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Rosetta 3 - General

Topic / Topic startersort descending Replies Views Last post
Normal topic fix backbone design of interface residue
by Lindsay » Tue, 2013-12-17 19:23
3
2,789 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Fix missing backbone residues
by Matthys » Mon, 2010-05-03 09:03
2
2,316 by Matthys
Mon, 2014-04-21 06:47
Normal topic fixbb and HETATM
by doranhen » Mon, 2013-01-14 07:50
2
2,127 by doranhen
Mon, 2014-04-21 06:47
Normal topic FixBB design design_contrast
by swoody » Tue, 2009-06-30 11:48
2
1,589 by swoody
Mon, 2014-04-21 06:47
Normal topic fixbb design use
by Lindsay » Fri, 2012-03-23 09:05
2
1,697 by Lindsay
Mon, 2014-04-21 06:47
Normal topic fixbb minimize sidechains with symmetric pose - recompile?
by Anonymous » Wed, 2012-08-22 06:14
13
6,087 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic fixbb program
by Lindsay » Tue, 2012-05-08 13:56
3
2,001 by AndrewLeaver-Fay
Mon, 2014-04-21 06:47
Normal topic Fixed bb design with hydrogen bond constraint
by bharat_46010 » Mon, 2012-04-30 22:56
6
3,434 by smlewis
Mon, 2014-04-21 06:47
Normal topic Fixing certain residues during refinement
by ckdenist » Thu, 2019-08-29 14:00
1
397 by jadolfbr
Thu, 2019-08-29 14:29
Normal topic Flag to not use PDB ligands
by matteoferla » Wed, 2019-08-21 10:14
2
487 by matteoferla
Wed, 2019-08-21 11:58
Normal topic flexible backbone design (fixbb+relax)
by sdh_h » Mon, 2013-02-04 03:19
9
6,966 by gsmurphy
Mon, 2014-04-21 06:47
Normal topic Flexible backbone design using PSSM
by kalicuta » Thu, 2012-07-26 13:38
4
2,943 by rmoretti
Mon, 2014-04-21 06:47
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
3,393 by knutjbj
Mon, 2014-04-21 06:47
Normal topic Fluctuations in I_sc
by eminegenetics » Thu, 2018-09-13 12:07
4
1,098 by eminegenetics
Fri, 2018-09-21 07:42
Normal topic Fold tree error
by mansi » Tue, 2010-05-18 07:43
2
2,561 by mansi
Mon, 2014-04-21 06:47
Normal topic force field, energy function
by masterofpuppets » Wed, 2015-01-21 11:06
3
3,345 by masterofpuppets
Tue, 2015-01-27 07:07
Normal topic force hydrogen rebuild on input
by jtmacd » Mon, 2013-11-18 08:28
2
1,684 by jtmacd
Mon, 2014-04-21 06:48
Normal topic force point mutation with fixbb
by Anonymous » Wed, 2012-06-13 09:15
3
2,320 by smlewis
Mon, 2014-04-21 06:47
Normal topic Fragment file viewers
by MajorID » Fri, 2012-02-24 20:57
2
1,652 by smlewis
Mon, 2014-04-21 06:47
Normal topic Fragment files
by exchhattu » Fri, 2009-09-18 01:04
4
2,685 by rmoretti
Tue, 2015-01-06 09:58
Normal topic Fragment picker
by phanvy » Mon, 2014-12-08 04:25
2
1,722 by phanvy
Wed, 2014-12-10 00:17
Normal topic fragment picking with 100% sequence identity
by nawsad » Thu, 2013-12-05 07:12
1
2,145 by rmoretti
Mon, 2014-04-21 06:48
Normal topic fragment-based loop modeling to get a helix at the loop site
by berk » Wed, 2013-05-29 06:00
11
5,369 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Fragments for short peptides using Robetta
by renedominik » Wed, 2018-05-16 14:21
3
1,202 by renedominik
Mon, 2018-06-04 00:04
Normal topic fragment_picker error secondarysimilarity.cc line:132
by leanawen » Mon, 2013-04-15 14:33
1
1,201 by smlewis
Mon, 2014-04-21 06:47
Normal topic fragment_picker problem
by adva » Tue, 2012-12-18 01:15
13
7,514 by sabine
Mon, 2014-04-21 06:47
Normal topic Free FSC score for validating refinement
by ahmadkhalifa » Thu, 2018-05-10 05:53
2
895 by ahmadkhalifa
Fri, 2018-06-29 07:54
Normal topic Fusing C-terminal or N-terminal segments onto proteins using Remodel
by achambe » Tue, 2016-01-05 09:39
1
1,394 by achambe
Wed, 2016-01-13 10:46
Normal topic Gaussian Constraint For Dihedrals
by jinli711 » Thu, 2020-07-23 10:47
1
121 by matteoferla
Fri, 2020-07-24 03:06
Normal topic General Forum Suggestion
by jadolfbr » Thu, 2011-09-29 08:11
0
2,131 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic General Protein Folding Question
by twopint23oz » Sun, 2012-04-01 22:57
7
3,597 by smlewis
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
1,608 by smlewis
Tue, 2016-12-20 10:40
Normal topic general question about protein docking
by albumns » Mon, 2010-12-13 23:26
1
1,623 by JeffreyGray
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
1,982 by Trentage
Mon, 2014-04-21 06:47
Normal topic Generate full symmetric assembly from subsystem
by lj269 » Thu, 2011-04-28 20:04
1
1,533 by IAndre
Mon, 2014-04-21 06:47
Normal topic Generate structural fragments
by kingljy » Tue, 2011-05-10 20:18
2
3,781 by pepfolder
Mon, 2014-04-21 06:47
Normal topic generating 10 lowest energy structures from abinitio
by isengupta13 » Fri, 2010-05-07 11:44
2
1,435 by ndousis
Mon, 2014-04-21 06:47
Normal topic Generating Fragment Libraries for Metal Binding Proteins
by buzb » Wed, 2011-01-26 12:43
1
1,968 by kaue
Mon, 2014-04-21 06:47
Normal topic Generating Protein/NA decoys
by rbeier1 » Mon, 2016-01-11 03:25
1
1,225 by rmoretti
Thu, 2016-04-28 16:25
Normal topic Get nchi for heavy atoms
by pachecoj » Tue, 2014-11-04 19:04
1
1,207 by rmoretti
Tue, 2014-11-11 13:22
Normal topic Getting an interface score from RosettaDock without docking
by rosend » Fri, 2015-12-18 14:02
3
3,586 by rosend
Fri, 2015-12-18 19:39
Normal topic Getting started with Rosetta
by myang » Tue, 2009-04-07 16:25
1
1,591 by smlewis
Mon, 2014-04-21 06:47
Normal topic get_distances command in rosetta 3.5
by pramod » Mon, 2014-01-20 11:31
3
1,929 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Give diferent chain information for a single sequence (comparative modeling)
by Martin Floor » Tue, 2013-04-02 08:59
4
2,615 by Martin Floor
Mon, 2014-04-21 06:47
Normal topic Give preference to native residue during fixed backbone designing
by tusharranjanmoharana » Mon, 2016-04-04 12:43
6
2,820 by rmoretti
Thu, 2016-04-28 15:19
Normal topic Good baseline settings for side chain packing
by pachecoj » Tue, 2015-01-13 19:25
2
2,631 by rmoretti
Wed, 2015-01-21 10:05
Normal topic H3 modelling scoring function
by aneamtu » Wed, 2017-12-27 23:10
2
900 by aneamtu
Mon, 2018-01-08 23:49
Normal topic Handling peptide with noncanonical aminoacids
by tigerous » Sat, 2013-12-28 17:16
1
2,372 by rmoretti
Mon, 2014-04-21 06:48
Normal topic harmonic_Calphas in RosettaLigand flags.txt
by cpkuntz » Wed, 2010-07-14 08:57
2
1,423 by smlewis
Mon, 2014-04-21 06:47
Normal topic have trouble with "relax" models
by wszjzhang » Thu, 2010-01-28 10:02
1
1,262 by smlewis
Mon, 2014-04-21 06:47
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
1,761 by burkheadlab
Mon, 2014-04-21 06:47
Normal topic hbnet
by mintseris » Mon, 2018-03-19 09:02
1
639 by rmoretti
Mon, 2018-03-19 09:08
Normal topic HBNetStapleInterface
by sdh_h » Wed, 2016-08-24 03:30
1
855 by smlewis
Wed, 2016-08-24 07:23
Normal topic Hbond tripped
by alejandro » Mon, 2011-11-21 04:17
3
2,290 by alejandro
Mon, 2014-04-21 06:47
Normal topic header pathways not accessable: No such file or directory
by rlwoltz » Tue, 2012-09-18 17:44
1
1,424 by smlewis
Mon, 2014-04-21 06:47
Normal topic Helical symmetry for cryo-EM refinement
by fmerino » Mon, 2017-10-16 04:02
0
703 by fmerino
Mon, 2017-10-16 04:02
Normal topic Helix at loop site
by berk » Fri, 2013-05-31 07:04
1
1,314 by smlewis
Mon, 2014-04-21 06:48
Normal topic Help with get_pdb.py for PDB file cleaning
by lzx32 » Mon, 2011-03-28 02:11
7
6,023 by smlewis
Mon, 2014-04-21 06:47
Normal topic help with perturbation docking please
by einew » Fri, 2011-03-25 16:16
2
2,049 by einew
Mon, 2014-04-21 06:47
Hot topic high resolution protein docking doesn't work
by albumns » Thu, 2010-12-02 02:36
17
8,107 by albumns
Mon, 2014-04-21 06:47
Normal topic Histidine phosphorylation by a patch
by felipet » Sat, 2016-07-09 06:51
2
1,610 by felipet
Sat, 2016-07-09 09:50
Normal topic Histidine protonation
by DmitriiN » Mon, 2016-09-26 13:15
11
9,479 by rmoretti
Mon, 2018-01-15 15:37
Normal topic homo-oligomeric proteins.............folddock+symmetry+abinito
by anusmita_sahoo » Thu, 2010-04-29 02:59
2
2,393 by biofisikx
Mon, 2014-04-21 06:47
Normal topic Homology Model gives output - but completely wrong!
by Julix » Wed, 2012-10-31 10:10
1
2,342 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Homology modeling
by mchldln » Mon, 2009-08-17 13:04
2
2,371 by smlewis
Mon, 2014-04-21 06:47
Normal topic Homology modeling starter script
by gobli033 » Thu, 2010-04-01 07:27
0
938 by gobli033
Mon, 2014-04-21 06:47
Normal topic how build (N-terminal 17 residues) structre /fragment file generation
by venkatazb » Wed, 2016-07-27 23:56
3
1,758 by smlewis
Fri, 2016-07-29 07:43
Normal topic How can move peptide on cleft of enzyme on Flexpepdock?
by phanvy » Thu, 2014-06-05 02:22
4
2,514 by zaldini
Fri, 2015-01-02 05:38
Normal topic How did you begin to learn Rosetta?
by mdeklotz » Mon, 2018-07-30 10:08
1
702 by jkleman
Tue, 2018-07-31 13:19
Normal topic How do I add hydrogen atoms to my PDB file?
by monos_morpheus » Wed, 2011-03-30 03:30
6
8,952 by rmoretti
Mon, 2014-04-21 06:47
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
1,976 by monos_morpheus
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
1,212 by smlewis
Mon, 2014-04-21 06:47
Normal topic How do you implement phosphoserine in ab -initio folding?
by smiruthi » Fri, 2011-12-16 14:45
10
5,849 by brspurri
Mon, 2014-04-21 06:47
Normal topic How does one prevent Rosetta from connecting two separate chains?
by jhbrown » Thu, 2011-12-15 14:08
7
4,019 by Anonymous
Mon, 2014-04-21 06:47
Normal topic How NMR structures can be inputted to Rosetta?
by exchhattu » Mon, 2015-02-09 17:44
1
1,211 by rmoretti
Wed, 2015-02-18 09:19
Normal topic How RosettaCM can perform part of C terminal domain (CTD) structure prediction without proper template structures (coordinates)
by haom » Tue, 2020-09-01 13:21
0
97 by haom
Tue, 2020-09-01 18:50
Normal topic how same random seeds can be used in rosetta for mpi run.
by exchhattu » Wed, 2009-10-28 22:09
1
1,690 by smlewis
Mon, 2014-04-21 06:47
Normal topic How the Rosetta score (dG) is actually related to dH (enthalpy) and dS (entropy)?
by lanselibai » Thu, 2014-12-04 13:16
4
3,766 by lanselibai
Fri, 2014-12-12 10:27
Normal topic How to set the cyana format of distance restraint in rosetta?
by zhisheng » Mon, 2011-04-25 02:21
1
2,234 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to add constrains in flexible peptide docking
by kingbo2008 » Fri, 2011-04-29 07:55
1
1,556 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to allow rosetta to recognize the ASP and protonated ASP?
by Jeffrey_Chen » Mon, 2014-03-24 20:34
2
2,331 by Jeffrey_Chen
Tue, 2014-03-25 23:06
Normal topic How to automatically position new peptides into the binding site of a enzime, in order to run peptide-protein docking approaches
by zaldini » Fri, 2015-01-02 05:53
4
2,644 by zaldini
Wed, 2015-01-07 20:35
Normal topic how to build homology based models?
by albumns » Thu, 2010-06-24 10:27
0
947 by albumns
Mon, 2014-04-21 06:47
Normal topic How to calculate the binding energy of peptide and a protein?
by tianbu » Thu, 2014-02-13 20:44
9
6,738 by tianbu
Mon, 2014-02-17 03:36
Normal topic how to cluster loop?
by albumns » Wed, 2011-01-05 19:48
6
4,112 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to convert fragments to PDB format?
by JadAbbass » Wed, 2015-08-19 04:05
1
1,142 by rmoretti
Wed, 2015-09-02 12:48
Normal topic How to create a native file for Protein-Protein docking
by Kotimedidhi » Mon, 2020-06-22 08:10
0
114 by Kotimedidhi
Mon, 2020-06-22 08:10
Normal topic How to create a rotamer set that includes all possible rotamers of all possible amino acids
by AyushGoyal » Thu, 2014-11-06 10:37
1
1,292 by smlewis
Fri, 2014-11-07 12:03
Normal topic How to deal with Cu-as a ligand or as part of the receptor?
by hanypao » Fri, 2011-09-30 18:50
7
6,701 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How to define a theozyme from the .pdb crystal structure without ligand?
by weifulei » Mon, 2019-05-20 21:18
1
526 by rmoretti
Tue, 2019-07-09 12:31
Normal topic How to define specific residues in alascan ?
by Park » Mon, 2011-06-13 19:56
6
4,477 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to define the surface (???.surf) for surface_docking?
by Anpu » Thu, 2018-09-27 07:34
0
353 by Anpu
Thu, 2018-09-27 23:36
Normal topic how to design a protein complex
by Lindsay » Tue, 2013-11-05 20:24
11
7,788 by Lindsay
Mon, 2014-04-21 06:48
Normal topic How to design a stand-alone loop from a binding interface?
by guangdianzi3 » Fri, 2011-02-11 21:11
1
1,383 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to design binding interface?
by Lindsay » Mon, 2013-12-02 19:06
8
6,641 by rmoretti
Tue, 2019-07-09 12:50
Normal topic How to determine the value size in block of *.cst files?
by weifulei » Sun, 2019-05-05 19:56
1
365 by rmoretti
Tue, 2019-07-09 15:59
Normal topic How to determine the value size in block of *.cst files?
by weifulei » Sun, 2019-05-05 19:56
1
424 by rmoretti
Tue, 2019-07-09 15:48
Normal topic How to do ab initio with fixed part of protein
by eunwook » Tue, 2013-04-16 03:00
11
7,022 by rmoretti
Mon, 2014-04-21 06:47
Normal topic how to do cluster after low resolution protein-protein docking?
by albumns » Sat, 2010-11-27 01:17
4
2,790 by albumns
Mon, 2014-04-21 06:47
Normal topic how to do ensemble docking using rosetta3.1
by lqzhang » Mon, 2010-01-11 10:31
1
1,176 by sid
Mon, 2014-04-21 06:47
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