You are here

Rosetta 3 - General

Topic / Topic startersort descending Replies Views Last post
Normal topic Good baseline settings for side chain packing
by pachecoj » Tue, 2015-01-13 19:25
2
3,439 by rmoretti
Wed, 2015-01-21 10:05
Normal topic H3 modelling scoring function
by aneamtu » Wed, 2017-12-27 23:10
2
1,605 by aneamtu
Mon, 2018-01-08 23:49
Normal topic Handling peptide with noncanonical aminoacids
by tigerous » Sat, 2013-12-28 17:16
1
2,971 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
1,969 by smlewis
Mon, 2014-04-21 06:47
Normal topic have trouble with "relax" models
by wszjzhang » Thu, 2010-01-28 10:02
1
1,696 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
2,372 by burkheadlab
Mon, 2014-04-21 06:47
Normal topic hbnet
by mintseris » Mon, 2018-03-19 09:02
1
1,109 by rmoretti
Mon, 2018-03-19 09:08
Normal topic HBNetStapleInterface
by sdh_h » Wed, 2016-08-24 03:30
1
1,255 by smlewis
Wed, 2016-08-24 07:23
Normal topic Hbond tripped
by alejandro » Mon, 2011-11-21 04:17
3
3,073 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
1,880 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
1,042 by fmerino
Mon, 2017-10-16 04:02
Normal topic Helix at loop site
by berk » Fri, 2013-05-31 07:04
1
1,763 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
611 by rmoretti
Tue, 2021-02-09 10:29
Normal topic Help deciphering an input
by Elijah_Hix » Wed, 2021-09-22 11:12
2
510 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
266 by Wenithor
Sat, 2021-10-09 07:23
Normal topic Help with filtering (Rosetta scripts)
by wentlewi » Sat, 2020-10-24 10:12
1
818 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
7,639 by smlewis
Mon, 2014-04-21 06:47
Normal topic help with perturbation docking please
by einew » Fri, 2011-03-25 16:16
2
2,584 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
11,278 by albumns
Mon, 2014-04-21 06:47
Normal topic Histidine phosphorylation by a patch
by felipet » Sat, 2016-07-09 06:51
2
2,273 by felipet
Sat, 2016-07-09 09:50
Normal topic Histidine protonation
by DmitriiN » Mon, 2016-09-26 13:15
11
13,900 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
3,014 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
2,876 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Homology modeling
by mchldln » Mon, 2009-08-17 13:04
2
3,049 by smlewis
Mon, 2014-04-21 06:47
Normal topic Homology modeling starter script
by gobli033 » Thu, 2010-04-01 07:27
0
1,226 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
2,557 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
426 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
3,548 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
1,531 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
11,395 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
2,668 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
1,622 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
7,916 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
5,633 by Anonymous
Mon, 2014-04-21 06:47
Normal topic how does rosetta handle hydrogens?
by patcD » Tue, 2021-08-31 00:48
2
583 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
1,646 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
565 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
2,206 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
5,080 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
2,665 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
1,960 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
9 by mb0261
Thu, 2022-06-30 10:48
Normal topic How to allow rosetta to recognize the ASP and protonated ASP?
by Jeffrey_Chen » Mon, 2014-03-24 20:34
2
3,066 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
3,573 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
1,226 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
9,064 by tianbu
Mon, 2014-02-17 03:36
Normal topic how to cluster loop?
by albumns » Wed, 2011-01-05 19:48
6
5,333 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
1,668 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
508 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
1,856 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
8,714 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
1,178 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
5,863 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
698 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
10,260 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
1,767 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to design binding interface?
by Lindsay » Mon, 2013-12-02 19:06
8
8,768 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
907 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
1,052 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
9,790 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
3,630 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
1,691 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
3,984 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to docking including HETATM
by tricia » Tue, 2009-05-05 22:03
1
2,068 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
429 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
1,061 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
12,675 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
2,075 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
2,913 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
2,697 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
2,380 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
968 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
7,516 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
4,136 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
4,525 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
2,859 by rmoretti
Wed, 2014-12-03 18:52
Normal topic how to identify selected interface residues
by vijayaraj81 » Mon, 2014-03-31 01:40
3
3,341 by rmoretti
Tue, 2014-04-01 08:12
Normal topic How to import SymmDock models into Rosetta for local docking and energy minimization
by devroop » Fri, 2012-07-20 13:20
1
2,710 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to input constraints?
by violetsha7 » Wed, 2009-05-13 00:13
7
7,568 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
3,478 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
2,724 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
4,807 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to integrate Rosetta code to my program?
by Lsg » Tue, 2011-06-28 07:18
3
3,513 by smlewis
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
2,138 by rmoretti
Tue, 2015-07-14 15:27
Normal topic how to keep modeling ignored ERROR?
by eunwook » Sat, 2013-04-27 05:44
3
3,004 by eunwook
Mon, 2014-04-21 06:47
Normal topic how to keep native structure when do loop modeling
by zlni » Sun, 2009-05-03 10:12
4
3,216 by zlni
Mon, 2014-04-21 06:47
Normal topic how to make a combined PDB file?
by fenghc » Mon, 2013-04-01 06:27
3
13,627 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to make a resfile
by dflaher » Fri, 2017-11-03 10:26
3
3,042 by smlewis
Wed, 2017-11-08 12:08
Hot topic how to make benchmark?
by albumns » Wed, 2012-04-04 05:23
23
23,072 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How to make Rosetta's sampling more aggresive ?
by jiongzhang » Mon, 2012-03-12 11:04
1
1,814 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How to minimize only a few key residues' orientation
by Ronghai Cheng » Mon, 2018-11-05 18:37
2
1,711 by Ronghai Cheng
Tue, 2018-11-13 21:56
Normal topic How to model a protein that dimerizes to a small molecule?
by pholland » Wed, 2011-05-25 07:29
3
4,185 by pholland
Mon, 2014-04-21 06:47
Normal topic How to modify disulfide bonds constrain in homology modeling
by eunwook » Mon, 2013-05-13 04:56
1
2,344 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to obtain alignment file for comparative modeling under Rosetta 3.1?
by lennylv » Tue, 2010-05-25 01:29
11
14,720 by sabine
Mon, 2014-04-21 06:47
Normal topic how to optimize the weights?
by Lindsay » Tue, 2012-04-10 07:40
7
4,937 by rmoretti
Mon, 2014-04-21 06:47
Normal topic how to output a structure when scoring it?
by tianbu » Tue, 2012-07-31 09:38
3
3,469 by rmoretti
Mon, 2014-04-21 06:47
Normal topic how to perform model quality assessment of rosetta generated models?
by Danielsebas » Tue, 2019-09-24 05:03
0
633 by Danielsebas
Tue, 2019-09-24 05:03
Normal topic How to prepare the pdblist file for docking_ensmble in Rosetta3.4
by sunlufinal » Mon, 2015-06-01 19:27
1
2,087 by rmoretti
Fri, 2015-07-03 12:58
Normal topic How to prevent rotamers from being pruned from the interaction graph?
by msun » Wed, 2013-04-17 14:19
2
2,195 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to provide multiple templates for Robetta with RosettaCM option?
by lanselibai » Wed, 2021-06-23 14:06
1
455 by lanselibai
Wed, 2021-06-23 14:53
New posts
No new posts
Hot topic with new posts
Hot topic without new posts
Sticky topic
Locked topic
Subscribe to RSS - Rosetta 3 - General