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Rosetta 3 - Applications

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Sticky topic Sticky: FAQ
by admin » Mon, 2010-08-30 04:18
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7,235 by admin
Fri, 2015-09-04 16:17
Normal topic I want some help for pHDock application
by leygkn » Mon, 2020-09-21 18:38
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16 by leygkn
Mon, 2020-09-21 18:38
Normal topic When using "screening job files" in small molecule-docking I get: Residue type already exists in the cache Error
by Martin Floor » Thu, 2020-09-17 06:01
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86 by nannemdp
Mon, 2020-09-21 08:50
Normal topic minimize_with_cst and convert_to_cst_file for ddG_monomer issues/confusion
by Kharlamov1317a » Mon, 2020-09-21 08:46
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22 by Kharlamov1317a
Mon, 2020-09-21 08:46
Normal topic Trouble running MPI docking protocol, please help!
by Rob_Barringer » Tue, 2020-08-18 06:40
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87 by ssrb
Sun, 2020-09-20 16:06
Normal topic Strong bias in sampling observed in RosettaDock
by chenna » Thu, 2020-08-27 22:23
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111 by ssrb
Sun, 2020-09-20 15:50
Normal topic Building loop extensions in a membrane protein with Remodel
by benhardy » Tue, 2020-06-02 08:21
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209 by benhardy
Sun, 2020-09-20 11:15
Normal topic Pepspec Anchor Dock
by Soler » Fri, 2020-09-18 08:09
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36 by Soler
Fri, 2020-09-18 08:09
Normal topic Segmentation fault (core dumped) in rosetta_scripts.default.linuxgccrelease after blueprint file reading
by Corvin » Tue, 2020-06-30 00:36
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371 by matteoferla
Fri, 2020-09-18 01:24
Normal topic FASTA for Octopus
by Smbat » Wed, 2020-09-16 05:40
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36 by rmoretti
Wed, 2020-09-16 22:11
Normal topic Pepspec Anchor Dock
by Soler » Wed, 2020-09-16 19:08
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39 by Soler
Wed, 2020-09-16 19:08
Normal topic BuildPeptide - Using Phosphorylated and Sulfated Tyrosine
by jlawrie » Thu, 2020-09-03 14:29
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119 by jlawrie
Wed, 2020-09-16 10:05
Normal topic FlexPepDocking
by jlawrie » Tue, 2020-09-15 12:52
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31 by jlawrie
Tue, 2020-09-15 12:52
Normal topic 'standard.wts' does not exist
by almeida85 » Mon, 2020-09-14 02:26
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56 by rmoretti
Mon, 2020-09-14 06:36
Normal topic Number of max allowed mutations from WT sequence
by mouung » Fri, 2020-09-04 02:33
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116 by rmoretti
Sun, 2020-09-06 10:10
Normal topic Scoring docking error
by almeida85 » Wed, 2020-09-02 01:32
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103 by almeida85
Wed, 2020-09-02 06:14
Normal topic make_fragments.pl error
by almeida85 » Mon, 2020-08-31 04:39
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96 by almeida85
Tue, 2020-09-01 01:29
Normal topic Extracting top score PIPER models
by almeida85 » Mon, 2020-08-31 07:17
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74 by almeida85
Mon, 2020-08-31 07:17
Normal topic density scoring
by Tianyang89 » Sat, 2020-08-29 04:54
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104 by danpf
Sun, 2020-08-30 22:23
Normal topic RosettaAntibody3 - How can I model an extended H3?
by brspurri » Fri, 2020-08-28 09:11
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91 by brspurri
Fri, 2020-08-28 09:11
Normal topic Rosetta_CM error unrecognized atom 'CS' this atom is not in PDB
by rlwoltz » Thu, 2019-01-24 19:43
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1,103 by bjharris
Sun, 2020-08-23 14:03
Normal topic Global Docking with carbohydrates
by ChiauShu » Sat, 2020-08-22 20:16
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72 by ChiauShu
Sat, 2020-08-22 20:16
Normal topic Successful RosettaCM?
by jlawrie » Wed, 2020-08-19 06:53
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85 by jlawrie
Thu, 2020-08-20 11:00
Normal topic Fewer than expected structures in clustering output
by fabiotrovato » Thu, 2020-08-20 00:59
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53 by fabiotrovato
Thu, 2020-08-20 00:59
Normal topic RosettaAntibody3 is failing with "Error: no input sequences were specified!"
by brspurri » Sun, 2020-08-16 16:16
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135 by brspurri
Tue, 2020-08-18 09:57
Normal topic clustering output file has few structures
by fabiotrovato » Mon, 2020-08-17 11:37
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63 by fabiotrovato
Mon, 2020-08-17 11:37
Normal topic RosettaCM
by jlawrie » Fri, 2020-08-14 14:09
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73 by jlawrie
Fri, 2020-08-14 14:09
Normal topic mpirun docking_protocol
by NanB » Mon, 2020-08-03 11:38
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121 by ssrb
Fri, 2020-08-14 09:18
Normal topic Docking-I_sc values do not correlate
by jlawrie » Wed, 2020-08-12 08:08
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92 by jlawrie
Wed, 2020-08-12 08:57
Normal topic Homology Modeling-no PDB output
by jlawrie » Wed, 2020-08-12 06:30
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84 by jlawrie
Wed, 2020-08-12 08:56
Normal topic Modeling-Using RosettaCM
by jlawrie » Wed, 2020-08-12 08:46
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60 by jlawrie
Wed, 2020-08-12 08:47
Normal topic Docking-RMS value nan
by jlawrie » Wed, 2020-08-12 07:03
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84 by jlawrie
Wed, 2020-08-12 07:27
Normal topic Error when trying docking protocol with different ligand
by scyphs » Wed, 2020-08-05 04:37
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116 by scyphs
Mon, 2020-08-10 08:09
Normal topic how to know the precedure of solving a actural bio problem? like interface design?
by qq7678500549 » Thu, 2020-08-06 18:45
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100 by qq7678500549
Sun, 2020-08-09 18:59
Normal topic De novo water predictions using SPaDES
by MNP1986 » Mon, 2019-03-25 07:53
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433 by matteoferla
Tue, 2020-08-04 09:30
Normal topic Bug Report - Encoding issue
by daniloboskovic » Tue, 2020-08-04 07:02
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46 by daniloboskovic
Tue, 2020-08-04 07:02
Normal topic pepspec anchor dock
by Andre Serobian » Tue, 2020-07-28 05:51
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97 by Andre Serobian
Tue, 2020-07-28 23:26
Normal topic Zero residues error in docking
by cjy318 » Tue, 2020-07-28 19:47
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69 by cjy318
Tue, 2020-07-28 19:47
Normal topic RosettaAntibody3 core.pose.util error
by linhhoang157 » Tue, 2020-07-28 12:40
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82 by linhhoang157
Tue, 2020-07-28 12:40
Normal topic clean_pdb not working
by Andre Serobian » Thu, 2020-07-23 04:48
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167 by rmoretti
Tue, 2020-07-28 08:24
Normal topic Comparative modeling of metalloproteins
by ctqwong » Sun, 2020-07-12 13:51
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187 by ctqwong
Mon, 2020-07-27 01:48
Normal topic How to choose designed antibody
by Sunyp_IM » Wed, 2020-06-24 10:06
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319 by jadolfbr
Fri, 2020-07-24 07:24
Normal topic How many iterations of remodel is enough?
by daniloboskovic » Thu, 2020-07-16 08:07
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92 by daniloboskovic
Thu, 2020-07-16 08:14
Normal topic Translate mover chain X doesnot exist.
by surya » Thu, 2020-07-09 08:36
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321 by rmoretti
Tue, 2020-07-14 10:54
Normal topic Warning: Fold tree is not set properly for density scoring
by ahansel » Mon, 2020-07-13 10:50
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131 by danpf
Tue, 2020-07-14 10:27
Normal topic manually defining CDRs in antibody modelling
by gard.nelson » Fri, 2020-07-10 13:31
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131 by gard.nelson
Fri, 2020-07-10 13:31
Normal topic Problem with mpirun/mpiexec
by ahansel » Fri, 2020-07-10 08:37
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185 by rmoretti
Fri, 2020-07-10 09:59
Normal topic Segmentation Fault during prepacking
by Sunyp_IM » Fri, 2020-06-12 11:24
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320 by Sunyp_IM
Thu, 2020-07-09 18:40
Normal topic Metal Ion in symmetric design
by tschiex » Wed, 2020-07-08 05:28
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117 by tschiex
Wed, 2020-07-08 05:28
Normal topic PEPSPEC
by Neeraj » Wed, 2018-01-03 02:24
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595 by Andre Serobian
Wed, 2020-07-08 04:44
Normal topic Does antibody_numbering_converter support camelid antibody?
by mxp » Tue, 2020-07-07 01:21
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69 by mxp
Tue, 2020-07-07 01:21
Normal topic zero standard deviation of I_sc in protein-protein docking
by rohi » Fri, 2020-07-03 22:19
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101 by rohi
Fri, 2020-07-03 22:20
Normal topic OptimizeMembranePositionMover - This element is not expected
by bjharris » Wed, 2020-07-01 23:21
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190 by bjharris
Thu, 2020-07-02 11:09
Normal topic LoopModeler mover unable to determine cut point
by gszwabowski » Mon, 2020-06-01 13:12
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168 by matteoferla
Thu, 2020-07-02 07:27
Normal topic ligand_docking: ligand preparation
by Alison_Yajie » Thu, 2020-07-02 07:05
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107 by Alison_Yajie
Thu, 2020-07-02 07:10
Normal topic kcenters_clustering_of_fragments
by bjharris » Mon, 2019-07-01 16:16
1
353 by bjharris
Wed, 2020-07-01 23:25
Normal topic Scoring after HBNet
by HHL_SIUC » Wed, 2020-07-01 10:49
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96 by HHL_SIUC
Wed, 2020-07-01 10:49
Normal topic Noncanonical amino acids
by wsgosal » Tue, 2014-03-18 05:29
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3,196 by Nolanm15
Tue, 2020-06-30 08:43
Normal topic "core.kinematics.FoldTree" error upon running RAbD
by Sunyp_IM » Fri, 2020-06-26 17:27
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187 by Sunyp_IM
Fri, 2020-06-26 20:57
Normal topic ligand_docking ligand preparation
by Alison_Yajie » Thu, 2020-05-21 10:21
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248 by Alison_Yajie
Wed, 2020-06-24 12:38
Normal topic Ligand docking with constraint
by Alison_Yajie » Wed, 2020-06-24 12:34
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100 by Alison_Yajie
Wed, 2020-06-24 12:34
Normal topic How to create a native file for Protein-Protein docking
by Kotimedidhi » Fri, 2020-06-19 08:58
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216 by Kotimedidhi
Mon, 2020-06-22 16:19
Normal topic How to select docked models
by Sunyp_IM » Mon, 2020-06-22 00:50
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134 by ssrb
Mon, 2020-06-22 13:12
Normal topic Coupled Moves crash with Membrane Protein - residue_edge is undefined for root vertex
by benhardy » Mon, 2020-06-15 09:33
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219 by benhardy
Fri, 2020-06-19 07:55
Normal topic Residue selector
by Alison_Yajie » Wed, 2020-06-17 19:57
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122 by Alison_Yajie
Thu, 2020-06-18 09:47
Normal topic Constraint generator
by Alison_Yajie » Wed, 2020-06-17 20:14
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157 by Alison_Yajie
Wed, 2020-06-17 20:35
Normal topic metalloprotein ab initio with glutamic acid
by inorgchem » Tue, 2020-06-16 20:45
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98 by inorgchem
Tue, 2020-06-16 20:45
Normal topic RosettaCM: An internal error has occurred when "Running the Hybridize mover"
by haom » Mon, 2020-06-15 05:56
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232 by haom
Tue, 2020-06-16 05:55
Normal topic The difference between the H1 regions of modeled camelid antibody and the crystal structure.
by Sunyp_IM » Sun, 2020-06-07 02:34
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171 by nannemdp
Sun, 2020-06-07 08:01
Normal topic The usage of antibody_H3.linuxgccrelease
by Sunyp_IM » Thu, 2020-05-28 22:50
2
226 by Sunyp_IM
Thu, 2020-06-04 08:20
Normal topic "Residue 7 was disulfide bonded but had no partner" with antibody.linuxgccrelease
by Sunyp_IM » Thu, 2020-06-04 05:53
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110 by Sunyp_IM
Thu, 2020-06-04 05:54
Normal topic RosettaAntibodyDesign: How can I run the protocol without allowing design?
by brspurri » Tue, 2020-05-26 08:12
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355 by brspurri
Wed, 2020-06-03 13:20
Normal topic AbinitioRelax detect_disulf_tolerance
by aarono » Tue, 2020-06-02 00:13
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164 by aarono
Tue, 2020-06-02 00:13
Normal topic ligand_docking_error
by Alison_Yajie » Mon, 2020-04-20 12:27
3
422 by YuFei
Sat, 2020-05-30 00:12
Normal topic Problems with mpi version of antibody.linuxgccrelease
by Sunyp_IM » Thu, 2020-05-28 23:06
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154 by Sunyp_IM
Thu, 2020-05-28 23:07
Normal topic mp_transform optimize with franklin2019 scoring
by benhardy » Thu, 2020-05-28 08:35
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188 by benhardy
Thu, 2020-05-28 08:45
Normal topic What is a rational minimal value for the "-nstruct" option
by Sunyp_IM » Fri, 2020-05-22 01:28
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312 by nannemdp
Sun, 2020-05-24 14:46
Normal topic cartesian_ddg crashes when the mutfile contains multiple mutations to non-canonical residues
by ValentinaSora » Sun, 2020-05-24 12:32
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167 by ValentinaSora
Sun, 2020-05-24 12:32
Normal topic relax and movemap
by Alison_Yajie » Wed, 2020-05-20 21:27
3
295 by smlewis
Thu, 2020-05-21 21:05
Normal topic Changing rosetta scoring to favour less hydrophobic areas
by daniloboskovic » Thu, 2020-05-21 03:03
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177 by vmulligan
Thu, 2020-05-21 18:33
Normal topic ligand_docking: ligand preparation
by Alison_Yajie » Thu, 2020-05-21 09:42
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115 by Alison_Yajie
Thu, 2020-05-21 09:42
Normal topic Modelling temperature dependent RNA structures
by tuleshwori » Tue, 2020-05-19 01:16
2
214 by tuleshwori
Thu, 2020-05-21 02:08
Normal topic Rosetta Antibody Design: Error with foldtree: problem with the fold_tree:biggest_label != num_jump 2 1
by cm21 » Wed, 2020-05-20 08:55
2
240 by cm21
Wed, 2020-05-20 11:22
Normal topic Rna Denovo
by helderveras » Wed, 2020-05-06 08:40
5
437 by everyday847
Wed, 2020-05-20 08:52
Normal topic Side-chain grafting at the fixed protein and position
by Kazu » Wed, 2020-05-20 08:49
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115 by Kazu
Wed, 2020-05-20 08:49
Normal topic Transmembrane helix fold-and-dock?
by sarah_b » Tue, 2020-05-12 02:09
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341 by jkleman
Tue, 2020-05-19 15:02
Normal topic protein relax
by Alison_Yajie » Tue, 2020-05-19 08:29
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123 by Alison_Yajie
Tue, 2020-05-19 08:29
Normal topic RosettaAntibodyDesign] How can I use run_relax and run_snugdock as part of my command and workflow?
by brspurri » Thu, 2020-05-14 11:15
2
232 by brspurri
Thu, 2020-05-14 12:24
Normal topic Multistate design issues with -run:msd_job_dist option and MSDMover
by elaine.thai » Wed, 2020-05-13 18:07
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172 by elaine.thai
Wed, 2020-05-13 18:07
Normal topic Flex_ddG crashes when attempting to move 2 chains (e.g. chains_to_move = A,C)
by jcampecino » Wed, 2020-05-13 12:22
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151 by jcampecino
Wed, 2020-05-13 12:22
Normal topic How to run partial_thread in RosettaCM when residure are more than 9999?
by lanselibai » Mon, 2020-05-11 22:43
2
291 by lanselibai
Tue, 2020-05-12 20:25
Normal topic How to concatenate the 3-mer and 9-mer files for RosettaCM?
by lanselibai » Fri, 2020-05-08 05:38
5
462 by danpf
Tue, 2020-05-12 10:58
Normal topic Template/Input length mismatch error during RosettaCM
by marinok » Mon, 2020-05-04 13:12
4
359 by marinok
Mon, 2020-05-11 12:48
Normal topic General question regarding ligand-docking
by Alison_Yajie » Thu, 2020-05-07 09:48
0
143 by Alison_Yajie
Thu, 2020-05-07 09:48
Normal topic Can the Rosetta Antibody Design (RAbD) protocol incorporate glycans?
by ccottrell » Tue, 2020-05-05 20:30
5
413 by jadolfbr
Wed, 2020-05-06 11:37
Normal topic Ligand docking at specific orientation
by ShiranBZ » Mon, 2020-04-13 20:46
1
225 by matteoferla
Mon, 2020-05-04 02:02
Normal topic can remodel add loops in one chain in multichain PDB structure?
by ksteczk » Fri, 2020-05-01 06:26
1
191 by matteoferla
Mon, 2020-05-04 01:43
Normal topic BUG REPORT: Remodel Resfile ERROR: LEU was added more than once?
by daniloboskovic » Wed, 2020-04-29 01:17
2
265 by daniloboskovic
Wed, 2020-04-29 05:51
Normal topic RosettaDesign error with Option file open failed
by xingqing326 » Sun, 2020-04-19 01:56
4
409 by xingqing326
Tue, 2020-04-21 19:11
Normal topic DNA-protein docking
by ksteczk » Sat, 2020-04-11 11:23
0
208 by ksteczk
Sat, 2020-04-11 11:23

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