T0203 At5g08170, Arabidopsis
| Description | Link to file | Date |
| Inputs |
| Submitted sequence(s) | T0203.a2m | 2004 Jun 14 16:44:26 |
| README file | README | 2004 Jul 2 18:34:32 |
| Provided documentation | T0203.doc.html | 2004 Jun 15 8:02:32 |
| Multiple alignment |
| SAM_t04 multiple alignment in a2m format | T0203.t04.a2m.gz | 2004 Jun 15 8:36:35 |
| SAM_t04 multiple alignment in pretty html format | T0203.t04.pa.html | 2004 Jun 15 8:36:42 |
| SAM_t04 target hidden Markov model | T0203.t04.w0.5.mod | 2004 Jun 15 8:36:46 |
| SAM_t04 multiple alignment---sequence logo (eps format) (pdf format) | T0203.t04.w0.5-logo | 2004 Jun 16 7:59:24 |
| Script for highlighting in rasmol | conserved_t04 | 2004 Jul 1 6:48:40 |
| SAM_t2k multiple alignment in a2m format | T0203.t2k.a2m.gz | 2004 Jun 15 8:44:29 |
| SAM_t2k multiple alignment in pretty html format | T0203.t2k.pa.html | 2004 Jun 15 8:44:34 |
| SAM_t2k target hidden Markov model | T0203.t2k.w0.5.mod | 2004 Jun 15 8:44:37 |
| SAM_t2k multiple alignment---sequence logo (eps format) (pdf format) | T0203.t2k.w0.5-logo | 2004 Jun 15 9:35:51 |
| Script for highlighting in rasmol | conserved_t2k | 2004 Jul 1 6:48:40 |
| Secondary Structure Prediction (Explanation of secondary-structure predictions) |
| str2 structure prediction (rdb format) (seq format) | T0203.t2k.str2 | 2004 Jun 15 8:44:43 |
| Script for T0203.t2k.str2 coloring in rasmol | T0203.t2k.str2-color.rasmol | 2004 Jun 15 8:44:43 |
| str2---sequence logo (eps format) (pdf format) | T0203.t2k.str2-logo | 2004 Jun 15 8:44:47 |
| stride-ebghtl structure prediction (rdb format) (seq format) | T0203.t2k.stride-ebghtl | 2004 Jun 15 8:44:39 |
| Script for T0203.t2k.stride-ebghtl coloring in rasmol | T0203.t2k.stride-ebghtl-color.rasmol | 2004 Jun 15 8:44:48 |
| stride-ebghtl---sequence logo (eps format) (pdf format) | T0203.t2k.stride-ebghtl-logo | 2004 Jun 15 8:44:51 |
| dssp-ebghstl structure prediction (rdb format) (seq format) | T0203.t2k.dssp-ebghstl | 2004 Jun 15 8:44:51 |
| Script for T0203.t2k.dssp-ebghstl coloring in rasmol | T0203.t2k.dssp-ebghstl-color.rasmol | 2004 Jun 15 8:44:52 |
| dssp-ebghstl---sequence logo (eps format) (pdf format) | T0203.t2k.dssp-ebghstl-logo | 2004 Jun 15 8:44:55 |
| alpha structure prediction (rdb format) (seq format) | T0203.t2k.alpha | 2004 Jun 15 8:44:56 |
| Script for T0203.t2k.alpha coloring in rasmol | T0203.t2k.alpha-color.rasmol | 2004 Jun 15 8:44:56 |
| alpha---sequence logo (eps format) (pdf format) | T0203.t2k.alpha-logo | 2004 Jun 15 8:45:00 |
| bys structure prediction (rdb format) (seq format) | T0203.t2k.bys | 2004 Jun 15 8:45:01 |
| Script for T0203.t2k.bys coloring in rasmol | T0203.t2k.bys-color.rasmol | 2004 Jun 15 8:45:01 |
| dssp-ehl2 structure prediction (rdb format) (seq format) | T0203.t2k.dssp-ehl2 | 2004 Jun 15 8:45:02 |
| Script for T0203.t2k.dssp-ehl2 coloring in rasmol | T0203.t2k.dssp-ehl2-color.rasmol | 2004 Jun 15 8:45:02 |
| dssp-ehl2---sequence logo (eps format) (pdf format) | T0203.t2k.dssp-ehl2-logo | 2004 Jun 15 8:45:05 |
| CB_burial_14_7 structure prediction (rdb format) (seq format) | T0203.t2k.CB_burial_14_7 | 2004 Jun 15 9:35:55 |
| Script for T0203.t2k.CB_burial_14_7 coloring in rasmol | T0203.t2k.CB_burial_14_7-color.rasmol | 2004 Jun 15 9:35:55 |
| CB_burial_14_7---sequence logo (eps format) (pdf format) | T0203.t2k.CB_burial_14_7-logo | 2004 Jun 15 9:36:00 |
| near-backbone-11 structure prediction (rdb format) (seq format) | T0203.t2k.near-backbone-11 | 2004 Jul 1 6:38:51 |
| Script for T0203.t2k.near-backbone-11 coloring in rasmol | T0203.t2k.near-backbone-11-color.rasmol | 2004 Jul 1 6:38:51 |
| str2 structure prediction (rdb format) (seq format) | T0203.t04.str2 | 2004 Jun 16 7:59:33 |
| Script for T0203.t04.str2 coloring in rasmol | T0203.t04.str2-color.rasmol | 2004 Jun 16 7:59:33 |
| str2---sequence logo (eps format) (pdf format) | T0203.t04.str2-logo | 2004 Jun 16 7:59:37 |
| stride-ebghtl structure prediction (rdb format) (seq format) | T0203.t04.stride-ebghtl | 2004 Jun 16 7:59:21 |
| Script for T0203.t04.stride-ebghtl coloring in rasmol | T0203.t04.stride-ebghtl-color.rasmol | 2004 Jun 16 7:59:38 |
| stride-ebghtl---sequence logo (eps format) (pdf format) | T0203.t04.stride-ebghtl-logo | 2004 Jun 16 7:59:41 |
| dssp-ebghstl structure prediction (rdb format) (seq format) | T0203.t04.dssp-ebghstl | 2004 Jun 16 7:59:43 |
| Script for T0203.t04.dssp-ebghstl coloring in rasmol | T0203.t04.dssp-ebghstl-color.rasmol | 2004 Jun 16 7:59:43 |
| dssp-ebghstl---sequence logo (eps format) (pdf format) | T0203.t04.dssp-ebghstl-logo | 2004 Jun 16 7:59:46 |
| alpha structure prediction (rdb format) (seq format) | T0203.t04.alpha | 2004 Jun 16 7:59:47 |
| Script for T0203.t04.alpha coloring in rasmol | T0203.t04.alpha-color.rasmol | 2004 Jun 16 7:59:48 |
| alpha---sequence logo (eps format) (pdf format) | T0203.t04.alpha-logo | 2004 Jun 16 7:59:51 |
| bys structure prediction (rdb format) (seq format) | T0203.t04.bys | 2004 Jun 16 7:59:52 |
| Script for T0203.t04.bys coloring in rasmol | T0203.t04.bys-color.rasmol | 2004 Jun 16 7:59:53 |
| dssp-ehl2 structure prediction (rdb format) (seq format) | T0203.t04.dssp-ehl2 | 2004 Jun 16 7:59:54 |
| Script for T0203.t04.dssp-ehl2 coloring in rasmol | T0203.t04.dssp-ehl2-color.rasmol | 2004 Jun 16 7:59:54 |
| dssp-ehl2---sequence logo (eps format) (pdf format) | T0203.t04.dssp-ehl2-logo | 2004 Jun 16 7:59:57 |
| CB_burial_14_7 structure prediction (rdb format) (seq format) | T0203.t04.CB_burial_14_7 | 2004 Jun 16 7:59:58 |
| Script for T0203.t04.CB_burial_14_7 coloring in rasmol | T0203.t04.CB_burial_14_7-color.rasmol | 2004 Jun 16 7:59:59 |
| CB_burial_14_7---sequence logo (eps format) (pdf format) | T0203.t04.CB_burial_14_7-logo | 2004 Jun 16 8:00:03 |
| near-backbone-11 structure prediction (rdb format) (seq format) | T0203.t04.near-backbone-11 | 2004 Jul 1 6:38:58 |
| Script for T0203.t04.near-backbone-11 coloring in rasmol | T0203.t04.near-backbone-11-color.rasmol | 2004 Jul 1 6:38:58 |
| Target model scores |
| amino acid single-track target model scores of PDB | T0203.t2k-w0.5-scores.html | 2004 Jul 2 14:49:24 |
| amino acid single-track target model scores of PDB | T0203.t04-w0.5-scores.html | 2004 Jul 2 22:27:04 |
| amino acid/100-30-str2 two-track target model scores | T0203.t2k-100-30-str2-scores.html | 2004 Jul 2 14:49:28 |
| amino acid/100-30-stride-ebghtl two-track target model scores | T0203.t2k-100-30-stride-ebghtl-scores.html | 2004 Jul 2 22:27:05 |
| amino acid/100-30-dssp-ebghstl two-track target model scores | T0203.t2k-100-30-dssp-ebghstl-scores.html | 2004 Jul 2 14:49:33 |
| amino acid/100-30-alpha two-track target model scores | T0203.t2k-100-30-alpha-scores.html | 2004 Jul 2 14:49:35 |
| amino acid/100-30-dssp-ehl2 two-track target model scores | T0203.t2k-100-30-dssp-ehl2-scores.html | 2004 Jul 2 14:49:39 |
| amino acid/100-30-CB_burial_14_7 two-track target model scores | T0203.t2k-100-30-CB_burial_14_7-scores.html | 2004 Jul 2 22:27:11 |
| amino acid/100-40-40-str2+CB_burial_14_7 two-track target model scores | T0203.t2k-100-40-40-str2+CB_burial_14_7-scores.html | 2004 Jul 2 14:56:32 |
| amino acid/100-30-str2 two-track target model scores | T0203.t04-100-30-str2-scores.html | 2004 Jul 2 14:56:35 |
| amino acid/100-30-stride-ebghtl two-track target model scores | T0203.t04-100-30-stride-ebghtl-scores.html | 2004 Jul 2 22:27:13 |
| amino acid/100-30-dssp-ebghstl two-track target model scores | T0203.t04-100-30-dssp-ebghstl-scores.html | 2004 Jul 2 14:56:40 |
| amino acid/100-30-alpha two-track target model scores | T0203.t04-100-30-alpha-scores.html | 2004 Jul 2 14:56:42 |
| amino acid/100-30-dssp-ehl2 two-track target model scores | T0203.t04-100-30-dssp-ehl2-scores.html | 2004 Jul 2 14:56:46 |
| amino acid/100-30-CB_burial_14_7 two-track target model scores | T0203.t04-100-30-CB_burial_14_7-scores.html | 2004 Jul 2 22:27:16 |
| amino acid/100-40-40-str2+CB_burial_14_7 two-track target model scores | T0203.t04-100-40-40-str2+CB_burial_14_7-scores.html | 2004 Jul 2 15:01:22 |
| Template model scores |
| Annotated template model scores | T0203.template-lib-scores.html | 2004 Jun 15 9:11:17 |
| Top Hits |
| Best scoring hits from all models | T0203.t04.best-scores.html | 2004 Jul 2 22:27:18 |
| Alignments for Top Hits |
| T02 Many Alignments Summary | T0203.t04.many_alignments.html | 2004 Jul 2 22:27:19 |
| T02 Top Models Summary | T0203.t04.top_reported_alignments.html | 2004 Jul 2 22:27:19 |
| multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2004 Jul 1 6:49:02 |
| Undertaker (3d) files |
| Multiple alignment for undertaker templates | T0203.t04-2track-undertaker.a2m | 2004 Jul 1 6:45:34 |
| Undertaker input for top alignments | T0203.t04.undertaker-align.under | 2004 Jul 2 22:27:21 |
| Fragment list for undertaker (from fragfinder) | T0203.t04.many.frag.gz | 2004 Jun 18 16:23:53 |
| First attempted model using undertaker | decoys/T0203.try1-opt2.pdb.gz | 2004 Jun 15 16:49:45 |
| Significant mutual information between column pairs |
| Mutual information table (align thinned to 30% ID) | T0203.t2k-thin30.mi.rdb | 2004 Jul 2 22:31:51 |
| Mutual information table (align thinned to 35% ID) | T0203.t2k-thin35.mi.rdb | 2004 Jul 2 22:21:38 |
| Mutual information table (align thinned to 40% ID) | T0203.t2k-thin40.mi.rdb | 2004 Jul 2 22:32:18 |
| Mutual information table (align thinned to 50% ID) | T0203.t2k-thin50.mi.rdb | 2004 Jul 2 22:23:10 |
| Mutual information table (align thinned to 62% ID) | T0203.t2k-thin62.mi.rdb | 2004 Jul 2 22:33:15 |
| Mutual information table (align thinned to 30% ID) | T0203.t04-thin30.mi.rdb | 2004 Jul 2 22:34:12 |
| Mutual information table (align thinned to 35% ID) | T0203.t04-thin35.mi.rdb | 2004 Jul 2 22:34:44 |
| Mutual information table (align thinned to 40% ID) | T0203.t04-thin40.mi.rdb | 2004 Jul 2 22:35:14 |
| Mutual information table (align thinned to 50% ID) | T0203.t04-thin50.mi.rdb | 2004 Jul 2 22:35:45 |
| Mutual information table (align thinned to 62% ID) | T0203.t04-thin62.mi.rdb | 2004 Jul 2 22:36:47 |
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