T0263 1wd6, Escherichia coli
| Description | Link to file | Date |
| Inputs |
| Submitted sequence(s) | T0263.a2m | 2004 Aug 4 12:40:51 |
| README file | README | 2004 Aug 4 15:17:22 |
| Provided documentation | T0263.doc.html | 2004 Aug 4 12:40:51 |
| Multiple alignment |
| SAM_t04 multiple alignment in a2m format | T0263.t04.a2m.gz | 2004 Aug 4 15:39:52 |
| SAM_t04 multiple alignment in pretty html format | T0263.t04.pa.html | 2004 Aug 4 15:40:00 |
| SAM_t04 target hidden Markov model | T0263.t04.w0.5.mod | 2004 Aug 4 15:40:05 |
| SAM_t04 multiple alignment---sequence logo (eps format) (pdf format) | T0263.t04.w0.5-logo | 2004 Aug 4 15:40:17 |
| Script for highlighting in rasmol | conserved_t04 | 2004 Aug 4 15:40:18 |
| SAM_t2k multiple alignment in a2m format | T0263.t2k.a2m.gz | 2004 Aug 6 10:39:08 |
| SAM_t2k multiple alignment in pretty html format | T0263.t2k.pa.html | 2004 Aug 6 10:39:19 |
| SAM_t2k target hidden Markov model | T0263.t2k.w0.5.mod | 2004 Aug 6 10:39:26 |
| SAM_t2k multiple alignment---sequence logo (eps format) (pdf format) | T0263.t2k.w0.5-logo | 2004 Aug 6 10:39:46 |
| Script for highlighting in rasmol | conserved_t2k | 2004 Aug 6 10:39:47 |
| Secondary Structure Prediction (Explanation of secondary-structure predictions) |
| str2 structure prediction (rdb format) (seq format) | T0263.t2k.str2 | 2004 Aug 6 10:39:54 |
| Script for T0263.t2k.str2 coloring in rasmol | T0263.t2k.str2-color.rasmol | 2004 Aug 6 10:39:57 |
| str2---sequence logo (eps format) (pdf format) | T0263.t2k.str2-logo | 2004 Aug 6 10:40:06 |
| stride-ebghtl structure prediction (rdb format) (seq format) | T0263.t2k.stride-ebghtl | 2004 Aug 6 10:39:42 |
| Script for T0263.t2k.stride-ebghtl coloring in rasmol | T0263.t2k.stride-ebghtl-color.rasmol | 2004 Aug 6 10:40:07 |
| stride-ebghtl---sequence logo (eps format) (pdf format) | T0263.t2k.stride-ebghtl-logo | 2004 Aug 6 10:40:14 |
| dssp-ebghstl structure prediction (rdb format) (seq format) | T0263.t2k.dssp-ebghstl | 2004 Aug 6 10:40:23 |
| Script for T0263.t2k.dssp-ebghstl coloring in rasmol | T0263.t2k.dssp-ebghstl-color.rasmol | 2004 Aug 6 10:40:23 |
| dssp-ebghstl---sequence logo (eps format) (pdf format) | T0263.t2k.dssp-ebghstl-logo | 2004 Aug 6 10:40:30 |
| alpha structure prediction (rdb format) (seq format) | T0263.t2k.alpha | 2004 Aug 6 10:40:38 |
| Script for T0263.t2k.alpha coloring in rasmol | T0263.t2k.alpha-color.rasmol | 2004 Aug 6 10:40:40 |
| alpha---sequence logo (eps format) (pdf format) | T0263.t2k.alpha-logo | 2004 Aug 6 10:40:44 |
| bys structure prediction (rdb format) (seq format) | T0263.t2k.bys | 2004 Aug 6 10:40:50 |
| Script for T0263.t2k.bys coloring in rasmol | T0263.t2k.bys-color.rasmol | 2004 Aug 6 10:40:52 |
| bys---sequence logo (eps format) (pdf format) | T0263.t2k.bys-logo | 2004 Aug 6 10:40:59 |
| dssp-ehl2 structure prediction (rdb format) (seq format) | T0263.t2k.dssp-ehl2 | 2004 Aug 6 10:41:00 |
| Script for T0263.t2k.dssp-ehl2 coloring in rasmol | T0263.t2k.dssp-ehl2-color.rasmol | 2004 Aug 6 10:41:01 |
| dssp-ehl2---sequence logo (eps format) (pdf format) | T0263.t2k.dssp-ehl2-logo | 2004 Aug 6 10:41:08 |
| CB_burial_14_7 structure prediction (rdb format) (seq format) | T0263.t2k.CB_burial_14_7 | 2004 Aug 6 10:41:17 |
| Script for T0263.t2k.CB_burial_14_7 coloring in rasmol | T0263.t2k.CB_burial_14_7-color.rasmol | 2004 Aug 6 10:41:19 |
| CB_burial_14_7---sequence logo (eps format) (pdf format) | T0263.t2k.CB_burial_14_7-logo | 2004 Aug 6 10:41:23 |
| near-backbone-11 structure prediction (rdb format) (seq format) | T0263.t2k.near-backbone-11 | 2004 Aug 6 10:41:28 |
| Script for T0263.t2k.near-backbone-11 coloring in rasmol | T0263.t2k.near-backbone-11-color.rasmol | 2004 Aug 6 10:41:30 |
| near-backbone-11---sequence logo (eps format) (pdf format) | T0263.t2k.near-backbone-11-logo | 2004 Aug 6 10:41:35 |
| str2 structure prediction (rdb format) (seq format) | T0263.t04.str2 | 2004 Aug 4 15:57:16 |
| Script for T0263.t04.str2 coloring in rasmol | T0263.t04.str2-color.rasmol | 2004 Aug 4 15:57:16 |
| str2---sequence logo (eps format) (pdf format) | T0263.t04.str2-logo | 2004 Aug 4 15:57:24 |
| stride-ebghtl structure prediction (rdb format) (seq format) | T0263.t04.stride-ebghtl | 2004 Aug 4 15:40:09 |
| Script for T0263.t04.stride-ebghtl coloring in rasmol | T0263.t04.stride-ebghtl-color.rasmol | 2004 Aug 4 15:57:24 |
| stride-ebghtl---sequence logo (eps format) (pdf format) | T0263.t04.stride-ebghtl-logo | 2004 Aug 4 15:57:33 |
| dssp-ebghstl structure prediction (rdb format) (seq format) | T0263.t04.dssp-ebghstl | 2004 Aug 4 15:57:34 |
| Script for T0263.t04.dssp-ebghstl coloring in rasmol | T0263.t04.dssp-ebghstl-color.rasmol | 2004 Aug 4 15:57:34 |
| dssp-ebghstl---sequence logo (eps format) (pdf format) | T0263.t04.dssp-ebghstl-logo | 2004 Aug 4 15:57:42 |
| alpha structure prediction (rdb format) (seq format) | T0263.t04.alpha | 2004 Aug 4 15:57:42 |
| Script for T0263.t04.alpha coloring in rasmol | T0263.t04.alpha-color.rasmol | 2004 Aug 4 15:57:42 |
| alpha---sequence logo (eps format) (pdf format) | T0263.t04.alpha-logo | 2004 Aug 4 15:57:50 |
| bys structure prediction (rdb format) (seq format) | T0263.t04.bys | 2004 Aug 4 15:57:51 |
| Script for T0263.t04.bys coloring in rasmol | T0263.t04.bys-color.rasmol | 2004 Aug 4 15:57:51 |
| bys---sequence logo (eps format) (pdf format) | T0263.t04.bys-logo | 2004 Aug 4 15:58:00 |
| dssp-ehl2 structure prediction (rdb format) (seq format) | T0263.t04.dssp-ehl2 | 2004 Aug 4 15:58:00 |
| Script for T0263.t04.dssp-ehl2 coloring in rasmol | T0263.t04.dssp-ehl2-color.rasmol | 2004 Aug 4 15:58:00 |
| dssp-ehl2---sequence logo (eps format) (pdf format) | T0263.t04.dssp-ehl2-logo | 2004 Aug 4 15:58:12 |
| CB_burial_14_7 structure prediction (rdb format) (seq format) | T0263.t04.CB_burial_14_7 | 2004 Aug 4 15:58:12 |
| Script for T0263.t04.CB_burial_14_7 coloring in rasmol | T0263.t04.CB_burial_14_7-color.rasmol | 2004 Aug 4 15:58:12 |
| CB_burial_14_7---sequence logo (eps format) (pdf format) | T0263.t04.CB_burial_14_7-logo | 2004 Aug 4 15:58:20 |
| near-backbone-11 structure prediction (rdb format) (seq format) | T0263.t04.near-backbone-11 | 2004 Aug 4 15:58:20 |
| Script for T0263.t04.near-backbone-11 coloring in rasmol | T0263.t04.near-backbone-11-color.rasmol | 2004 Aug 4 15:58:21 |
| near-backbone-11---sequence logo (eps format) (pdf format) | T0263.t04.near-backbone-11-logo | 2004 Aug 4 15:58:28 |
| Target model scores |
| amino acid single-track target model scores of PDB | T0263.t2k-w0.5-scores.html | 2004 Aug 6 10:44:37 |
| amino acid single-track target model scores of PDB | T0263.t04-w0.5-scores.html | 2004 Aug 4 16:00:55 |
| amino acid/100-30-str2 two-track target model scores | T0263.t2k-100-30-str2-scores.html | 2004 Aug 6 10:47:18 |
| amino acid/100-30-stride-ebghtl two-track target model scores | T0263.t2k-100-30-stride-ebghtl-scores.html | 2004 Aug 6 10:51:06 |
| amino acid/100-30-dssp-ebghstl two-track target model scores | T0263.t2k-100-30-dssp-ebghstl-scores.html | 2004 Aug 6 10:54:51 |
| amino acid/100-30-alpha two-track target model scores | T0263.t2k-100-30-alpha-scores.html | 2004 Aug 6 10:59:03 |
| amino acid/100-30-bys two-track target model scores | T0263.t2k-100-30-bys-scores.html | 2004 Aug 6 11:02:57 |
| amino acid/100-30-dssp-ehl2 two-track target model scores | T0263.t2k-100-30-dssp-ehl2-scores.html | 2004 Aug 6 11:06:37 |
| amino acid/100-30-CB_burial_14_7 two-track target model scores | T0263.t2k-100-30-CB_burial_14_7-scores.html | 2004 Aug 6 11:10:16 |
| amino acid/100-30-near-backbone-11 two-track target model scores | T0263.t2k-100-30-near-backbone-11-scores.html | 2004 Aug 6 11:14:14 |
| amino acid/100-40-40-str2+CB_burial_14_7 two-track target model scores | T0263.t2k-100-40-40-str2+CB_burial_14_7-scores.html | 2004 Aug 6 11:18:26 |
| amino acid/100-30-str2 two-track target model scores | T0263.t04-100-30-str2-scores.html | 2004 Aug 4 16:14:17 |
| amino acid/100-30-stride-ebghtl two-track target model scores | T0263.t04-100-30-stride-ebghtl-scores.html | 2004 Aug 4 16:15:13 |
| amino acid/100-30-dssp-ebghstl two-track target model scores | T0263.t04-100-30-dssp-ebghstl-scores.html | 2004 Aug 4 16:16:08 |
| amino acid/100-30-alpha two-track target model scores | T0263.t04-100-30-alpha-scores.html | 2004 Aug 4 16:17:02 |
| amino acid/100-30-bys two-track target model scores | T0263.t04-100-30-bys-scores.html | 2004 Aug 4 16:17:55 |
| amino acid/100-30-dssp-ehl2 two-track target model scores | T0263.t04-100-30-dssp-ehl2-scores.html | 2004 Aug 4 16:18:50 |
| amino acid/100-30-CB_burial_14_7 two-track target model scores | T0263.t04-100-30-CB_burial_14_7-scores.html | 2004 Aug 4 16:19:42 |
| amino acid/100-30-near-backbone-11 two-track target model scores | T0263.t04-100-30-near-backbone-11-scores.html | 2004 Aug 4 16:20:34 |
| amino acid/100-40-40-str2+CB_burial_14_7 two-track target model scores | T0263.t04-100-40-40-str2+CB_burial_14_7-scores.html | 2004 Aug 4 16:21:34 |
| Template model scores |
| Annotated template model scores | T0263.template-lib-scores.html | 2004 Aug 6 11:23:17 |
| Top Hits |
| Best scoring hits from all models | T0263.t2k.best-scores.html | 2004 Aug 6 11:23:20 |
| Alignments for Top Hits |
| T02 Many Alignments Summary | T0263.t2k.many_alignments.html | 2004 Aug 6 11:40:08 |
| T02 Top Models Summary | T0263.t2k.top_reported_alignments.html | 2004 Aug 6 11:42:23 |
| multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2004 Aug 6 11:42:49 |
| Undertaker (3d) files |
| Multiple alignment for undertaker templates | T0263.t2k-2track-undertaker.a2m | 2004 Aug 6 11:44:36 |
| Undertaker input for top alignments | T0263.t2k.undertaker-align.under | 2004 Aug 6 11:44:37 |
| PDB file with model(s) for top alignments | T0263.t2k.undertaker-align.pdb.gz | 2004 Aug 6 11:52:09 |
| Fragment list for undertaker (from fragfinder) | T0263.t2k.many.frag.gz | 2004 Aug 6 11:53:02 |
| First attempted model using undertaker | decoys/T0263.try1-opt2.pdb.gz | 2004 Aug 6 15:26:11 |
| Significant mutual information between column pairs |
| Mutual information table (align thinned to 30% ID) | T0263.t2k-thin30.mi.rdb | 2004 Aug 6 15:28:46 |
| Mutual information table (align thinned to 35% ID) | T0263.t2k-thin35.mi.rdb | 2004 Aug 6 15:30:06 |
| Mutual information table (align thinned to 40% ID) | T0263.t2k-thin40.mi.rdb | 2004 Aug 6 15:30:57 |
| Mutual information table (align thinned to 50% ID) | T0263.t2k-thin50.mi.rdb | 2004 Aug 6 15:31:41 |
| Mutual information table (align thinned to 62% ID) | T0263.t2k-thin62.mi.rdb | 2004 Aug 6 15:32:08 |
| Mutual information table (align thinned to 30% ID) | T0263.t04-thin30.mi.rdb | 2004 Aug 4 17:41:59 |
| Mutual information table (align thinned to 35% ID) | T0263.t04-thin35.mi.rdb | 2004 Aug 4 17:42:43 |
| Mutual information table (align thinned to 40% ID) | T0263.t04-thin40.mi.rdb | 2004 Aug 4 17:43:09 |
| Mutual information table (align thinned to 50% ID) | T0263.t04-thin50.mi.rdb | 2004 Aug 4 17:43:21 |
| Mutual information table (align thinned to 62% ID) | T0263.t04-thin62.mi.rdb | 2004 Aug 4 17:43:33 |
| contact predictions (rr format) (rr.constraints format) | T0263.280 | 2004 Aug 6 15:32:12 |
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