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Rosetta 3 - General

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Normal topic General Forum Suggestion
by jadolfbr » Thu, 2011-09-29 08:11
0
2,572 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic General Protein Folding Question
by twopint23oz » Sun, 2012-04-01 22:57
7
5,677 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
2,682 by smlewis
Tue, 2016-12-20 10:40
Normal topic general question about protein docking
by albumns » Mon, 2010-12-13 23:26
1
2,210 by JeffreyGray
Mon, 2014-04-21 06:47
Normal topic GeneralizedKIC disulfide closure
by Ken » Tue, 2022-08-16 13:32
2
363 by Ken
Wed, 2022-08-17 08:04
Normal topic GeneralizedKIC side chain closure.
by almeida85 » Mon, 2022-09-19 06:13
0
203 by almeida85
Mon, 2022-09-19 07:22
Normal topic generate full atom coordinates with abinitio rosetta structure prediction
by anusmita_sahoo » Tue, 2010-03-30 00:11
2
2,802 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
2,133 by IAndre
Mon, 2014-04-21 06:47
Normal topic Generate structural fragments
by kingljy » Tue, 2011-05-10 20:18
2
4,754 by pepfolder
Mon, 2014-04-21 06:47
Normal topic Generate template parameter file for a polymer
by anarob » Fri, 2022-06-10 11:05
1
375 by matteoferla
Fri, 2022-06-17 10:38
Normal topic generating 10 lowest energy structures from abinitio
by isengupta13 » Fri, 2010-05-07 11:44
2
2,242 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
2,552 by kaue
Mon, 2014-04-21 06:47
Normal topic Generating Protein/NA decoys
by rbeier1 » Mon, 2016-01-11 03:25
1
2,072 by rmoretti
Thu, 2016-04-28 16:25
Normal topic genkic mover produced an unwanted HN - CA bond
by cttm4a1 » Mon, 2022-06-20 14:25
2
420 by cttm4a1
Mon, 2022-06-20 16:58
Normal topic Get fasta from PDB script correction - Solved
by ialvy » Tue, 2022-08-30 00:00
0
208 by ialvy
Tue, 2022-08-30 00:00
Normal topic Get nchi for heavy atoms
by pachecoj » Tue, 2014-11-04 19:04
1
1,854 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
5,596 by rosend
Fri, 2015-12-18 19:39
Normal topic Getting started with Rosetta
by myang » Tue, 2009-04-07 16:25
1
2,294 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
3,014 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
4,084 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
4,747 by rmoretti
Thu, 2016-04-28 15:19
Normal topic Global ligand docking with Rosetta script and PyRosetta
by tisozaki » Tue, 2021-12-14 17:16
0
450 by tisozaki
Tue, 2021-12-14 17:16
Normal topic Good baseline settings for side chain packing
by pachecoj » Tue, 2015-01-13 19:25
2
3,734 by rmoretti
Wed, 2015-01-21 10:05
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
128 by rmoretti
Mon, 2023-02-06 14:35
Normal topic H3 modelling scoring function
by aneamtu » Wed, 2017-12-27 23:10
2
1,857 by aneamtu
Mon, 2018-01-08 23:49
Normal topic Handling peptide with noncanonical aminoacids
by tigerous » Sat, 2013-12-28 17:16
1
3,174 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
2,207 by smlewis
Mon, 2014-04-21 06:47
Normal topic have trouble with "relax" models
by wszjzhang » Thu, 2010-01-28 10:02
1
1,852 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
2,600 by burkheadlab
Mon, 2014-04-21 06:47
Normal topic hbnet
by mintseris » Mon, 2018-03-19 09:02
1
1,304 by rmoretti
Mon, 2018-03-19 09:08
Normal topic HBNetStapleInterface
by sdh_h » Wed, 2016-08-24 03:30
1
1,445 by smlewis
Wed, 2016-08-24 07:23
Normal topic Hbond tripped
by alejandro » Mon, 2011-11-21 04:17
3
3,318 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
2,075 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
1,188 by fmerino
Mon, 2017-10-16 04:02
Normal topic Helix at loop site
by berk » Fri, 2013-05-31 07:04
1
1,952 by smlewis
Mon, 2014-04-21 06:48
Normal topic Help - Protein-Protein interface design
by Dinesh Kumar » Thu, 2021-01-28 00:47
1
795 by rmoretti
Tue, 2021-02-09 10:29
Normal topic Help deciphering an input
by Elijah_Hix » Wed, 2021-09-22 11:12
2
896 by Elijah_Hix
Thu, 2021-09-23 10:13
Normal topic Help with file in article Kemp elimination catalysts by computational enzyme design
by Wenithor » Sat, 2021-10-09 07:23
0
450 by Wenithor
Sat, 2021-10-09 07:23
Normal topic Help with filtering (Rosetta scripts)
by wentlewi » Sat, 2020-10-24 10:12
1
1,040 by rmoretti
Tue, 2021-02-09 12:35
Normal topic Help with get_pdb.py for PDB file cleaning
by lzx32 » Mon, 2011-03-28 02:11
7
8,187 by smlewis
Mon, 2014-04-21 06:47
Normal topic help with perturbation docking please
by einew » Fri, 2011-03-25 16:16
2
2,771 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
12,290 by albumns
Mon, 2014-04-21 06:47
Normal topic Histidine phosphorylation by a patch
by felipet » Sat, 2016-07-09 06:51
2
2,583 by felipet
Sat, 2016-07-09 09:50
Normal topic Histidine protonation
by DmitriiN » Mon, 2016-09-26 13:15
11
15,451 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
3,252 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
3,063 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Homology modeling
by mchldln » Mon, 2009-08-17 13:04
2
3,299 by smlewis
Mon, 2014-04-21 06:47
Normal topic Homology modeling starter script
by gobli033 » Thu, 2010-04-01 07:27
0
1,348 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
2,869 by smlewis
Fri, 2016-07-29 07:43
Normal topic How can I use InterfaceScore terms in docking as GenericMonteCarlo criterion
by wwwmrzkwww » Sun, 2021-08-15 00:19
0
598 by wwwmrzkwww
Sun, 2021-08-15 00:19
Normal topic How can move peptide on cleft of enzyme on Flexpepdock?
by phanvy » Thu, 2014-06-05 02:22
4
3,942 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
1,778 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
12,439 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
2,935 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
1,792 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
8,664 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
6,117 by Anonymous
Mon, 2014-04-21 06:47
Normal topic how does rosetta handle hydrogens?
by patcD » Tue, 2021-08-31 00:48
2
931 by patcD
Wed, 2021-09-01 06:54
Normal topic How NMR structures can be inputted to Rosetta?
by exchhattu » Mon, 2015-02-09 17:44
1
1,815 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
690 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
2,413 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
5,535 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
2,840 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
2,109 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to add new Movers to Rosetta
by mb0261 » Thu, 2022-06-30 10:48
0
220 by mb0261
Thu, 2022-06-30 10:48
Normal topic How to add uncommon metal elements into Rosetta and make it recognizable?
by JasonIsaac » Thu, 2023-02-09 00:08
4
154 by JasonIsaac
Sat, 2023-02-11 00:44
Normal topic How to allow rosetta to recognize the ASP and protonated ASP?
by Jeffrey_Chen » Mon, 2014-03-24 20:34
2
3,399 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
3,952 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
1,335 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
9,789 by tianbu
Mon, 2014-02-17 03:36
Normal topic how to cluster loop?
by albumns » Wed, 2011-01-05 19:48
6
5,704 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
1,887 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
632 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
2,087 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
9,365 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
1,445 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
6,361 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
825 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
11,096 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
1,925 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to design binding interface?
by Lindsay » Mon, 2013-12-02 19:06
8
9,442 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
1,097 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
1,291 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
10,670 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
3,937 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
1,877 by sid
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
4,249 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to docking including HETATM
by tricia » Tue, 2009-05-05 22:03
1
2,279 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to export high energy state pdb out of backrub?
by whiteqiu » Mon, 2021-03-01 18:32
0
568 by whiteqiu
Mon, 2021-03-01 18:32
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
1,265 by ac.research
Sat, 2017-11-18 06:54
Normal topic How to extract specific pdb from silent files
by eunwook » Tue, 2013-05-14 05:29
5
13,807 by nawsad
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
2,263 by Anonymous
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
3,210 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic How to generate score file for loop refinement or modelling?
by zhisheng » Fri, 2011-12-09 05:15
2
2,902 by zhisheng
Mon, 2014-04-21 06:47
Normal topic How to generate symmdef file for translational symmetry only?
by pitmand » Thu, 2015-05-14 11:34
2
2,655 by pitmand
Tue, 2015-05-26 12:20
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
1,171 by rmoretti
Wed, 2019-09-18 10:49
Normal topic How to get multiple chains in PDB from Fold and Dock
by arthuc01 » Tue, 2012-05-29 02:05
9
8,229 by arthuc01
Mon, 2014-04-21 06:47
Normal topic how to get reliable results for carbohydrate docking?
by albumns » Sun, 2010-09-05 23:12
3
4,446 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to get the GDT_TS?
by JadAbbass » Thu, 2013-09-05 11:59
3
4,895 by rmoretti
Mon, 2014-04-21 06:48
Normal topic How to get the RMSD between two .pdb structures?
by cossio » Wed, 2014-12-03 05:33
1
3,144 by rmoretti
Wed, 2014-12-03 18:52
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