis
Mon, 2014-04-21 06:47
Normal topic Fragments for short peptides using Robetta
by renedominik » Wed, 2018-05-16 14:21 		3
 3,041 by renedominik
Mon, 2018-06-04 00:04
Normal topic fragment-based loop modeling to get a helix at the loop site
by berk » Wed, 2013-05-29 06:00 		11
 10,632 by rmoretti
Mon, 2014-04-21 06:47
Normal topic fragment picking with 100% sequence identity
by nawsad » Thu, 2013-12-05 07:12 		1
 3,157 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Fragment Picker score type weights
by wellsm10 » Mon, 2020-12-14 13:05 		1
 1,537 by dgront
Thu, 2021-02-11 08:30
Normal topic Fragment picker
by phanvy » Mon, 2014-12-08 04:25 		2
 3,405 by phanvy
Wed, 2014-12-10 00:17
Normal topic Fragment files
by exchhattu » Fri, 2009-09-18 01:04 		4
 4,820 by rmoretti
Tue, 2015-01-06 09:58
Normal topic Fragment file viewers
by MajorID » Fri, 2012-02-24 20:57 		2
 2,875 by smlewis
Mon, 2014-04-21 06:47
Normal topic force point mutation with fixbb
by Anonymous » Wed, 2012-06-13 09:15 		3
 4,093 by smlewis
Mon, 2014-04-21 06:47
Normal topic force hydrogen rebuild on input
by jtmacd » Mon, 2013-11-18 08:28 		2
 3,148 by jtmacd
Mon, 2014-04-21 06:48
Normal topic force field, energy function
by masterofpuppets » Wed, 2015-01-21 11:06 		3
 6,285 by masterofpuppets
Tue, 2015-01-27 07:07
Normal topic Fold tree error
by mansi » Tue, 2010-05-18 07:43 		2
 4,019 by mansi
Mon, 2014-04-21 06:47
Normal topic Fluctuations in I_sc
by eminegenetics » Thu, 2018-09-13 12:07 		4
 3,368 by eminegenetics
Fri, 2018-09-21 07:42
Normal topic FlexPepDocking.mpi.linuxgccrelease bails out ERROR: total_residue() != 0 ERROR:: Exit from: src/core/pose/Pose.cc line: 1369
by knutjbj » Thu, 2011-02-03 03:24 		2
 4,577 by knutjbj
Mon, 2014-04-21 06:47
Normal topic Flexible backbone design using PSSM
by kalicuta » Thu, 2012-07-26 13:38 		4
 5,155 by rmoretti
Mon, 2014-04-21 06:47
Normal topic flexible backbone design (fixbb+relax)
by sdh_h » Mon, 2013-02-04 03:19 		9
 12,279 by gsmurphy
Mon, 2014-04-21 06:47
Normal topic Flex-pep-docking (ab-initio mode)
by ate » Wed, 2021-06-16 19:19 		0
 795 by ate
Wed, 2021-06-16 19:19
Normal topic Flag to not use PDB ligands
by matteoferla » Wed, 2019-08-21 10:14 		2
 2,028 by matteoferla
Wed, 2019-08-21 11:58
Normal topic Fixing certain residues during refinement
by ckdenist » Thu, 2019-08-29 14:00 		1
 1,901 by jadolfbr
Thu, 2019-08-29 14:29
Normal topic Fixed bb design with hydrogen bond constraint
by bharat_46010 » Mon, 2012-04-30 22:56 		6
 6,147 by smlewis
Mon, 2014-04-21 06:47
Normal topic fixbb program
by Lindsay » Tue, 2012-05-08 13:56 		3
 3,558 by AndrewLeaver-Fay
Mon, 2014-04-21 06:47
Normal topic fixbb minimize sidechains with symmetric pose - recompile?
by Anonymous » Wed, 2012-08-22 06:14 		13
 11,303 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic fixbb design use
by Lindsay » Fri, 2012-03-23 09:05 		2
 2,971 by Lindsay
Mon, 2014-04-21 06:47
Normal topic FixBB design design_contrast
by swoody » Tue, 2009-06-30 11:48 		2
 3,020 by swoody
Mon, 2014-04-21 06:47
Normal topic fixbb and HETATM
by doranhen » Mon, 2013-01-14 07:50 		2
 3,684 by doranhen
Mon, 2014-04-21 06:47
Normal topic Fix missing backbone residues
by Matthys » Mon, 2010-05-03 09:03 		2
 3,777 by Matthys
Mon, 2014-04-21 06:47
Normal topic fix backbone design of interface residue
by Lindsay » Tue, 2013-12-17 19:23 		3
 4,604 by rmoretti
Mon, 2014-04-21 06:48
Hot topic Fix back bone design fixbb
by Lindsay » Tue, 2012-03-06 12:30 		26
 23,521 by Anonymous
Mon, 2014-04-21 06:47
Normal topic Fitting a structure with an unrecognized residue to an EM density
by ahmadkhalifa » Tue, 2017-12-05 14:44 		2
 2,369 by ahmadkhalifa
Wed, 2017-12-06 12:30
Normal topic first try at relaxing a structure
by einew » Wed, 2011-01-05 11:09 		4
 6,843 by einew
Mon, 2014-04-21 06:47
Normal topic first run of abinitio in rosetta 3.2 produces an error right away
by burkheadlab » Fri, 2011-03-04 22:50 		3
 3,734 by smlewis
Mon, 2014-04-21 06:47
Normal topic Finding affinity-reducing mutants towards a ligand in Ligand-based interface design protocol
by adityapadhi » Wed, 2020-06-24 01:29 		0
 925 by adityapadhi
Wed, 2020-06-24 01:29
Normal topic Filters saying atom type does not exist on residue
by mdm95 » Mon, 2024-03-04 15:13 		1
 352 by mdm95
Tue, 2024-03-05 14:05
Normal topic filter score by I_sc and keep top 1000
by aaj » Tue, 2016-01-19 07:13 		2
 2,997 by aaj
Mon, 2016-02-22 07:43
Normal topic File specification of binary part of silent file (especially PDB section)
by m.ebert » Wed, 2019-05-29 01:52 		1
 1,492 by smlewis
Wed, 2019-05-29 13:21