T0204 At5g18200, Arabidopsis
| Description | Link to file | Date |
| Inputs |
| Submitted sequence(s) | T0204.a2m | 2004 Jun 15 8:06:18 |
| README file | README | 2004 Jul 2 15:34:15 |
| Provided documentation | T0204.doc.html | 2004 Jun 15 8:03:28 |
| Multiple alignment |
| SAM_t04 multiple alignment in a2m format | T0204.t04.a2m.gz | 2004 Jun 15 8:41:47 |
| SAM_t04 multiple alignment in pretty html format | T0204.t04.pa.html | 2004 Jun 15 9:41:05 |
| SAM_t04 target hidden Markov model | T0204.t04.w0.5.mod | 2004 Jun 15 8:41:54 |
| SAM_t04 multiple alignment---sequence logo (eps format) (pdf format) | T0204.t04.w0.5-logo | 2004 Jun 16 8:15:14 |
| Script for highlighting in rasmol | conserved_t04 | 2004 Jun 16 8:15:16 |
| SAM_t2k multiple alignment in a2m format | T0204.t2k.a2m.gz | 2004 Jun 15 9:50:41 |
| SAM_t2k multiple alignment in pretty html format | T0204.t2k.pa.html | 2004 Jun 15 9:50:46 |
| SAM_t2k target hidden Markov model | T0204.t2k.w0.5.mod | 2004 Jun 15 9:50:49 |
| SAM_t2k multiple alignment---sequence logo (eps format) (pdf format) | T0204.t2k.w0.5-logo | 2004 Jun 15 9:50:53 |
| Script for highlighting in rasmol | conserved_t2k | 2004 Jun 15 9:50:54 |
| Secondary Structure Prediction (Explanation of secondary-structure predictions) |
| str2 structure prediction (rdb format) (seq format) | T0204.t2k.str2 | 2004 Jun 15 9:51:02 |
| Script for T0204.t2k.str2 coloring in rasmol | T0204.t2k.str2-color.rasmol | 2004 Jun 15 9:51:04 |
| str2---sequence logo (eps format) (pdf format) | T0204.t2k.str2-logo | 2004 Jun 15 9:51:13 |
| stride-ebghtl structure prediction (rdb format) (seq format) | T0204.t2k.stride-ebghtl | 2004 Jun 15 9:50:49 |
| Script for T0204.t2k.stride-ebghtl coloring in rasmol | T0204.t2k.stride-ebghtl-color.rasmol | 2004 Jun 15 9:51:15 |
| stride-ebghtl---sequence logo (eps format) (pdf format) | T0204.t2k.stride-ebghtl-logo | 2004 Jun 15 9:51:22 |
| dssp-ebghstl structure prediction (rdb format) (seq format) | T0204.t2k.dssp-ebghstl | 2004 Jun 15 9:51:25 |
| Script for T0204.t2k.dssp-ebghstl coloring in rasmol | T0204.t2k.dssp-ebghstl-color.rasmol | 2004 Jun 15 9:51:26 |
| dssp-ebghstl---sequence logo (eps format) (pdf format) | T0204.t2k.dssp-ebghstl-logo | 2004 Jun 15 9:51:31 |
| alpha structure prediction (rdb format) (seq format) | T0204.t2k.alpha | 2004 Jun 15 9:51:32 |
| Script for T0204.t2k.alpha coloring in rasmol | T0204.t2k.alpha-color.rasmol | 2004 Jun 15 9:51:33 |
| alpha---sequence logo (eps format) (pdf format) | T0204.t2k.alpha-logo | 2004 Jun 15 9:51:38 |
| bys structure prediction (rdb format) (seq format) | T0204.t2k.bys | 2004 Jun 15 9:51:40 |
| Script for T0204.t2k.bys coloring in rasmol | T0204.t2k.bys-color.rasmol | 2004 Jun 15 9:51:41 |
| dssp-ehl2 structure prediction (rdb format) (seq format) | T0204.t2k.dssp-ehl2 | 2004 Jun 15 9:51:43 |
| Script for T0204.t2k.dssp-ehl2 coloring in rasmol | T0204.t2k.dssp-ehl2-color.rasmol | 2004 Jun 15 9:51:43 |
| dssp-ehl2---sequence logo (eps format) (pdf format) | T0204.t2k.dssp-ehl2-logo | 2004 Jun 15 9:51:47 |
| CB_burial_14_7 structure prediction (rdb format) (seq format) | T0204.t2k.CB_burial_14_7 | 2004 Jun 15 9:51:49 |
| Script for T0204.t2k.CB_burial_14_7 coloring in rasmol | T0204.t2k.CB_burial_14_7-color.rasmol | 2004 Jun 15 9:51:50 |
| CB_burial_14_7---sequence logo (eps format) (pdf format) | T0204.t2k.CB_burial_14_7-logo | 2004 Jun 15 9:52:01 |
| near-backbone-11 structure prediction (rdb format) (seq format) | T0204.t2k.near-backbone-11 | 2004 Jul 2 17:43:25 |
| Script for T0204.t2k.near-backbone-11 coloring in rasmol | T0204.t2k.near-backbone-11-color.rasmol | 2004 Jul 2 17:43:25 |
| str2 structure prediction (rdb format) (seq format) | T0204.t04.str2 | 2004 Jun 16 8:15:40 |
| Script for T0204.t04.str2 coloring in rasmol | T0204.t04.str2-color.rasmol | 2004 Jun 16 8:15:42 |
| str2---sequence logo (eps format) (pdf format) | T0204.t04.str2-logo | 2004 Jun 16 8:15:47 |
| stride-ebghtl structure prediction (rdb format) (seq format) | T0204.t04.stride-ebghtl | 2004 Jun 16 8:15:10 |
| Script for T0204.t04.stride-ebghtl coloring in rasmol | T0204.t04.stride-ebghtl-color.rasmol | 2004 Jun 16 8:15:49 |
| stride-ebghtl---sequence logo (eps format) (pdf format) | T0204.t04.stride-ebghtl-logo | 2004 Jun 16 8:15:54 |
| dssp-ebghstl structure prediction (rdb format) (seq format) | T0204.t04.dssp-ebghstl | 2004 Jun 16 8:15:56 |
| Script for T0204.t04.dssp-ebghstl coloring in rasmol | T0204.t04.dssp-ebghstl-color.rasmol | 2004 Jun 16 8:15:57 |
| dssp-ebghstl---sequence logo (eps format) (pdf format) | T0204.t04.dssp-ebghstl-logo | 2004 Jun 16 8:16:02 |
| alpha structure prediction (rdb format) (seq format) | T0204.t04.alpha | 2004 Jun 16 8:16:04 |
| Script for T0204.t04.alpha coloring in rasmol | T0204.t04.alpha-color.rasmol | 2004 Jun 16 8:16:05 |
| alpha---sequence logo (eps format) (pdf format) | T0204.t04.alpha-logo | 2004 Jun 16 8:16:10 |
| bys structure prediction (rdb format) (seq format) | T0204.t04.bys | 2004 Jun 16 8:16:13 |
| Script for T0204.t04.bys coloring in rasmol | T0204.t04.bys-color.rasmol | 2004 Jun 16 8:16:14 |
| dssp-ehl2 structure prediction (rdb format) (seq format) | T0204.t04.dssp-ehl2 | 2004 Jun 16 8:16:17 |
| Script for T0204.t04.dssp-ehl2 coloring in rasmol | T0204.t04.dssp-ehl2-color.rasmol | 2004 Jun 16 8:16:18 |
| dssp-ehl2---sequence logo (eps format) (pdf format) | T0204.t04.dssp-ehl2-logo | 2004 Jun 16 8:16:22 |
| CB_burial_14_7 structure prediction (rdb format) (seq format) | T0204.t04.CB_burial_14_7 | 2004 Jun 16 8:16:25 |
| Script for T0204.t04.CB_burial_14_7 coloring in rasmol | T0204.t04.CB_burial_14_7-color.rasmol | 2004 Jun 16 8:16:26 |
| CB_burial_14_7---sequence logo (eps format) (pdf format) | T0204.t04.CB_burial_14_7-logo | 2004 Jun 16 8:16:30 |
| near-backbone-11 structure prediction (rdb format) (seq format) | T0204.t04.near-backbone-11 | 2004 Jul 2 17:43:38 |
| Script for T0204.t04.near-backbone-11 coloring in rasmol | T0204.t04.near-backbone-11-color.rasmol | 2004 Jul 2 17:43:38 |
| Target model scores |
| amino acid single-track target model scores of PDB | T0204.t2k-w0.5-scores.html | 2004 Jun 15 9:57:56 |
| amino acid single-track target model scores of PDB | T0204.t04-w0.5-scores.html | 2004 Jun 16 1:49:41 |
| amino acid/100-30-str2 two-track target model scores | T0204.t2k-100-30-str2-scores.html | 2004 Jun 15 10:02:05 |
| amino acid/100-30-stride-ebghtl two-track target model scores | T0204.t2k-100-30-stride-ebghtl-scores.html | 2004 Jun 15 10:06:12 |
| amino acid/100-30-dssp-ebghstl two-track target model scores | T0204.t2k-100-30-dssp-ebghstl-scores.html | 2004 Jun 15 10:10:23 |
| amino acid/100-30-alpha two-track target model scores | T0204.t2k-100-30-alpha-scores.html | 2004 Jun 15 10:14:10 |
| amino acid/100-30-dssp-ehl2 two-track target model scores | T0204.t2k-100-30-dssp-ehl2-scores.html | 2004 Jun 15 17:44:03 |
| amino acid/100-30-CB_burial_14_7 two-track target model scores | T0204.t2k-100-30-CB_burial_14_7-scores.html | 2004 Jun 15 10:26:25 |
| amino acid/100-40-40-str2+CB_burial_14_7 two-track target model scores | T0204.t2k-100-40-40-str2+CB_burial_14_7-scores.html | 2004 Jun 15 10:33:43 |
| amino acid/100-30-str2 two-track target model scores | T0204.t04-100-30-str2-scores.html | 2004 Jun 16 8:22:51 |
| amino acid/100-30-stride-ebghtl two-track target model scores | T0204.t04-100-30-stride-ebghtl-scores.html | 2004 Jun 16 8:26:58 |
| amino acid/100-30-dssp-ebghstl two-track target model scores | T0204.t04-100-30-dssp-ebghstl-scores.html | 2004 Jun 16 8:30:05 |
| amino acid/100-30-alpha two-track target model scores | T0204.t04-100-30-alpha-scores.html | 2004 Jun 16 8:32:56 |
| amino acid/100-30-dssp-ehl2 two-track target model scores | T0204.t04-100-30-dssp-ehl2-scores.html | 2004 Jun 16 8:35:47 |
| amino acid/100-30-CB_burial_14_7 two-track target model scores | T0204.t04-100-30-CB_burial_14_7-scores.html | 2004 Jun 16 8:38:46 |
| amino acid/100-40-40-str2+CB_burial_14_7 two-track target model scores | T0204.t04-100-40-40-str2+CB_burial_14_7-scores.html | 2004 Jun 16 8:42:44 |
| Template model scores |
| Annotated template model scores | T0204.template-lib-scores.html | 2004 Jun 15 10:55:01 |
| Top Hits |
| Best scoring hits from all models | T0204.t2k.best-scores.html | 2004 Jun 15 17:44:07 |
| Alignments for Top Hits |
| T02 Many Alignments Summary | T0204.t2k.many_alignments.html | 2004 Jul 2 17:53:20 |
| T02 Top Models Summary | T0204.t2k.top_reported_alignments.html | 2004 Jul 2 17:53:24 |
| multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2004 Jul 2 17:53:29 |
| Undertaker (3d) files |
| Multiple alignment for undertaker templates | T0204.t2k-2track-undertaker.a2m | 2004 Jun 15 11:00:07 |
| Undertaker input for top alignments | T0204.t2k.undertaker-align.under | 2004 Jul 2 17:53:29 |
| PDB file with model(s) for top alignments | T0204.t2k.undertaker-align.pdb.gz | 2004 Jul 2 17:54:45 |
| Fragment list for undertaker (from fragfinder) | T0204.t2k.many.frag.gz | 2004 Jun 15 11:02:19 |
| First attempted model using undertaker | decoys/T0204.try1-opt2.pdb.gz | 2004 Jun 15 16:25:37 |
| Significant mutual information between column pairs |
| Mutual information table (align thinned to 30% ID) | T0204.t2k-thin30.mi.rdb | 2004 Jul 2 18:01:13 |
| Mutual information table (align thinned to 35% ID) | T0204.t2k-thin35.mi.rdb | 2004 Jul 2 18:01:19 |
| Mutual information table (align thinned to 40% ID) | T0204.t2k-thin40.mi.rdb | 2004 Jul 2 18:01:23 |
| Mutual information table (align thinned to 50% ID) | T0204.t2k-thin50.mi.rdb | 2004 Jul 2 18:01:32 |
| Mutual information table (align thinned to 62% ID) | T0204.t2k-thin62.mi.rdb | 2004 Jul 2 18:01:55 |
| Mutual information table (align thinned to 30% ID) | T0204.t04-thin30.mi.rdb | 2004 Jul 2 18:01:59 |
| Mutual information table (align thinned to 35% ID) | T0204.t04-thin35.mi.rdb | 2004 Jul 2 18:02:04 |
| Mutual information table (align thinned to 40% ID) | T0204.t04-thin40.mi.rdb | 2004 Jul 2 18:02:14 |
| Mutual information table (align thinned to 50% ID) | T0204.t04-thin50.mi.rdb | 2004 Jul 2 18:03:04 |
| Mutual information table (align thinned to 62% ID) | T0204.t04-thin62.mi.rdb | 2004 Jul 2 18:05:30 |
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