T0209 IR47, H.influenzae
| Description | Link to file | Date |
| Inputs |
| Submitted sequence(s) | T0209.a2m | 2004 Jul 11 8:04:16 |
| Multiple alignment |
| SAM_t04 multiple alignment in a2m format | T0209.t04.a2m.gz | 2004 Jul 11 8:09:26 |
| SAM_t04 target hidden Markov model | T0209.t04.w0.5.mod | 2004 Jul 11 8:09:30 |
| SAM_t04 multiple alignment---sequence logo (eps format) (pdf format) | T0209.t04.w0.5-logo | 2004 Jul 11 8:09:36 |
| Script for highlighting in rasmol | conserved_t04 | 2004 Jul 11 8:09:38 |
| SAM_t2k multiple alignment in a2m format | T0209.t2k.a2m.gz | 2004 Jul 11 9:46:23 |
| SAM_t2k target hidden Markov model | T0209.t2k.w0.5.mod | 2004 Jul 11 9:46:27 |
| SAM_t2k multiple alignment---sequence logo (eps format) (pdf format) | T0209.t2k.w0.5-logo | 2004 Jul 11 9:46:35 |
| Script for highlighting in rasmol | conserved_t2k | 2004 Jul 11 9:46:35 |
| Secondary Structure Prediction (Explanation of secondary-structure predictions) |
| str2 structure prediction (rdb format) (seq format) | T0209.t2k.str2 | 2004 Jul 11 9:46:36 |
| Script for T0209.t2k.str2 coloring in rasmol | T0209.t2k.str2-color.rasmol | 2004 Jul 11 9:46:38 |
| str2---sequence logo (eps format) (pdf format) | T0209.t2k.str2-logo | 2004 Jul 11 9:46:42 |
| stride-ebghtl structure prediction (rdb format) (seq format) | T0209.t2k.stride-ebghtl | 2004 Jul 11 9:46:28 |
| Script for T0209.t2k.stride-ebghtl coloring in rasmol | T0209.t2k.stride-ebghtl-color.rasmol | 2004 Jul 11 9:46:42 |
| stride-ebghtl---sequence logo (eps format) (pdf format) | T0209.t2k.stride-ebghtl-logo | 2004 Jul 11 9:46:47 |
| dssp-ebghstl structure prediction (rdb format) (seq format) | T0209.t2k.dssp-ebghstl | 2004 Jul 11 9:46:46 |
| Script for T0209.t2k.dssp-ebghstl coloring in rasmol | T0209.t2k.dssp-ebghstl-color.rasmol | 2004 Jul 11 9:46:47 |
| dssp-ebghstl---sequence logo (eps format) (pdf format) | T0209.t2k.dssp-ebghstl-logo | 2004 Jul 11 9:46:52 |
| alpha structure prediction (rdb format) (seq format) | T0209.t2k.alpha | 2004 Jul 11 9:46:52 |
| Script for T0209.t2k.alpha coloring in rasmol | T0209.t2k.alpha-color.rasmol | 2004 Jul 11 9:46:52 |
| alpha---sequence logo (eps format) (pdf format) | T0209.t2k.alpha-logo | 2004 Jul 11 9:46:57 |
| bys structure prediction (rdb format) (seq format) | T0209.t2k.bys | 2004 Jul 11 9:46:57 |
| Script for T0209.t2k.bys coloring in rasmol | T0209.t2k.bys-color.rasmol | 2004 Jul 11 9:46:57 |
| dssp-ehl2 structure prediction (rdb format) (seq format) | T0209.t2k.dssp-ehl2 | 2004 Jul 11 9:47:00 |
| Script for T0209.t2k.dssp-ehl2 coloring in rasmol | T0209.t2k.dssp-ehl2-color.rasmol | 2004 Jul 11 9:47:02 |
| dssp-ehl2---sequence logo (eps format) (pdf format) | T0209.t2k.dssp-ehl2-logo | 2004 Jul 11 9:47:06 |
| CB_burial_14_7 structure prediction (rdb format) (seq format) | T0209.t2k.CB_burial_14_7 | 2004 Jul 11 9:47:06 |
| Script for T0209.t2k.CB_burial_14_7 coloring in rasmol | T0209.t2k.CB_burial_14_7-color.rasmol | 2004 Jul 11 9:47:06 |
| CB_burial_14_7---sequence logo (eps format) (pdf format) | T0209.t2k.CB_burial_14_7-logo | 2004 Jul 11 9:47:11 |
| near-backbone-11 structure prediction (rdb format) (seq format) | T0209.t2k.near-backbone-11 | 2004 Jul 11 9:47:11 |
| Script for T0209.t2k.near-backbone-11 coloring in rasmol | T0209.t2k.near-backbone-11-color.rasmol | 2004 Jul 11 9:47:11 |
| str2 structure prediction (rdb format) (seq format) | T0209.t04.str2 | 2004 Jul 11 9:47:13 |
| Script for T0209.t04.str2 coloring in rasmol | T0209.t04.str2-color.rasmol | 2004 Jul 11 9:47:13 |
| str2---sequence logo (eps format) (pdf format) | T0209.t04.str2-logo | 2004 Jul 11 9:47:18 |
| stride-ebghtl structure prediction (rdb format) (seq format) | T0209.t04.stride-ebghtl | 2004 Jul 11 8:09:32 |
| Script for T0209.t04.stride-ebghtl coloring in rasmol | T0209.t04.stride-ebghtl-color.rasmol | 2004 Jul 11 9:47:18 |
| stride-ebghtl---sequence logo (eps format) (pdf format) | T0209.t04.stride-ebghtl-logo | 2004 Jul 11 9:47:23 |
| dssp-ebghstl structure prediction (rdb format) (seq format) | T0209.t04.dssp-ebghstl | 2004 Jul 11 9:47:23 |
| Script for T0209.t04.dssp-ebghstl coloring in rasmol | T0209.t04.dssp-ebghstl-color.rasmol | 2004 Jul 11 9:47:23 |
| dssp-ebghstl---sequence logo (eps format) (pdf format) | T0209.t04.dssp-ebghstl-logo | 2004 Jul 11 9:47:28 |
| alpha structure prediction (rdb format) (seq format) | T0209.t04.alpha | 2004 Jul 11 9:47:28 |
| Script for T0209.t04.alpha coloring in rasmol | T0209.t04.alpha-color.rasmol | 2004 Jul 11 9:47:28 |
| alpha---sequence logo (eps format) (pdf format) | T0209.t04.alpha-logo | 2004 Jul 11 9:47:33 |
| bys structure prediction (rdb format) (seq format) | T0209.t04.bys | 2004 Jul 11 9:47:33 |
| Script for T0209.t04.bys coloring in rasmol | T0209.t04.bys-color.rasmol | 2004 Jul 11 9:47:33 |
| dssp-ehl2 structure prediction (rdb format) (seq format) | T0209.t04.dssp-ehl2 | 2004 Jul 11 9:47:37 |
| Script for T0209.t04.dssp-ehl2 coloring in rasmol | T0209.t04.dssp-ehl2-color.rasmol | 2004 Jul 11 9:47:36 |
| dssp-ehl2---sequence logo (eps format) (pdf format) | T0209.t04.dssp-ehl2-logo | 2004 Jul 11 9:47:41 |
| CB_burial_14_7 structure prediction (rdb format) (seq format) | T0209.t04.CB_burial_14_7 | 2004 Jul 11 9:47:41 |
| Script for T0209.t04.CB_burial_14_7 coloring in rasmol | T0209.t04.CB_burial_14_7-color.rasmol | 2004 Jul 11 9:47:43 |
| CB_burial_14_7---sequence logo (eps format) (pdf format) | T0209.t04.CB_burial_14_7-logo | 2004 Jul 11 9:47:46 |
| near-backbone-11 structure prediction (rdb format) (seq format) | T0209.t04.near-backbone-11 | 2004 Jul 11 9:47:46 |
| Script for T0209.t04.near-backbone-11 coloring in rasmol | T0209.t04.near-backbone-11-color.rasmol | 2004 Jul 11 9:47:46 |
| Target model scores |
| amino acid single-track target model scores of PDB | T0209.t2k-w0.5-scores.html | 2004 Jul 11 9:49:04 |
| amino acid single-track target model scores of PDB | T0209.t04-w0.5-scores.html | 2004 Jul 11 9:50:10 |
| amino acid/100-30-str2 two-track target model scores | T0209.t2k-100-30-str2-scores.html | 2004 Jul 11 9:51:25 |
| amino acid/100-30-stride-ebghtl two-track target model scores | T0209.t2k-100-30-stride-ebghtl-scores.html | 2004 Jul 11 9:52:42 |
| amino acid/100-30-dssp-ebghstl two-track target model scores | T0209.t2k-100-30-dssp-ebghstl-scores.html | 2004 Jul 11 9:54:00 |
| amino acid/100-30-alpha two-track target model scores | T0209.t2k-100-30-alpha-scores.html | 2004 Jul 11 9:55:14 |
| amino acid/100-30-dssp-ehl2 two-track target model scores | T0209.t2k-100-30-dssp-ehl2-scores.html | 2004 Jul 11 9:56:31 |
| amino acid/100-30-CB_burial_14_7 two-track target model scores | T0209.t2k-100-30-CB_burial_14_7-scores.html | 2004 Jul 11 9:57:50 |
| amino acid/100-40-40-str2+CB_burial_14_7 two-track target model scores | T0209.t2k-100-40-40-str2+CB_burial_14_7-scores.html | 2004 Jul 11 9:59:16 |
| amino acid/100-30-str2 two-track target model scores | T0209.t04-100-30-str2-scores.html | 2004 Jul 11 10:00:11 |
| amino acid/100-30-stride-ebghtl two-track target model scores | T0209.t04-100-30-stride-ebghtl-scores.html | 2004 Jul 11 10:01:03 |
| amino acid/100-30-dssp-ebghstl two-track target model scores | T0209.t04-100-30-dssp-ebghstl-scores.html | 2004 Jul 11 10:01:56 |
| amino acid/100-30-alpha two-track target model scores | T0209.t04-100-30-alpha-scores.html | 2004 Jul 11 10:02:47 |
| amino acid/100-30-dssp-ehl2 two-track target model scores | T0209.t04-100-30-dssp-ehl2-scores.html | 2004 Jul 11 10:03:40 |
| amino acid/100-30-CB_burial_14_7 two-track target model scores | T0209.t04-100-30-CB_burial_14_7-scores.html | 2004 Jul 11 10:04:32 |
| amino acid/100-40-40-str2+CB_burial_14_7 two-track target model scores | T0209.t04-100-40-40-str2+CB_burial_14_7-scores.html | 2004 Jul 11 10:05:29 |
| Template model scores |
| Annotated template model scores | T0209.template-lib-scores.html | 2004 Jul 11 10:15:29 |
| Top Hits |
| Best scoring hits from all models | T0209.t2k.best-scores.html | 2004 Jul 11 10:15:32 |
| Alignments for Top Hits |
| T02 Many Alignments Summary | T0209.t2k.many_alignments.html | 2004 Jul 11 10:17:09 |
| T02 Top Models Summary | T0209.t2k.top_reported_alignments.html | 2004 Jul 11 10:17:45 |
| multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2004 Jul 11 10:17:48 |
| Undertaker (3d) files |
| Multiple alignment for undertaker templates | T0209.t2k-2track-undertaker.a2m | 2004 Jul 11 10:18:25 |
| Undertaker input for top alignments | T0209.t2k.undertaker-align.under | 2004 Jul 11 10:18:24 |
| PDB file with model(s) for top alignments | T0209.t2k.undertaker-align.pdb.gz | 2004 Jul 11 10:19:21 |
| Fragment list for undertaker (from fragfinder) | T0209.t2k.many.frag.gz | 2004 Jul 11 10:19:40 |
| First attempted model using undertaker | decoys/T0209.try1-opt2.pdb.gz | 2004 Jul 11 13:15:43 |
| Significant mutual information between column pairs |
| Mutual information table (align thinned to 30% ID) | T0209.t2k-thin30.mi.rdb | 2004 Jul 11 13:16:13 |
| Mutual information table (align thinned to 35% ID) | T0209.t2k-thin35.mi.rdb | 2004 Jul 11 13:16:30 |
| Mutual information table (align thinned to 40% ID) | T0209.t2k-thin40.mi.rdb | 2004 Jul 11 13:16:38 |
| Mutual information table (align thinned to 50% ID) | T0209.t2k-thin50.mi.rdb | 2004 Jul 11 13:16:45 |
| Mutual information table (align thinned to 62% ID) | T0209.t2k-thin62.mi.rdb | 2004 Jul 11 13:16:52 |
| Mutual information table (align thinned to 30% ID) | T0209.t04-thin30.mi.rdb | 2004 Jul 11 13:17:31 |
| Mutual information table (align thinned to 35% ID) | T0209.t04-thin35.mi.rdb | 2004 Jul 11 13:17:44 |
| Mutual information table (align thinned to 40% ID) | T0209.t04-thin40.mi.rdb | 2004 Jul 11 13:17:54 |
| Mutual information table (align thinned to 50% ID) | T0209.t04-thin50.mi.rdb | 2004 Jul 11 13:18:03 |
| Mutual information table (align thinned to 62% ID) | T0209.t04-thin62.mi.rdb | 2004 Jul 11 13:18:11 |
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