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Rosetta 3 - General

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Normal topic how to keep modeling ignored ERROR?
by eunwook » Sat, 2013-04-27 05:44
3
2,136 by eunwook
Mon, 2014-04-21 06:47
Normal topic How to judge docking success for two proteins without knowledge of native structure
by jasnyderjr » Fri, 2015-07-10 14:27
1
1,532 by rmoretti
Tue, 2015-07-14 15:27
Normal topic How to integrate Rosetta code to my program?
by Lsg » Tue, 2011-06-28 07:18
3
2,774 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to install Rosetta in Redhat Linux ?
by ajaniharesh » Fri, 2012-02-24 02:32
1
4,185 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to insert a TER line between docking partners
by devroop » Sun, 2012-07-29 13:48
1
2,284 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to input pdb to rosetta format add "missing" residues to pdb file
by zhisheng » Tue, 2011-06-07 09:51
1
2,999 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to input constraints?
by violetsha7 » Wed, 2009-05-13 00:13
7
5,872 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to import SymmDock models into Rosetta for local docking and energy minimization
by devroop » Fri, 2012-07-20 13:20
1
2,261 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to identify selected interface residues
by vijayaraj81 » Mon, 2014-03-31 01:40
3
2,399 by rmoretti
Tue, 2014-04-01 08:12
Normal topic How to get the RMSD between two .pdb structures?
by cossio » Wed, 2014-12-03 05:33
1
2,133 by rmoretti
Wed, 2014-12-03 18:52
Normal topic How to get the GDT_TS?
by JadAbbass » Thu, 2013-09-05 11:59
3
3,406 by rmoretti
Mon, 2014-04-21 06:48
Normal topic how to get reliable results for carbohydrate docking?
by albumns » Sun, 2010-09-05 23:12
3
3,367 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to get multiple chains in PDB from Fold and Dock
by arthuc01 » Tue, 2012-05-29 02:05
9
5,544 by arthuc01
Mon, 2014-04-21 06:47
Normal topic How to get fragment library from robetta server for mre than 1000 residue sequence?
by Danielsebas » Wed, 2019-09-18 07:53
1
429 by rmoretti
Wed, 2019-09-18 10:49
Normal topic How to generate symmdef file for translational symmetry only?
by pitmand » Thu, 2015-05-14 11:34
2
1,731 by pitmand
Tue, 2015-05-26 12:20
Normal topic How to generate score file for loop refinement or modelling?
by zhisheng » Fri, 2011-12-09 05:15
2
2,089 by zhisheng
Mon, 2014-04-21 06:47
Normal topic How to generate constraints of active sites from a pdb file of an enzyme
by Albert » Sun, 2013-05-26 20:07
3
2,181 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic How to generate a symmetry definition file for octahedral symmetry?
by Anonymous » Wed, 2012-08-15 05:20
0
1,718 by Anonymous
Mon, 2014-04-21 06:47
Normal topic How to extract specific pdb from silent files
by eunwook » Tue, 2013-05-14 05:29
5
10,023 by nawsad
Mon, 2014-04-21 06:47
Normal topic How to extract antibody from a set of pdb file may may contain antigen?
by Sunyp_IM » Mon, 2017-11-13 17:11
1
621 by ac.research
Sat, 2017-11-18 06:54
Normal topic how to docking including HETATM
by tricia » Tue, 2009-05-05 22:03
1
1,536 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to dock 3 missing domains onto a multi-domain protein
by tevang » Sun, 2011-04-10 15:22
3
3,265 by smlewis
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
1,208 by sid
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
2,831 by albumns
Mon, 2014-04-21 06:47
Normal topic How to do ab initio with fixed part of protein
by eunwook » Tue, 2013-04-16 03:00
11
7,203 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How to determine the value size in block of *.cst files?
by weifulei » Sun, 2019-05-05 19:56
1
460 by rmoretti
Tue, 2019-07-09 15:48
Normal topic How to determine the value size in block of *.cst files?
by weifulei » Sun, 2019-05-05 19:56
1
391 by rmoretti
Tue, 2019-07-09 15:59
Normal topic how to design binding interface?
by Lindsay » Mon, 2013-12-02 19:06
8
6,756 by rmoretti
Tue, 2019-07-09 12:50
Normal topic How to design a stand-alone loop from a binding interface?
by guangdianzi3 » Fri, 2011-02-11 21:11
1
1,402 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to design a protein complex
by Lindsay » Tue, 2013-11-05 20:24
11
7,924 by Lindsay
Mon, 2014-04-21 06:48
Normal topic How to define the surface (???.surf) for surface_docking?
by Anpu » Thu, 2018-09-27 07:34
0
367 by Anpu
Thu, 2018-09-27 23:36
Normal topic How to define specific residues in alascan ?
by Park » Mon, 2011-06-13 19:56
6
4,547 by smlewis
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
560 by rmoretti
Tue, 2019-07-09 12:31
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
6,801 by rmoretti
Mon, 2014-04-21 06:47
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
1,321 by smlewis
Fri, 2014-11-07 12:03
Normal topic How to create a native file for Protein-Protein docking
by Kotimedidhi » Mon, 2020-06-22 08:10
0
141 by Kotimedidhi
Mon, 2020-06-22 08:10
Normal topic How to convert fragments to PDB format?
by JadAbbass » Wed, 2015-08-19 04:05
1
1,171 by rmoretti
Wed, 2015-09-02 12:48
Normal topic how to cluster loop?
by albumns » Wed, 2011-01-05 19:48
6
4,180 by smlewis
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
6,874 by tianbu
Mon, 2014-02-17 03:36
Normal topic how to build homology based models?
by albumns » Thu, 2010-06-24 10:27
0
959 by albumns
Mon, 2014-04-21 06:47
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
2,690 by zaldini
Wed, 2015-01-07 20:35
Normal topic How to allow rosetta to recognize the ASP and protonated ASP?
by Jeffrey_Chen » Mon, 2014-03-24 20:34
2
2,372 by Jeffrey_Chen
Tue, 2014-03-25 23:06
Normal topic how to add constrains in flexible peptide docking
by kingbo2008 » Fri, 2011-04-29 07:55
1
1,577 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to set the cyana format of distance restraint in rosetta?
by zhisheng » Mon, 2011-04-25 02:21
1
2,246 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
3,823 by lanselibai
Fri, 2014-12-12 10:27
Normal topic how same random seeds can be used in rosetta for mpi run.
by exchhattu » Wed, 2009-10-28 22:09
1
1,713 by smlewis
Mon, 2014-04-21 06:47
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
136 by haom
Tue, 2020-09-01 18:50
Normal topic How NMR structures can be inputted to Rosetta?
by exchhattu » Mon, 2015-02-09 17:44
1
1,241 by rmoretti
Wed, 2015-02-18 09:19
Normal topic How does one prevent Rosetta from connecting two separate chains?
by jhbrown » Thu, 2011-12-15 14:08
7
4,129 by Anonymous
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
5,959 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
1,231 by smlewis
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
2,007 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
9,055 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
738 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
2,571 by zaldini
Fri, 2015-01-02 05:38
Normal topic how build (N-terminal 17 residues) structre /fragment file generation
by venkatazb » Wed, 2016-07-27 23:56
3
1,801 by smlewis
Fri, 2016-07-29 07:43
Normal topic Homology modeling starter script
by gobli033 » Thu, 2010-04-01 07:27
0
950 by gobli033
Mon, 2014-04-21 06:47
Normal topic Homology modeling
by mchldln » Mon, 2009-08-17 13:04
2
2,400 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
2,366 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
2,417 by biofisikx
Mon, 2014-04-21 06:47
Normal topic Histidine protonation
by DmitriiN » Mon, 2016-09-26 13:15
11
9,696 by rmoretti
Mon, 2018-01-15 15:37
Normal topic Histidine phosphorylation by a patch
by felipet » Sat, 2016-07-09 06:51
2
1,662 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
8,260 by albumns
Mon, 2014-04-21 06:47
Normal topic help with perturbation docking please
by einew » Fri, 2011-03-25 16:16
2
2,084 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
6,117 by smlewis
Mon, 2014-04-21 06:47
Normal topic Helix at loop site
by berk » Fri, 2013-05-31 07:04
1
1,331 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
725 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
1,445 by smlewis
Mon, 2014-04-21 06:47
Normal topic Hbond tripped
by alejandro » Mon, 2011-11-21 04:17
3
2,336 by alejandro
Mon, 2014-04-21 06:47
Normal topic HBNetStapleInterface
by sdh_h » Wed, 2016-08-24 03:30
1
877 by smlewis
Wed, 2016-08-24 07:23
Normal topic hbnet
by mintseris » Mon, 2018-03-19 09:02
1
658 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
1,794 by burkheadlab
Mon, 2014-04-21 06:47
Normal topic have trouble with "relax" models
by wszjzhang » Thu, 2010-01-28 10:02
1
1,289 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
1,456 by smlewis
Mon, 2014-04-21 06:47
Normal topic Handling peptide with noncanonical aminoacids
by tigerous » Sat, 2013-12-28 17:16
1
2,401 by rmoretti
Mon, 2014-04-21 06:48
Normal topic H3 modelling scoring function
by aneamtu » Wed, 2017-12-27 23:10
2
937 by aneamtu
Mon, 2018-01-08 23:49
Normal topic Good baseline settings for side chain packing
by pachecoj » Tue, 2015-01-13 19:25
2
2,687 by rmoretti
Wed, 2015-01-21 10:05
Normal topic Give preference to native residue during fixed backbone designing
by tusharranjanmoharana » Mon, 2016-04-04 12:43
6
2,879 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
2,673 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
1,963 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Getting started with Rosetta
by myang » Tue, 2009-04-07 16:25
1
1,616 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
3,649 by rosend
Fri, 2015-12-18 19:39
Normal topic Get nchi for heavy atoms
by pachecoj » Tue, 2014-11-04 19:04
1
1,228 by rmoretti
Tue, 2014-11-11 13:22
Normal topic Generating Protein/NA decoys
by rbeier1 » Mon, 2016-01-11 03:25
1
1,253 by rmoretti
Thu, 2016-04-28 16:25
Normal topic Generating Fragment Libraries for Metal Binding Proteins
by buzb » Wed, 2011-01-26 12:43
1
1,998 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
1,463 by ndousis
Mon, 2014-04-21 06:47
Normal topic Generate structural fragments
by kingljy » Tue, 2011-05-10 20:18
2
3,813 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
1,547 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
2,012 by Trentage
Mon, 2014-04-21 06:47
Normal topic general question about protein docking
by albumns » Mon, 2010-12-13 23:26
1
1,648 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
1,648 by smlewis
Tue, 2016-12-20 10:40
Normal topic General Protein Folding Question
by twopint23oz » Sun, 2012-04-01 22:57
7
3,677 by smlewis
Mon, 2014-04-21 06:47
Normal topic General Forum Suggestion
by jadolfbr » Thu, 2011-09-29 08:11
0
2,155 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic Gaussian Constraint For Dihedrals
by jinli711 » Thu, 2020-07-23 10:47
1
163 by matteoferla
Fri, 2020-07-24 03:06
Normal topic Fusing C-terminal or N-terminal segments onto proteins using Remodel
by achambe » Tue, 2016-01-05 09:39
1
1,425 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
933 by ahmadkhalifa
Fri, 2018-06-29 07:54
Normal topic fragment_picker problem
by adva » Tue, 2012-12-18 01:15
13
7,638 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
1,220 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
1,253 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
5,492 by rmoretti
Mon, 2014-04-21 06:47
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