YBL008W (HIR1) SGDID:S0000104, Chr II from 209614-212136
| Description | Link to file | Date |
| Inputs |
| Submitted sequence(s) | YBL008W.a2m | 2002 Oct 30 17:49:47 |
| README file | README | 2002 Oct 28 17:35:09 |
| Multiple alignment |
| SAM_T02 multiple alignment in a2m format | YBL008W.t2k.a2m.gz | 2002 Nov 3 20:23:39 |
| SAM_T02 multiple alignment in pretty html format | YBL008W.t2k.pa.html | 2002 Nov 3 20:23:44 |
| SAM_T02 target hidden Markov model | YBL008W.t2k-w0.5.mod | 2002 Nov 3 20:24:13 |
| SAM_T02 multiple alignment---sequence logo (eps format) (pdf format) | YBL008W.t2k.w0.5-logo | 2004 Nov 11 13:35:09 |
| Secondary Structure Prediction (Explanation of secondary-structure predictions) |
| Str2 structure prediction (rdb format) (seq format) | YBL008W.t2k.str2 | 2004 Nov 11 13:35:12 |
| Str2 prediction---sequence logo (eps format) (pdf format) | YBL008W.t2k.str2-logo | 2005 Aug 1 13:32:11 |
| DSSP EBGHSTL structure prediction (rdb format) (seq format) | YBL008W.t2k.dssp-ebghstl | 2004 Nov 11 13:34:46 |
| DSSP EBGHSTL prediction---sequence logo (eps format) (pdf format) | YBL008W.t2k.dssp-ebghstl-logo | 2005 Aug 1 13:32:17 |
| Stride EBGHTL structure prediction (rdb format) (seq format) | YBL008W.t2k.stride-ebghtl | 2004 Nov 11 13:36:10 |
| Stride EBGHTL prediction---sequence logo (eps format) (pdf format) | YBL008W.t2k.stride-ebghtl-logo | 2005 Aug 1 13:32:23 |
| Alpha angle prediction (rdb format) (seq format) | YBL008W.t2k.alpha | 2002 Nov 3 20:24:47 |
| Alpha angle prediction---sequence logo (eps format) (pdf format) | YBL008W.t2k.alpha-logo | 2005 Aug 1 13:32:29 |
| Burial (CB_14_7) prediction (rdb format) (seq format) | YBL008W.t2k.CB_burial_14_7 | 2004 Nov 11 13:37:04 |
| Burial CB_14_7 prediction---sequence logo (eps format) (pdf format) | YBL008W.t2k.CB_burial_14_7-logo | 2005 Aug 1 13:32:36 |
| DSSP 3-value prediction (rdb format) | YBL008W.t2k.dssp-ehl2 | 2004 Nov 11 13:37:35 |
| DSSP 3-value prediction---sequence logo (eps format) (pdf format) | YBL008W.t2k.dssp-ehl2-logo | 2005 Aug 1 13:32:51 |
| Target model scores |
| Annotated amino acid single-track target model scores of PDB | YBL008W.t2k-w0.5-scores.html | 2005 Aug 1 11:20:23 |
| Annotated amino acid/100-30-str2 two-track target model scores | YBL008W.t2k-100-30-str2-scores.html | 2005 Aug 3 9:36:49 |
| Annotated amino acid/100-30-dssp-ebghstl two-track target model scores | YBL008W.t2k-100-30-dssp-ebghstl-scores.html | 2005 Aug 3 10:00:09 |
| Annotated amino acid/100-30-stride-ebghtl two-track target model scores | YBL008W.t2k-100-30-stride-ebghtl-scores.html | 2005 Aug 3 10:21:58 |
| Annotated amino acid/100-30-alpha two-track target model scores | YBL008W.t2k-100-30-alpha-scores.html | 2005 Aug 3 10:44:13 |
| Annotated amino acid/100-30-dssp-ehl2 two-track target model scores | YBL008W.t2k-100-30-dssp-ehl2-scores.html | 2005 Aug 1 17:09:18 |
| Annotated amino acid/100-30-CB_burial_14_7 two-track target model scores | YBL008W.t2k-100-30-CB_burial_14_7-scores.html | 2005 Aug 1 17:52:51 |
| Annotated amino acid/100-40-40-str2+CB_burial_14_7 two-track target model scores | YBL008W.t2k-100-40-40-str2+CB_burial_14_7-scores.html | 2005 Aug 1 18:40:09 |
| Template model scores |
| Annotated template model scores | YBL008W.template-lib-scores.html | 2005 Aug 1 19:01:10 |
| Top Hits |
| Best scoring hits from all models | YBL008W.t2k.best-scores.html | 2005 Aug 3 10:44:16 |
| Alignments for Top Hits |
| T02 Many Alignments Summary | YBL008W.t2k.many_alignments.html | 2005 Aug 3 11:10:39 |
| T02 Top Models Summary | YBL008W.t2k.top_reported_alignments.html | 2005 Aug 3 11:10:46 |
| Undertaker (3d) files |
| Script for dssp coloring in rasmol | YBL008W.t2k.dssp-color.rasmol | 2004 Nov 11 13:35:42 |
| Script for stride coloring in rasmol | YBL008W.t2k.stride-color.rasmol | 2004 Nov 11 13:36:11 |
| Script for str2 coloring in rasmol | YBL008W.t2k.str2-color.rasmol | 2004 Nov 11 13:35:14 |
| Script for CB_burial_14_7 coloring in rasmol | YBL008W.t2k.CB_burial_14_7-color.rasmol | 2004 Nov 11 13:37:06 |
| Script for alpha coloring in rasmol | YBL008W.t2k.alpha-color.rasmol | 2002 Nov 3 20:24:48 |
| Script for coloring in rasmol | conserved | 2004 Nov 11 18:30:10 |
| Multiple alignment for undertaker templates | YBL008W.t2k-2track-undertaker.a2m | 2005 Aug 1 19:23:07 |
| Undertaker input for top alignments | YBL008W.t2k.undertaker-align.under | 2005 Aug 3 11:10:48 |
| PDB file with model(s) for top alignments | YBL008W.t2k.undertaker-align.pdb.gz | 2005 Aug 3 11:12:40 |
Images of the first model, created by sidechain replacement on the backbone of the template in the first alignment. Coloring is with the YBL008W.t2k.dssp-color.rasmol script, to show predicted secondary structure (red for helix, yellow for strand, blue for turn, grey for other).
| Front | Top | Side |
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|
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| 500x500 | 500x500 | 500x500 |
| Fragment list for undertaker (from fragfinder) | YBL008W.t2k.frag.gz | 2005 Aug 1 19:32:14 |
| Significant mutual information between column pairs |
| Mutual information table (align thinned to 30% ID) | YBL008W.t2k-thin30.mi.rdb | 2004 Nov 11 19:00:09 |
| Mutual information table (align thinned to 40% ID) | YBL008W.t2k-thin40.mi.rdb | 2004 Nov 11 19:03:36 |
| Mutual information table (align thinned to 50% ID) | YBL008W.t2k-thin50.mi.rdb | 2004 Nov 11 19:11:39 |
| Mutual information table (align thinned to 62% ID) | YBL008W.t2k-thin62.mi.rdb | 2004 Nov 11 19:30:25 |
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
