T0207 XcR50, X. campestris
| Description | Link to file | Date |
| Inputs |
| Submitted sequence(s) | T0207.a2m | 2004 Jun 16 15:16:27 |
| README file | README | 2004 Jun 17 11:48:32 |
| Provided documentation | T0207.doc.html | 2004 Jun 16 15:51:43 |
| Multiple alignment |
| SAM_t04 multiple alignment in a2m format | T0207.t04.a2m.gz | 2004 Jun 16 16:12:35 |
| SAM_t04 multiple alignment in pretty html format | T0207.t04.pa.html | 2004 Jun 16 16:12:46 |
| SAM_t04 target hidden Markov model | T0207.t04.w0.5.mod | 2004 Jun 16 16:12:48 |
| SAM_t04 multiple alignment---sequence logo (eps format) (pdf format) | T0207.t04.w0.5-logo | 2004 Jun 16 16:12:53 |
| Script for highlighting in rasmol | conserved_t04 | 2004 Jun 16 16:12:53 |
| SAM_t2k multiple alignment in a2m format | T0207.t2k.a2m.gz | 2004 Jun 16 16:23:03 |
| SAM_t2k multiple alignment in pretty html format | T0207.t2k.pa.html | 2004 Jun 16 16:23:12 |
| SAM_t2k target hidden Markov model | T0207.t2k.w0.5.mod | 2004 Jun 16 16:23:13 |
| SAM_t2k multiple alignment---sequence logo (eps format) (pdf format) | T0207.t2k.w0.5-logo | 2004 Jun 16 16:23:16 |
| Script for highlighting in rasmol | conserved_t2k | 2004 Jun 16 16:23:17 |
| Secondary Structure Prediction (Explanation of secondary-structure predictions) |
| str2 structure prediction (rdb format) (seq format) | T0207.t2k.str2 | 2004 Jun 16 16:23:18 |
| Script for T0207.t2k.str2 coloring in rasmol | T0207.t2k.str2-color.rasmol | 2004 Jun 16 16:23:18 |
| str2---sequence logo (eps format) (pdf format) | T0207.t2k.str2-logo | 2004 Jun 16 16:23:21 |
| stride-ebghtl structure prediction (rdb format) (seq format) | T0207.t2k.stride-ebghtl | 2004 Jun 16 16:23:14 |
| Script for T0207.t2k.stride-ebghtl coloring in rasmol | T0207.t2k.stride-ebghtl-color.rasmol | 2004 Jun 16 16:23:22 |
| stride-ebghtl---sequence logo (eps format) (pdf format) | T0207.t2k.stride-ebghtl-logo | 2004 Jun 16 16:23:24 |
| dssp-ebghstl structure prediction (rdb format) (seq format) | T0207.t2k.dssp-ebghstl | 2004 Jun 16 16:23:25 |
| Script for T0207.t2k.dssp-ebghstl coloring in rasmol | T0207.t2k.dssp-ebghstl-color.rasmol | 2004 Jun 16 16:23:25 |
| dssp-ebghstl---sequence logo (eps format) (pdf format) | T0207.t2k.dssp-ebghstl-logo | 2004 Jun 16 16:23:28 |
| alpha structure prediction (rdb format) (seq format) | T0207.t2k.alpha | 2004 Jun 16 16:23:28 |
| Script for T0207.t2k.alpha coloring in rasmol | T0207.t2k.alpha-color.rasmol | 2004 Jun 16 16:23:28 |
| alpha---sequence logo (eps format) (pdf format) | T0207.t2k.alpha-logo | 2004 Jun 16 16:23:31 |
| bys structure prediction (rdb format) (seq format) | T0207.t2k.bys | 2004 Jun 16 16:23:32 |
| Script for T0207.t2k.bys coloring in rasmol | T0207.t2k.bys-color.rasmol | 2004 Jun 16 16:23:32 |
| dssp-ehl2 structure prediction (rdb format) (seq format) | T0207.t2k.dssp-ehl2 | 2004 Jun 16 16:23:33 |
| Script for T0207.t2k.dssp-ehl2 coloring in rasmol | T0207.t2k.dssp-ehl2-color.rasmol | 2004 Jun 16 16:23:33 |
| dssp-ehl2---sequence logo (eps format) (pdf format) | T0207.t2k.dssp-ehl2-logo | 2004 Jun 16 16:23:36 |
| CB_burial_14_7 structure prediction (rdb format) (seq format) | T0207.t2k.CB_burial_14_7 | 2004 Jun 16 16:23:36 |
| Script for T0207.t2k.CB_burial_14_7 coloring in rasmol | T0207.t2k.CB_burial_14_7-color.rasmol | 2004 Jun 16 16:23:37 |
| CB_burial_14_7---sequence logo (eps format) (pdf format) | T0207.t2k.CB_burial_14_7-logo | 2004 Jun 16 16:23:39 |
| str2 structure prediction (rdb format) (seq format) | T0207.t04.str2 | 2004 Jun 16 16:23:40 |
| Script for T0207.t04.str2 coloring in rasmol | T0207.t04.str2-color.rasmol | 2004 Jun 16 16:23:41 |
| str2---sequence logo (eps format) (pdf format) | T0207.t04.str2-logo | 2004 Jun 16 16:23:43 |
| stride-ebghtl structure prediction (rdb format) (seq format) | T0207.t04.stride-ebghtl | 2004 Jun 16 16:12:49 |
| Script for T0207.t04.stride-ebghtl coloring in rasmol | T0207.t04.stride-ebghtl-color.rasmol | 2004 Jun 16 16:23:44 |
| stride-ebghtl---sequence logo (eps format) (pdf format) | T0207.t04.stride-ebghtl-logo | 2004 Jun 16 16:23:47 |
| dssp-ebghstl structure prediction (rdb format) (seq format) | T0207.t04.dssp-ebghstl | 2004 Jun 16 16:23:48 |
| Script for T0207.t04.dssp-ebghstl coloring in rasmol | T0207.t04.dssp-ebghstl-color.rasmol | 2004 Jun 16 16:23:48 |
| dssp-ebghstl---sequence logo (eps format) (pdf format) | T0207.t04.dssp-ebghstl-logo | 2004 Jun 16 16:23:51 |
| alpha structure prediction (rdb format) (seq format) | T0207.t04.alpha | 2004 Jun 16 16:23:52 |
| Script for T0207.t04.alpha coloring in rasmol | T0207.t04.alpha-color.rasmol | 2004 Jun 16 16:23:52 |
| alpha---sequence logo (eps format) (pdf format) | T0207.t04.alpha-logo | 2004 Jun 16 16:23:55 |
| bys structure prediction (rdb format) (seq format) | T0207.t04.bys | 2004 Jun 16 16:23:56 |
| Script for T0207.t04.bys coloring in rasmol | T0207.t04.bys-color.rasmol | 2004 Jun 16 16:23:56 |
| dssp-ehl2 structure prediction (rdb format) (seq format) | T0207.t04.dssp-ehl2 | 2004 Jun 16 16:23:57 |
| Script for T0207.t04.dssp-ehl2 coloring in rasmol | T0207.t04.dssp-ehl2-color.rasmol | 2004 Jun 16 16:23:57 |
| dssp-ehl2---sequence logo (eps format) (pdf format) | T0207.t04.dssp-ehl2-logo | 2004 Jun 16 16:24:00 |
| CB_burial_14_7 structure prediction (rdb format) (seq format) | T0207.t04.CB_burial_14_7 | 2004 Jun 16 16:24:00 |
| Script for T0207.t04.CB_burial_14_7 coloring in rasmol | T0207.t04.CB_burial_14_7-color.rasmol | 2004 Jun 16 16:24:01 |
| CB_burial_14_7---sequence logo (eps format) (pdf format) | T0207.t04.CB_burial_14_7-logo | 2004 Jun 16 16:24:04 |
| Target model scores |
| amino acid single-track target model scores of PDB | T0207.t2k-w0.5-scores.html | 2004 Jun 16 16:25:00 |
| amino acid single-track target model scores of PDB | T0207.t04-w0.5-scores.html | 2004 Jun 16 16:25:51 |
| amino acid/100-30-str2 two-track target model scores | T0207.t2k-100-30-str2-scores.html | 2004 Jun 16 16:26:49 |
| amino acid/100-30-stride-ebghtl two-track target model scores | T0207.t2k-100-30-stride-ebghtl-scores.html | 2004 Jun 16 16:27:49 |
| amino acid/100-30-dssp-ebghstl two-track target model scores | T0207.t2k-100-30-dssp-ebghstl-scores.html | 2004 Jun 16 16:28:48 |
| amino acid/100-30-alpha two-track target model scores | T0207.t2k-100-30-alpha-scores.html | 2004 Jun 16 16:29:45 |
| amino acid/100-30-dssp-ehl2 two-track target model scores | T0207.t2k-100-30-dssp-ehl2-scores.html | 2004 Jun 16 16:30:41 |
| amino acid/100-30-CB_burial_14_7 two-track target model scores | T0207.t2k-100-30-CB_burial_14_7-scores.html | 2004 Jun 16 16:31:36 |
| amino acid/100-40-40-str2+CB_burial_14_7 two-track target model scores | T0207.t2k-100-40-40-str2+CB_burial_14_7-scores.html | 2004 Jun 16 16:32:43 |
| amino acid/100-30-str2 two-track target model scores | T0207.t04-100-30-str2-scores.html | 2004 Jun 16 16:33:24 |
| amino acid/100-30-stride-ebghtl two-track target model scores | T0207.t04-100-30-stride-ebghtl-scores.html | 2004 Jun 16 16:34:03 |
| amino acid/100-30-dssp-ebghstl two-track target model scores | T0207.t04-100-30-dssp-ebghstl-scores.html | 2004 Jun 16 16:34:42 |
| amino acid/100-30-alpha two-track target model scores | T0207.t04-100-30-alpha-scores.html | 2004 Jun 16 16:35:24 |
| amino acid/100-30-dssp-ehl2 two-track target model scores | T0207.t04-100-30-dssp-ehl2-scores.html | 2004 Jun 16 16:36:09 |
| amino acid/100-30-CB_burial_14_7 two-track target model scores | T0207.t04-100-30-CB_burial_14_7-scores.html | 2004 Jun 16 16:36:53 |
| amino acid/100-40-40-str2+CB_burial_14_7 two-track target model scores | T0207.t04-100-40-40-str2+CB_burial_14_7-scores.html | 2004 Jun 16 16:37:40 |
| Template model scores |
| Annotated template model scores | T0207.template-lib-scores.html | 2004 Jun 16 16:43:45 |
| Top Hits |
| Best scoring hits from all models | T0207.t2k.best-scores.html | 2004 Jun 16 16:43:47 |
| Alignments for Top Hits |
| T02 Many Alignments Summary | T0207.t2k.many_alignments.html | 2004 Jun 16 16:55:25 |
| T02 Top Models Summary | T0207.t2k.top_reported_alignments.html | 2004 Jun 16 16:55:40 |
| multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2004 Jun 16 16:55:43 |
| Undertaker (3d) files |
| Multiple alignment for undertaker templates | T0207.t2k-2track-undertaker.a2m | 2004 Jun 16 16:56:10 |
| Undertaker input for top alignments | T0207.t2k.undertaker-align.under | 2004 Jun 16 16:56:10 |
| PDB file with model(s) for top alignments | T0207.t2k.undertaker-align.pdb.gz | 2004 Jun 16 16:56:58 |
| Fragment list for undertaker (from fragfinder) | T0207.t2k.many.frag.gz | 2004 Jun 16 16:57:12 |
| First attempted model using undertaker | decoys/T0207.try1-opt2.pdb.gz | 2004 Jun 16 17:37:28 |
| Significant mutual information between column pairs |
| Mutual information table (align thinned to 30% ID) | T0207.t2k-thin30.mi.rdb | 2004 Jun 16 17:37:36 |
| Mutual information table (align thinned to 35% ID) | T0207.t2k-thin35.mi.rdb | 2004 Jun 17 13:41:04 |
| Mutual information table (align thinned to 40% ID) | T0207.t2k-thin40.mi.rdb | 2004 Jun 16 17:37:37 |
| Mutual information table (align thinned to 50% ID) | T0207.t2k-thin50.mi.rdb | 2004 Jun 16 17:37:38 |
| Mutual information table (align thinned to 62% ID) | T0207.t2k-thin62.mi.rdb | 2004 Jun 16 17:37:39 |
| Mutual information table (align thinned to 30% ID) | T0207.t04-thin30.mi.rdb | 2004 Jun 16 17:37:40 |
| Mutual information table (align thinned to 35% ID) | T0207.t04-thin35.mi.rdb | 2004 Jun 17 13:41:10 |
| Mutual information table (align thinned to 40% ID) | T0207.t04-thin40.mi.rdb | 2004 Jun 16 17:37:42 |
| Mutual information table (align thinned to 50% ID) | T0207.t04-thin50.mi.rdb | 2004 Jun 16 17:37:46 |
| Mutual information table (align thinned to 62% ID) | T0207.t04-thin62.mi.rdb | 2004 Jun 16 17:38:09 |
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