T0254 AAF93879, Vibrio cholerae O1 biovar eltor str. N16961
| Description | Link to file | Date |
| Inputs |
| Submitted sequence(s) | T0254.a2m | 2004 Jul 28 8:55:52 |
| README file | README | 2004 Aug 12 9:37:41 |
| Provided documentation | T0254.doc.html | 2004 Jul 28 8:55:52 |
| Multiple alignment |
| SAM_t04 multiple alignment in a2m format | T0254.t04.a2m.gz | 2004 Jul 29 12:09:04 |
| SAM_t04 multiple alignment in pretty html format | T0254.t04.pa.html | 2004 Jul 29 12:09:10 |
| SAM_t04 target hidden Markov model | T0254.t04.w0.5.mod | 2004 Jul 29 12:09:13 |
| SAM_t04 multiple alignment---sequence logo (eps format) (pdf format) | T0254.t04.w0.5-logo | 2004 Jul 29 12:09:22 |
| Script for highlighting in rasmol | conserved_t04 | 2004 Jul 29 12:09:23 |
| SAM_t2k multiple alignment in a2m format | T0254.t2k.a2m.gz | 2004 Jul 29 12:18:40 |
| SAM_t2k multiple alignment in pretty html format | T0254.t2k.pa.html | 2004 Jul 29 12:18:47 |
| SAM_t2k target hidden Markov model | T0254.t2k.w0.5.mod | 2004 Jul 29 12:18:49 |
| SAM_t2k multiple alignment---sequence logo (eps format) (pdf format) | T0254.t2k.w0.5-logo | 2004 Jul 29 12:18:54 |
| Script for highlighting in rasmol | conserved_t2k | 2004 Jul 29 12:18:54 |
| Secondary Structure Prediction (Explanation of secondary-structure predictions) |
| str2 structure prediction (rdb format) (seq format) | T0254.t2k.str2 | 2004 Jul 29 12:18:55 |
| Script for T0254.t2k.str2 coloring in rasmol | T0254.t2k.str2-color.rasmol | 2004 Jul 29 12:18:55 |
| str2---sequence logo (eps format) (pdf format) | T0254.t2k.str2-logo | 2004 Jul 29 12:18:59 |
| stride-ebghtl structure prediction (rdb format) (seq format) | T0254.t2k.stride-ebghtl | 2004 Jul 29 12:18:50 |
| Script for T0254.t2k.stride-ebghtl coloring in rasmol | T0254.t2k.stride-ebghtl-color.rasmol | 2004 Jul 29 12:19:00 |
| stride-ebghtl---sequence logo (eps format) (pdf format) | T0254.t2k.stride-ebghtl-logo | 2004 Jul 29 12:19:03 |
| dssp-ebghstl structure prediction (rdb format) (seq format) | T0254.t2k.dssp-ebghstl | 2004 Jul 29 12:19:03 |
| Script for T0254.t2k.dssp-ebghstl coloring in rasmol | T0254.t2k.dssp-ebghstl-color.rasmol | 2004 Jul 29 12:19:04 |
| dssp-ebghstl---sequence logo (eps format) (pdf format) | T0254.t2k.dssp-ebghstl-logo | 2004 Jul 29 12:19:07 |
| alpha structure prediction (rdb format) (seq format) | T0254.t2k.alpha | 2004 Jul 29 12:19:08 |
| Script for T0254.t2k.alpha coloring in rasmol | T0254.t2k.alpha-color.rasmol | 2004 Jul 29 12:19:08 |
| alpha---sequence logo (eps format) (pdf format) | T0254.t2k.alpha-logo | 2004 Jul 29 12:19:12 |
| bys structure prediction (rdb format) (seq format) | T0254.t2k.bys | 2004 Jul 29 12:19:13 |
| Script for T0254.t2k.bys coloring in rasmol | T0254.t2k.bys-color.rasmol | 2004 Jul 29 12:19:13 |
| bys---sequence logo (eps format) (pdf format) | T0254.t2k.bys-logo | 2004 Jul 29 12:19:17 |
| dssp-ehl2 structure prediction (rdb format) (seq format) | T0254.t2k.dssp-ehl2 | 2004 Jul 29 12:19:18 |
| Script for T0254.t2k.dssp-ehl2 coloring in rasmol | T0254.t2k.dssp-ehl2-color.rasmol | 2004 Jul 29 12:19:18 |
| dssp-ehl2---sequence logo (eps format) (pdf format) | T0254.t2k.dssp-ehl2-logo | 2004 Jul 29 12:19:22 |
| CB_burial_14_7 structure prediction (rdb format) (seq format) | T0254.t2k.CB_burial_14_7 | 2004 Jul 29 12:19:23 |
| Script for T0254.t2k.CB_burial_14_7 coloring in rasmol | T0254.t2k.CB_burial_14_7-color.rasmol | 2004 Jul 29 12:19:23 |
| CB_burial_14_7---sequence logo (eps format) (pdf format) | T0254.t2k.CB_burial_14_7-logo | 2004 Jul 29 12:19:27 |
| near-backbone-11 structure prediction (rdb format) (seq format) | T0254.t2k.near-backbone-11 | 2004 Jul 29 12:19:28 |
| Script for T0254.t2k.near-backbone-11 coloring in rasmol | T0254.t2k.near-backbone-11-color.rasmol | 2004 Jul 29 12:19:28 |
| near-backbone-11---sequence logo (eps format) (pdf format) | T0254.t2k.near-backbone-11-logo | 2004 Jul 29 12:19:32 |
| str2 structure prediction (rdb format) (seq format) | T0254.t04.str2 | 2004 Jul 29 12:19:33 |
| Script for T0254.t04.str2 coloring in rasmol | T0254.t04.str2-color.rasmol | 2004 Jul 29 12:19:33 |
| str2---sequence logo (eps format) (pdf format) | T0254.t04.str2-logo | 2004 Jul 29 12:19:37 |
| stride-ebghtl structure prediction (rdb format) (seq format) | T0254.t04.stride-ebghtl | 2004 Jul 29 12:09:16 |
| Script for T0254.t04.stride-ebghtl coloring in rasmol | T0254.t04.stride-ebghtl-color.rasmol | 2004 Jul 29 12:19:37 |
| stride-ebghtl---sequence logo (eps format) (pdf format) | T0254.t04.stride-ebghtl-logo | 2004 Jul 29 12:19:41 |
| dssp-ebghstl structure prediction (rdb format) (seq format) | T0254.t04.dssp-ebghstl | 2004 Jul 29 12:19:42 |
| Script for T0254.t04.dssp-ebghstl coloring in rasmol | T0254.t04.dssp-ebghstl-color.rasmol | 2004 Jul 29 12:19:42 |
| dssp-ebghstl---sequence logo (eps format) (pdf format) | T0254.t04.dssp-ebghstl-logo | 2004 Jul 29 12:19:46 |
| alpha structure prediction (rdb format) (seq format) | T0254.t04.alpha | 2004 Jul 29 12:19:46 |
| Script for T0254.t04.alpha coloring in rasmol | T0254.t04.alpha-color.rasmol | 2004 Jul 29 12:19:46 |
| alpha---sequence logo (eps format) (pdf format) | T0254.t04.alpha-logo | 2004 Jul 29 12:19:50 |
| bys structure prediction (rdb format) (seq format) | T0254.t04.bys | 2004 Jul 29 12:19:51 |
| Script for T0254.t04.bys coloring in rasmol | T0254.t04.bys-color.rasmol | 2004 Jul 29 12:19:52 |
| bys---sequence logo (eps format) (pdf format) | T0254.t04.bys-logo | 2004 Jul 29 12:19:56 |
| dssp-ehl2 structure prediction (rdb format) (seq format) | T0254.t04.dssp-ehl2 | 2004 Jul 29 12:19:57 |
| Script for T0254.t04.dssp-ehl2 coloring in rasmol | T0254.t04.dssp-ehl2-color.rasmol | 2004 Jul 29 12:19:57 |
| dssp-ehl2---sequence logo (eps format) (pdf format) | T0254.t04.dssp-ehl2-logo | 2004 Jul 29 12:20:01 |
| CB_burial_14_7 structure prediction (rdb format) (seq format) | T0254.t04.CB_burial_14_7 | 2004 Jul 29 12:20:02 |
| Script for T0254.t04.CB_burial_14_7 coloring in rasmol | T0254.t04.CB_burial_14_7-color.rasmol | 2004 Jul 29 12:20:02 |
| CB_burial_14_7---sequence logo (eps format) (pdf format) | T0254.t04.CB_burial_14_7-logo | 2004 Jul 29 12:20:06 |
| near-backbone-11 structure prediction (rdb format) (seq format) | T0254.t04.near-backbone-11 | 2004 Jul 29 12:20:07 |
| Script for T0254.t04.near-backbone-11 coloring in rasmol | T0254.t04.near-backbone-11-color.rasmol | 2004 Jul 29 12:20:07 |
| near-backbone-11---sequence logo (eps format) (pdf format) | T0254.t04.near-backbone-11-logo | 2004 Jul 29 12:20:11 |
| Target model scores |
| amino acid single-track target model scores of PDB | T0254.t2k-w0.5-scores.html | 2004 Jul 29 12:21:27 |
| amino acid single-track target model scores of PDB | T0254.t04-w0.5-scores.html | 2004 Jul 29 12:22:35 |
| amino acid/100-30-str2 two-track target model scores | T0254.t2k-100-30-str2-scores.html | 2004 Jul 29 12:23:58 |
| amino acid/100-30-stride-ebghtl two-track target model scores | T0254.t2k-100-30-stride-ebghtl-scores.html | 2004 Jul 29 12:25:20 |
| amino acid/100-30-dssp-ebghstl two-track target model scores | T0254.t2k-100-30-dssp-ebghstl-scores.html | 2004 Jul 29 12:26:41 |
| amino acid/100-30-alpha two-track target model scores | T0254.t2k-100-30-alpha-scores.html | 2004 Jul 29 12:28:04 |
| amino acid/100-30-bys two-track target model scores | T0254.t2k-100-30-bys-scores.html | 2004 Jul 29 12:29:25 |
| amino acid/100-30-dssp-ehl2 two-track target model scores | T0254.t2k-100-30-dssp-ehl2-scores.html | 2004 Jul 29 12:30:45 |
| amino acid/100-30-CB_burial_14_7 two-track target model scores | T0254.t2k-100-30-CB_burial_14_7-scores.html | 2004 Jul 29 12:32:04 |
| amino acid/100-30-near-backbone-11 two-track target model scores | T0254.t2k-100-30-near-backbone-11-scores.html | 2004 Jul 29 12:33:21 |
| amino acid/100-40-40-str2+CB_burial_14_7 two-track target model scores | T0254.t2k-100-40-40-str2+CB_burial_14_7-scores.html | 2004 Jul 29 12:34:48 |
| amino acid/100-30-str2 two-track target model scores | T0254.t04-100-30-str2-scores.html | 2004 Jul 29 12:35:41 |
| amino acid/100-30-stride-ebghtl two-track target model scores | T0254.t04-100-30-stride-ebghtl-scores.html | 2004 Jul 29 12:36:33 |
| amino acid/100-30-dssp-ebghstl two-track target model scores | T0254.t04-100-30-dssp-ebghstl-scores.html | 2004 Jul 29 12:37:28 |
| amino acid/100-30-alpha two-track target model scores | T0254.t04-100-30-alpha-scores.html | 2004 Jul 29 12:38:20 |
| amino acid/100-30-bys two-track target model scores | T0254.t04-100-30-bys-scores.html | 2004 Jul 29 12:39:15 |
| amino acid/100-30-dssp-ehl2 two-track target model scores | T0254.t04-100-30-dssp-ehl2-scores.html | 2004 Jul 29 12:40:08 |
| amino acid/100-30-CB_burial_14_7 two-track target model scores | T0254.t04-100-30-CB_burial_14_7-scores.html | 2004 Jul 29 12:41:02 |
| amino acid/100-30-near-backbone-11 two-track target model scores | T0254.t04-100-30-near-backbone-11-scores.html | 2004 Jul 29 12:41:55 |
| amino acid/100-40-40-str2+CB_burial_14_7 two-track target model scores | T0254.t04-100-40-40-str2+CB_burial_14_7-scores.html | 2004 Jul 29 12:42:53 |
| Template model scores |
| Annotated template model scores | T0254.template-lib-scores.html | 2004 Jul 29 12:50:35 |
| Top Hits |
| Best scoring hits from all models | T0254.t2k.best-scores.html | 2004 Jul 29 12:50:39 |
| Alignments for Top Hits |
| T02 Many Alignments Summary | T0254.t2k.many_alignments.html | 2004 Jul 29 12:51:35 |
| T02 Top Models Summary | T0254.t2k.top_reported_alignments.html | 2004 Jul 29 12:51:38 |
| multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2004 Jul 29 21:36:15 |
| Undertaker (3d) files |
| Multiple alignment for undertaker templates | T0254.t2k-2track-undertaker.a2m | 2004 Aug 12 9:40:24 |
| Undertaker input for top alignments | T0254.t2k.undertaker-align.under | 2004 Jul 29 12:52:17 |
| PDB file with model(s) for top alignments | T0254.t2k.undertaker-align.pdb.gz | 2004 Aug 12 9:41:27 |
| Fragment list for undertaker (from fragfinder) | T0254.t04.many.frag.gz | 2004 Aug 12 9:41:48 |
| Fragment list for undertaker (from fragfinder) | T0254.t2k.many.frag.gz | 2004 Jul 29 12:53:27 |
| First attempted model using undertaker | decoys/T0254.try1-opt2.pdb.gz | 2004 Jul 29 22:30:34 |
| Significant mutual information between column pairs |
| Mutual information table (align thinned to 30% ID) | T0254.t2k-thin30.mi.rdb | 2004 Jul 29 14:15:02 |
| Mutual information table (align thinned to 35% ID) | T0254.t2k-thin35.mi.rdb | 2004 Jul 29 14:15:33 |
| Mutual information table (align thinned to 40% ID) | T0254.t2k-thin40.mi.rdb | 2004 Jul 29 14:16:04 |
| Mutual information table (align thinned to 50% ID) | T0254.t2k-thin50.mi.rdb | 2004 Jul 29 14:16:23 |
| Mutual information table (align thinned to 62% ID) | T0254.t2k-thin62.mi.rdb | 2004 Jul 29 14:16:43 |
| Mutual information table (align thinned to 30% ID) | T0254.t04-thin30.mi.rdb | 2004 Jul 29 14:17:27 |
| Mutual information table (align thinned to 35% ID) | T0254.t04-thin35.mi.rdb | 2004 Jul 29 14:17:59 |
| Mutual information table (align thinned to 40% ID) | T0254.t04-thin40.mi.rdb | 2004 Jul 29 14:18:23 |
| Mutual information table (align thinned to 50% ID) | T0254.t04-thin50.mi.rdb | 2004 Jul 29 14:18:38 |
| Mutual information table (align thinned to 62% ID) | T0254.t04-thin62.mi.rdb | 2004 Jul 29 14:18:56 |
| contact predictions (rr format) (rr.constraints format) | T0254.280 | 2004 Aug 10 21:47:20 |
Please cite: Karplus, K. and Karchin, R. and Barrett, C. and Tu, S. and Cline, M. and Diekhans, M. and Grate, L. and Casper, J. and Hughey, R. ``What is the value added by human intervention in protein structure prediction?'' Proteins: Structure Function and Genetics 45(S5):86-91,2001
SAM_T02 web system designed by Rachel Karchin and Kevin Karplus rachelk@soe.ucsc.edu karplus@soe.ucsc.edu