miniAGRP
| Description | Link to file | Date |
| Inputs |
| Submitted sequence(s) | miniAGRP.a2m | 2005 May 20 12:21:20 |
| README file | README | 2005 May 20 12:26:42 |
| Multiple alignment |
| SAM_t04 multiple alignment in a2m format | miniAGRP.t04.a2m.gz | 2005 May 20 12:29:19 |
| SAM_t04 multiple alignment in pretty html format | miniAGRP.t04.pa.html | 2005 May 20 12:29:25 |
| SAM_t04 target hidden Markov model | miniAGRP.t04.w0.5.mod | 2005 May 20 12:29:29 |
| SAM_t04 multiple alignment---sequence logo (eps format) (pdf format) | miniAGRP.t04.w0.5-logo | 2005 May 20 12:45:51 |
| Script for highlighting in rasmol | conserved_t04 | 2005 May 20 12:45:52 |
| SAM_t2k multiple alignment in a2m format | miniAGRP.t2k.a2m.gz | 2005 May 20 12:37:27 |
| SAM_t2k multiple alignment in pretty html format | miniAGRP.t2k.pa.html | 2005 May 20 12:37:33 |
| SAM_t2k target hidden Markov model | miniAGRP.t2k.w0.5.mod | 2005 May 20 12:37:35 |
| SAM_t2k multiple alignment---sequence logo (eps format) (pdf format) | miniAGRP.t2k.w0.5-logo | 2005 May 20 12:46:02 |
| Script for highlighting in rasmol | conserved_t2k | 2005 May 20 12:46:02 |
| Secondary Structure Prediction (Explanation of secondary-structure predictions) |
| str2 structure prediction (rdb format) (seq format) | miniAGRP.t2k.str2 | 2005 May 20 12:37:37 |
| Script for miniAGRP.t2k.str2 coloring in rasmol | miniAGRP.t2k.str2-color.rasmol | 2005 May 20 12:37:37 |
| str2---sequence logo (eps format) (pdf format) | miniAGRP.t2k.str2-logo | 2005 May 20 12:37:50 |
| str2 structure prediction (rdb format) (seq format) | miniAGRP.t04.str2 | 2005 May 20 12:37:50 |
| Script for miniAGRP.t04.str2 coloring in rasmol | miniAGRP.t04.str2-color.rasmol | 2005 May 20 12:37:51 |
| str2---sequence logo (eps format) (pdf format) | miniAGRP.t04.str2-logo | 2005 May 20 12:38:01 |
| stride-ebghtl structure prediction (rdb format) (seq format) | miniAGRP.t2k.stride-ebghtl | 2005 May 20 12:37:36 |
| Script for miniAGRP.t2k.stride-ebghtl coloring in rasmol | miniAGRP.t2k.stride-ebghtl-color.rasmol | 2005 May 20 12:38:02 |
| stride-ebghtl---sequence logo (eps format) (pdf format) | miniAGRP.t2k.stride-ebghtl-logo | 2005 May 20 12:38:11 |
| stride-ebghtl structure prediction (rdb format) (seq format) | miniAGRP.t04.stride-ebghtl | 2005 May 20 12:29:31 |
| Script for miniAGRP.t04.stride-ebghtl coloring in rasmol | miniAGRP.t04.stride-ebghtl-color.rasmol | 2005 May 20 12:38:11 |
| stride-ebghtl---sequence logo (eps format) (pdf format) | miniAGRP.t04.stride-ebghtl-logo | 2005 May 20 12:38:22 |
| dssp-ebghstl structure prediction (rdb format) (seq format) | miniAGRP.t2k.dssp-ebghstl | 2005 May 20 12:38:23 |
| Script for miniAGRP.t2k.dssp-ebghstl coloring in rasmol | miniAGRP.t2k.dssp-ebghstl-color.rasmol | 2005 May 20 12:38:23 |
| dssp-ebghstl---sequence logo (eps format) (pdf format) | miniAGRP.t2k.dssp-ebghstl-logo | 2005 May 20 12:38:33 |
| dssp-ebghstl structure prediction (rdb format) (seq format) | miniAGRP.t04.dssp-ebghstl | 2005 May 20 12:38:34 |
| Script for miniAGRP.t04.dssp-ebghstl coloring in rasmol | miniAGRP.t04.dssp-ebghstl-color.rasmol | 2005 May 20 12:38:34 |
| dssp-ebghstl---sequence logo (eps format) (pdf format) | miniAGRP.t04.dssp-ebghstl-logo | 2005 May 20 12:38:43 |
| alpha structure prediction (rdb format) (seq format) | miniAGRP.t2k.alpha | 2005 May 20 12:38:44 |
| Script for miniAGRP.t2k.alpha coloring in rasmol | miniAGRP.t2k.alpha-color.rasmol | 2005 May 20 12:38:44 |
| alpha---sequence logo (eps format) (pdf format) | miniAGRP.t2k.alpha-logo | 2005 May 20 12:38:55 |
| alpha structure prediction (rdb format) (seq format) | miniAGRP.t04.alpha | 2005 May 20 12:38:56 |
| Script for miniAGRP.t04.alpha coloring in rasmol | miniAGRP.t04.alpha-color.rasmol | 2005 May 20 12:38:56 |
| alpha---sequence logo (eps format) (pdf format) | miniAGRP.t04.alpha-logo | 2005 May 20 12:39:07 |
| bys structure prediction (rdb format) (seq format) | miniAGRP.t2k.bys | 2005 May 20 12:39:08 |
| Script for miniAGRP.t2k.bys coloring in rasmol | miniAGRP.t2k.bys-color.rasmol | 2005 May 20 12:39:08 |
| bys---sequence logo (eps format) (pdf format) | miniAGRP.t2k.bys-logo | 2005 May 20 12:39:19 |
| bys structure prediction (rdb format) (seq format) | miniAGRP.t04.bys | 2005 May 20 12:39:21 |
| Script for miniAGRP.t04.bys coloring in rasmol | miniAGRP.t04.bys-color.rasmol | 2005 May 20 12:39:21 |
| bys---sequence logo (eps format) (pdf format) | miniAGRP.t04.bys-logo | 2005 May 20 12:39:31 |
| dssp-ehl2 structure prediction (rdb format) (seq format) | miniAGRP.t2k.dssp-ehl2 | 2005 May 20 12:39:31 |
| Script for miniAGRP.t2k.dssp-ehl2 coloring in rasmol | miniAGRP.t2k.dssp-ehl2-color.rasmol | 2005 May 20 12:39:31 |
| dssp-ehl2---sequence logo (eps format) (pdf format) | miniAGRP.t2k.dssp-ehl2-logo | 2005 May 20 12:39:42 |
| dssp-ehl2 structure prediction (rdb format) (seq format) | miniAGRP.t04.dssp-ehl2 | 2005 May 20 12:39:43 |
| Script for miniAGRP.t04.dssp-ehl2 coloring in rasmol | miniAGRP.t04.dssp-ehl2-color.rasmol | 2005 May 20 12:39:43 |
| dssp-ehl2---sequence logo (eps format) (pdf format) | miniAGRP.t04.dssp-ehl2-logo | 2005 May 20 12:39:54 |
| CB_burial_14_7 structure prediction (rdb format) (seq format) | miniAGRP.t2k.CB_burial_14_7 | 2005 May 20 12:39:55 |
| Script for miniAGRP.t2k.CB_burial_14_7 coloring in rasmol | miniAGRP.t2k.CB_burial_14_7-color.rasmol | 2005 May 20 12:39:55 |
| CB_burial_14_7---sequence logo (eps format) (pdf format) | miniAGRP.t2k.CB_burial_14_7-logo | 2005 May 20 12:40:05 |
| CB_burial_14_7 structure prediction (rdb format) (seq format) | miniAGRP.t04.CB_burial_14_7 | 2005 May 20 12:40:06 |
| Script for miniAGRP.t04.CB_burial_14_7 coloring in rasmol | miniAGRP.t04.CB_burial_14_7-color.rasmol | 2005 May 20 12:40:06 |
| CB_burial_14_7---sequence logo (eps format) (pdf format) | miniAGRP.t04.CB_burial_14_7-logo | 2005 May 20 12:40:17 |
| near-backbone-11 structure prediction (rdb format) (seq format) | miniAGRP.t2k.near-backbone-11 | 2005 May 20 12:40:18 |
| Script for miniAGRP.t2k.near-backbone-11 coloring in rasmol | miniAGRP.t2k.near-backbone-11-color.rasmol | 2005 May 20 12:40:18 |
| near-backbone-11---sequence logo (eps format) (pdf format) | miniAGRP.t2k.near-backbone-11-logo | 2005 May 20 12:40:28 |
| near-backbone-11 structure prediction (rdb format) (seq format) | miniAGRP.t04.near-backbone-11 | 2005 May 20 12:40:28 |
| Script for miniAGRP.t04.near-backbone-11 coloring in rasmol | miniAGRP.t04.near-backbone-11-color.rasmol | 2005 May 20 12:40:29 |
| near-backbone-11---sequence logo (eps format) (pdf format) | miniAGRP.t04.near-backbone-11-logo | 2005 May 20 12:40:39 |
| Target model scores |
| amino acid single-track target model scores of PDB | miniAGRP.t2k-w0.5-scores.html | 2005 May 20 12:41:07 |
| amino acid single-track target model scores of PDB | miniAGRP.t04-w0.5-scores.html | 2005 May 20 12:41:32 |
| amino acid/100-30-str2 two-track target model scores | miniAGRP.t2k-100-30-str2-scores.html | 2005 May 20 12:42:00 |
| amino acid/100-30-stride-ebghtl two-track target model scores | miniAGRP.t2k-100-30-stride-ebghtl-scores.html | 2005 May 20 12:42:27 |
| amino acid/100-30-dssp-ebghstl two-track target model scores | miniAGRP.t2k-100-30-dssp-ebghstl-scores.html | 2005 May 20 12:42:55 |
| amino acid/100-30-alpha two-track target model scores | miniAGRP.t2k-100-30-alpha-scores.html | 2005 May 20 12:43:23 |
| amino acid/100-30-bys two-track target model scores | miniAGRP.t2k-100-30-bys-scores.html | 2005 May 20 12:43:49 |
| amino acid/100-30-dssp-ehl2 two-track target model scores | miniAGRP.t2k-100-30-dssp-ehl2-scores.html | 2005 May 20 12:44:15 |
| amino acid/100-30-CB_burial_14_7 two-track target model scores | miniAGRP.t2k-100-30-CB_burial_14_7-scores.html | 2005 May 20 12:44:42 |
| amino acid/100-30-near-backbone-11 two-track target model scores | miniAGRP.t2k-100-30-near-backbone-11-scores.html | 2005 May 20 12:45:08 |
| amino acid/100-40-40-str2+CB_burial_14_7 two-track target model scores | miniAGRP.t2k-100-40-40-str2+CB_burial_14_7-scores.html | 2005 May 20 12:48:35 |
| amino acid/80-60-80-str2+near-backbone-11 two-track target model scores | miniAGRP.t2k-80-60-80-str2+near-backbone-11-scores.html | 2005 May 20 12:48:51 |
| amino acid/100-30-str2 two-track target model scores | miniAGRP.t04-100-30-str2-scores.html | 2005 May 20 12:49:13 |
| amino acid/100-30-stride-ebghtl two-track target model scores | miniAGRP.t04-100-30-stride-ebghtl-scores.html | 2005 May 20 12:49:32 |
| amino acid/100-30-dssp-ebghstl two-track target model scores | miniAGRP.t04-100-30-dssp-ebghstl-scores.html | 2005 May 20 12:49:52 |
| amino acid/100-30-alpha two-track target model scores | miniAGRP.t04-100-30-alpha-scores.html | 2005 May 20 12:50:15 |
| amino acid/100-30-bys two-track target model scores | miniAGRP.t04-100-30-bys-scores.html | 2005 May 20 12:50:38 |
| amino acid/100-30-dssp-ehl2 two-track target model scores | miniAGRP.t04-100-30-dssp-ehl2-scores.html | 2005 May 20 12:51:05 |
| amino acid/100-30-CB_burial_14_7 two-track target model scores | miniAGRP.t04-100-30-CB_burial_14_7-scores.html | 2005 May 20 12:51:25 |
| amino acid/100-30-near-backbone-11 two-track target model scores | miniAGRP.t04-100-30-near-backbone-11-scores.html | 2005 May 20 12:51:46 |
| amino acid/100-40-40-str2+CB_burial_14_7 two-track target model scores | miniAGRP.t04-100-40-40-str2+CB_burial_14_7-scores.html | 2005 May 20 12:52:09 |
| amino acid/80-60-80-str2+near-backbone-11 two-track target model scores | miniAGRP.t04-80-60-80-str2+near-backbone-11-scores.html | 2005 May 20 12:52:34 |
| Template model scores |
| Annotated t2k template model scores | miniAGRP.t2k-template-lib-scores.html | 2005 May 20 13:00:18 |
| Annotated t04 template model scores | miniAGRP.t04-template-lib-scores.html | 2005 May 20 13:06:36 |
| Top Hits |
| Best scoring hits from t2k HMMs | miniAGRP.t2k.best-scores.html | 2005 May 20 13:06:40 |
| Best scoring hits from t04 HMMs | miniAGRP.t04.best-scores.html | 2005 May 20 13:06:41 |
| Best scoring hits from combining t2k and t04 | miniAGRP.best-scores.html | 2005 May 20 13:06:38 |
| Alignments for Top Hits |
| Top alignments from t2k hits | miniAGRP.t2k.top_reported_alignments.html | 2005 May 20 13:17:48 |
| Top alignments from t04 hits | miniAGRP.t04.top_reported_alignments.html | 2005 May 20 13:18:14 |
| Top alignments from combined hits | miniAGRP.top_reported_alignments.html | 2005 May 20 13:18:29 |
| multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2005 May 20 13:19:03 |
| Undertaker (3d) files |
| Undertaker input for top t2k alignments | miniAGRP.t2k.undertaker-align.under | 2005 May 20 13:19:04 |
| Undertaker input for top t04 alignments | miniAGRP.t04.undertaker-align.under | 2005 May 20 13:19:05 |
| Undertaker input for top combined alignments | miniAGRP.undertaker-align.under | 2005 May 20 13:19:05 |
| PDB file with model(s) for top alignments | miniAGRP.undertaker-align.pdb.gz | 2005 May 20 13:20:23 |
Images of the first model, created by sidechain replacement on the backbone of the template in the first alignment. Coloring is with the miniAGRP.undertaker-align.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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| 500x500 | 500x500 | 500x500 |
| Fragment list for undertaker (from fragfinder) | miniAGRP.t04.many.frag.gz | 2005 May 20 13:22:02 |
| Fragment list for undertaker (from fragfinder) | miniAGRP.t2k.many.frag.gz | 2005 May 20 13:22:15 |
| First attempted model using undertaker | decoys/miniAGRP.try1-opt2.pdb.gz | 2005 May 20 13:34:31 |
Images of the first model, created by sidechain replacement on the backbone of the template in the first alignment. Coloring is with the decoys/miniAGRP.try1-opt2.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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 |
 |
| 500x500 | 500x500 | 500x500 |
| Contact predictions, based on significant mutual information between column pairs |
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
