Please cite the following papers:
When SAM_T06 finishes loading, you should see links to
You may also view the list of files created so far. This link gives access to the full directory of file produced, including query progress logs, and this html file (summary.html). When the process is finished, you may want to download the entire directory to your computer, using a tool such as "wget".
Description | Link to file | Date |
Inputs |
Submitted sequence(s) | T0294.a2m | 2006 May 17 20:25:57 |
README file | README | 2006 May 18 20:02:43 |
Provided documentation | T0294.doc.html | 2006 May 17 20:26:17 |
Quick blastp of non-redundant PDB | T0294.pdb.blast | 2006 May 18 15:45:28 |
Multiple alignment |
SAM_t06 multiple alignment in a2m format | T0294.t06.a2m.gz | 2006 May 18 10:29:15 |
SAM_t06 multiple alignment in pretty html format | T0294.t06.pa.html | 2006 May 18 10:30:10 |
SAM_t06 target hidden Markov model | T0294.t06.w0.5.mod | 2006 May 18 10:30:21 |
SAM_t06 multiple alignment---sequence logo (eps format) (pdf format) | T0294.t06.w0.5-logo | 2006 May 18 10:30:39 |
Script for highlighting in rasmol | conserved_t06 | 2006 May 18 10:30:41 |
SAM_t04 multiple alignment in a2m format | T0294.t04.a2m.gz | 2006 May 18 11:19:02 |
SAM_t04 multiple alignment in pretty html format | T0294.t04.pa.html | 2006 May 18 11:20:06 |
SAM_t04 target hidden Markov model | T0294.t04.w0.5.mod | 2006 May 18 11:20:14 |
SAM_t04 multiple alignment---sequence logo (eps format) (pdf format) | T0294.t04.w0.5-logo | 2006 May 18 11:20:30 |
Script for highlighting in rasmol | conserved_t04 | 2006 May 18 11:20:31 |
SAM_t2k multiple alignment in a2m format | T0294.t2k.a2m.gz | 2006 May 18 11:50:25 |
SAM_t2k multiple alignment in pretty html format | T0294.t2k.pa.html | 2006 May 18 11:50:57 |
SAM_t2k target hidden Markov model | T0294.t2k.w0.5.mod | 2006 May 18 11:51:03 |
SAM_t2k multiple alignment---sequence logo (eps format) (pdf format) | T0294.t2k.w0.5-logo | 2006 May 18 11:51:17 |
Script for highlighting in rasmol | conserved_t2k | 2006 May 18 11:51:18 |
Secondary Structure Prediction (Explanation of secondary-structure predictions) |
str2 structure prediction (rdb format) (seq format) | T0294.t06.str2 | 2006 May 18 10:30:34 |
Script for T0294.t06.str2 coloring in rasmol | T0294.t06.str2-color.rasmol | 2006 May 18 11:51:20 |
str2---sequence logo (eps format) (pdf format) | T0294.t06.str2-logo | 2006 May 18 11:51:25 |
str2 structure prediction (rdb format) (seq format) | T0294.t04.str2 | 2006 May 18 11:20:26 |
Script for T0294.t04.str2 coloring in rasmol | T0294.t04.str2-color.rasmol | 2006 May 18 11:51:26 |
str2---sequence logo (eps format) (pdf format) | T0294.t04.str2-logo | 2006 May 18 11:51:30 |
str2 structure prediction (rdb format) (seq format) | T0294.t2k.str2 | 2006 May 18 11:51:13 |
Script for T0294.t2k.str2 coloring in rasmol | T0294.t2k.str2-color.rasmol | 2006 May 18 11:51:31 |
str2---sequence logo (eps format) (pdf format) | T0294.t2k.str2-logo | 2006 May 18 11:51:36 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0294.t06.stride-ebghtl | 2006 May 18 11:51:41 |
Script for T0294.t06.stride-ebghtl coloring in rasmol | T0294.t06.stride-ebghtl-color.rasmol | 2006 May 18 11:51:41 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0294.t06.stride-ebghtl-logo | 2006 May 18 11:51:46 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0294.t04.stride-ebghtl | 2006 May 18 11:51:51 |
Script for T0294.t04.stride-ebghtl coloring in rasmol | T0294.t04.stride-ebghtl-color.rasmol | 2006 May 18 11:51:52 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0294.t04.stride-ebghtl-logo | 2006 May 18 11:51:57 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0294.t2k.stride-ebghtl | 2006 May 18 11:52:00 |
Script for T0294.t2k.stride-ebghtl coloring in rasmol | T0294.t2k.stride-ebghtl-color.rasmol | 2006 May 18 11:52:01 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0294.t2k.stride-ebghtl-logo | 2006 May 18 11:52:14 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0294.t06.dssp-ebghstl | 2006 May 18 11:52:19 |
Script for T0294.t06.dssp-ebghstl coloring in rasmol | T0294.t06.dssp-ebghstl-color.rasmol | 2006 May 18 11:52:19 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0294.t06.dssp-ebghstl-logo | 2006 May 18 11:52:23 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0294.t04.dssp-ebghstl | 2006 May 18 11:52:28 |
Script for T0294.t04.dssp-ebghstl coloring in rasmol | T0294.t04.dssp-ebghstl-color.rasmol | 2006 May 18 11:52:28 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0294.t04.dssp-ebghstl-logo | 2006 May 18 11:52:32 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0294.t2k.dssp-ebghstl | 2006 May 18 11:52:35 |
Script for T0294.t2k.dssp-ebghstl coloring in rasmol | T0294.t2k.dssp-ebghstl-color.rasmol | 2006 May 18 11:52:36 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0294.t2k.dssp-ebghstl-logo | 2006 May 18 11:52:42 |
alpha structure prediction (rdb format) (seq format) | T0294.t06.alpha | 2006 May 18 11:52:49 |
Script for T0294.t06.alpha coloring in rasmol | T0294.t06.alpha-color.rasmol | 2006 May 18 11:52:50 |
alpha---sequence logo (eps format) (pdf format) | T0294.t06.alpha-logo | 2006 May 18 11:52:55 |
alpha structure prediction (rdb format) (seq format) | T0294.t04.alpha | 2006 May 18 11:53:00 |
Script for T0294.t04.alpha coloring in rasmol | T0294.t04.alpha-color.rasmol | 2006 May 18 11:53:00 |
alpha---sequence logo (eps format) (pdf format) | T0294.t04.alpha-logo | 2006 May 18 11:53:05 |
alpha structure prediction (rdb format) (seq format) | T0294.t2k.alpha | 2006 May 18 11:53:07 |
Script for T0294.t2k.alpha coloring in rasmol | T0294.t2k.alpha-color.rasmol | 2006 May 18 11:53:07 |
alpha---sequence logo (eps format) (pdf format) | T0294.t2k.alpha-logo | 2006 May 18 11:53:11 |
bys structure prediction (rdb format) (seq format) | T0294.t06.bys | 2006 May 18 11:53:16 |
Script for T0294.t06.bys coloring in rasmol | T0294.t06.bys-color.rasmol | 2006 May 18 11:53:16 |
bys---sequence logo (eps format) (pdf format) | T0294.t06.bys-logo | 2006 May 18 11:53:21 |
bys structure prediction (rdb format) (seq format) | T0294.t04.bys | 2006 May 18 11:53:25 |
Script for T0294.t04.bys coloring in rasmol | T0294.t04.bys-color.rasmol | 2006 May 18 11:53:26 |
bys---sequence logo (eps format) (pdf format) | T0294.t04.bys-logo | 2006 May 18 11:53:31 |
bys structure prediction (rdb format) (seq format) | T0294.t2k.bys | 2006 May 18 11:53:39 |
Script for T0294.t2k.bys coloring in rasmol | T0294.t2k.bys-color.rasmol | 2006 May 18 11:53:40 |
bys---sequence logo (eps format) (pdf format) | T0294.t2k.bys-logo | 2006 May 18 11:53:45 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0294.t06.dssp-ehl2 | 2006 May 18 11:53:46 |
Script for T0294.t06.dssp-ehl2 coloring in rasmol | T0294.t06.dssp-ehl2-color.rasmol | 2006 May 18 11:53:47 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0294.t06.dssp-ehl2-logo | 2006 May 18 11:53:51 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0294.t04.dssp-ehl2 | 2006 May 18 11:53:52 |
Script for T0294.t04.dssp-ehl2 coloring in rasmol | T0294.t04.dssp-ehl2-color.rasmol | 2006 May 18 11:53:52 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0294.t04.dssp-ehl2-logo | 2006 May 18 11:53:56 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0294.t2k.dssp-ehl2 | 2006 May 18 11:53:57 |
Script for T0294.t2k.dssp-ehl2 coloring in rasmol | T0294.t2k.dssp-ehl2-color.rasmol | 2006 May 18 11:53:58 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0294.t2k.dssp-ehl2-logo | 2006 May 18 11:54:02 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0294.dssp-ehl2 | 2006 May 18 11:54:04 |
Script for T0294.dssp-ehl2 coloring in rasmol | T0294.dssp-ehl2-color.rasmol | 2006 May 18 11:54:04 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0294.dssp-ehl2-logo | 2006 May 18 11:54:08 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0294.t06.CB_burial_14_7 | 2006 May 18 11:54:13 |
Script for T0294.t06.CB_burial_14_7 coloring in rasmol | T0294.t06.CB_burial_14_7-color.rasmol | 2006 May 18 11:54:13 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0294.t06.CB_burial_14_7-logo | 2006 May 18 11:54:17 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0294.t04.CB_burial_14_7 | 2006 May 18 11:54:22 |
Script for T0294.t04.CB_burial_14_7 coloring in rasmol | T0294.t04.CB_burial_14_7-color.rasmol | 2006 May 18 11:54:22 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0294.t04.CB_burial_14_7-logo | 2006 May 18 11:54:27 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0294.t2k.CB_burial_14_7 | 2006 May 18 11:54:30 |
Script for T0294.t2k.CB_burial_14_7 coloring in rasmol | T0294.t2k.CB_burial_14_7-color.rasmol | 2006 May 18 11:54:31 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0294.t2k.CB_burial_14_7-logo | 2006 May 18 11:54:35 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0294.t06.near-backbone-11 | 2006 May 18 11:54:40 |
Script for T0294.t06.near-backbone-11 coloring in rasmol | T0294.t06.near-backbone-11-color.rasmol | 2006 May 18 11:54:41 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0294.t06.near-backbone-11-logo | 2006 May 18 11:54:45 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0294.t04.near-backbone-11 | 2006 May 18 11:54:50 |
Script for T0294.t04.near-backbone-11 coloring in rasmol | T0294.t04.near-backbone-11-color.rasmol | 2006 May 18 11:54:50 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0294.t04.near-backbone-11-logo | 2006 May 18 11:54:55 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0294.t2k.near-backbone-11 | 2006 May 18 11:54:59 |
Script for T0294.t2k.near-backbone-11 coloring in rasmol | T0294.t2k.near-backbone-11-color.rasmol | 2006 May 18 11:55:00 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0294.t2k.near-backbone-11-logo | 2006 May 18 11:55:04 |
Target model scores |
amino acid single-track target model scores of PDB | T0294.t06-w0.5-scores.html | 2006 May 18 11:59:46 |
amino acid single-track target model scores of PDB | T0294.t04-w0.5-scores.html | 2006 May 18 12:06:13 |
amino acid single-track target model scores of PDB | T0294.t2k-w0.5-scores.html | 2006 May 18 12:12:48 |
amino acid/100-30-str2 multi-track target model scores | T0294.t06-100-30-str2-scores.html | 2006 May 18 12:13:37 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0294.t06-100-30-stride-ebghtl-scores.html | 2006 May 18 12:14:34 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0294.t06-100-30-dssp-ebghstl-scores.html | 2006 May 18 12:15:24 |
amino acid/100-30-alpha multi-track target model scores | T0294.t06-100-30-alpha-scores.html | 2006 May 18 12:16:11 |
amino acid/100-30-bys multi-track target model scores | T0294.t06-100-30-bys-scores.html | 2006 May 18 12:16:57 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0294.t06-100-30-dssp-ehl2-scores.html | 2006 May 18 12:17:41 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0294.t06-100-30-CB_burial_14_7-scores.html | 2006 May 18 12:18:26 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0294.t06-100-30-near-backbone-11-scores.html | 2006 May 18 12:19:10 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0294.t06-100-40-40-str2+CB_burial_14_7-scores.html | 2006 May 18 12:20:00 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0294.t06-80-60-80-str2+near-backbone-11-scores.html | 2006 May 18 12:20:49 |
amino acid/100-30-str2 multi-track target model scores | T0294.t04-100-30-str2-scores.html | 2006 May 18 12:23:15 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0294.t04-100-30-stride-ebghtl-scores.html | 2006 May 18 12:25:57 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0294.t04-100-30-dssp-ebghstl-scores.html | 2006 May 18 12:28:20 |
amino acid/100-30-alpha multi-track target model scores | T0294.t04-100-30-alpha-scores.html | 2006 May 18 12:30:45 |
amino acid/100-30-bys multi-track target model scores | T0294.t04-100-30-bys-scores.html | 2006 May 18 12:33:11 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0294.t04-100-30-dssp-ehl2-scores.html | 2006 May 18 12:36:04 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0294.t04-100-30-CB_burial_14_7-scores.html | 2006 May 18 12:38:24 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0294.t04-100-30-near-backbone-11-scores.html | 2006 May 18 12:40:44 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0294.t04-100-40-40-str2+CB_burial_14_7-scores.html | 2006 May 18 12:43:24 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0294.t04-80-60-80-str2+near-backbone-11-scores.html | 2006 May 18 12:46:28 |
amino acid/100-30-str2 multi-track target model scores | T0294.t2k-100-30-str2-scores.html | 2006 May 18 12:49:50 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0294.t2k-100-30-stride-ebghtl-scores.html | 2006 May 18 12:53:12 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0294.t2k-100-30-dssp-ebghstl-scores.html | 2006 May 18 12:56:41 |
amino acid/100-30-alpha multi-track target model scores | T0294.t2k-100-30-alpha-scores.html | 2006 May 18 12:59:53 |
amino acid/100-30-bys multi-track target model scores | T0294.t2k-100-30-bys-scores.html | 2006 May 18 13:03:17 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0294.t2k-100-30-dssp-ehl2-scores.html | 2006 May 18 13:07:19 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0294.t2k-100-30-CB_burial_14_7-scores.html | 2006 May 18 13:10:23 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0294.t2k-100-30-near-backbone-11-scores.html | 2006 May 18 13:13:47 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0294.t2k-100-40-40-str2+CB_burial_14_7-scores.html | 2006 May 18 13:18:14 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0294.t2k-80-60-80-str2+near-backbone-11-scores.html | 2006 May 18 13:21:45 |
Template model scores |
Annotated t06 template model scores | T0294.t06-template-lib-scores.html | 2006 May 18 13:36:05 |
Annotated t04 template model scores | T0294.t04-template-lib-scores.html | 2006 May 18 14:20:36 |
Annotated t2k template model scores | T0294.t2k-template-lib-scores.html | 2006 May 18 15:24:31 |
Top Hits |
Best scoring hits from t06 HMMs | T0294.t06.best-scores.html | 2006 May 18 15:24:36 |
Best scoring hits from t04 HMMs | T0294.t04.best-scores.html | 2006 May 18 15:24:40 |
Best scoring hits from t2k HMMs | T0294.t2k.best-scores.html | 2006 May 18 15:24:44 |
Best scoring hits from combining t06 t04 t2k | T0294.best-scores.html | 2006 May 18 15:24:49 |
Alignments for Top Hits |
Top alignments from t06 hits | T0294.t06.top_reported_alignments.html | 2006 May 18 20:18:01 |
Top alignments from t04 hits | T0294.t04.top_reported_alignments.html | 2006 May 18 20:18:16 |
Top alignments from t2k hits | T0294.t2k.top_reported_alignments.html | 2006 May 18 20:18:26 |
Top alignments from combined hits | T0294.top_reported_alignments.html | 2006 May 18 20:18:36 |
multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2006 May 18 20:18:50 |
Undertaker (3d) files |
Undertaker input for top t06 alignments | T0294.t06.undertaker-align.under | 2006 May 18 20:18:52 |
Undertaker input for top t04 alignments | T0294.t04.undertaker-align.under | 2006 May 18 20:18:52 |
Undertaker input for top t2k alignments | T0294.t2k.undertaker-align.under | 2006 May 18 20:18:52 |
Undertaker input for top combined alignments | T0294.undertaker-align.under | 2006 May 18 20:18:53 |
PDB file with model(s) for top alignments | T0294.undertaker-align.pdb.gz | 2006 May 18 20:20:09 |
Images of an (incomplete) model created by sidechain replacement on the backbone of the highest scoring template.
Coloring is defined by the dssp rasmol script, to show predicted secondary structure (red for helix, yellow for strand, blue for turn, grey for other).
Front | Top | Side |
500x500 | 500x500 | 500x500 |
Fragment list for undertaker (from fragfinder) | T0294.t06.many.frag.gz | 2006 May 18 17:16:21 |
Fragment list for undertaker (from fragfinder) | T0294.t04.many.frag.gz | 2006 May 18 17:17:50 |
Fragment list for undertaker (from fragfinder) | T0294.t2k.many.frag.gz | 2006 May 18 17:19:33 |
Contact predictions, based on significance of mutual information, pairwise contact propensity, log(separation), predicted burial (near-backbone-11), predicted secondary structure(str2), amino acid profile, log(protein length) |
contact predictions (rr format) (rr.constraints format) | T0294.352_28 | 2006 May 18 17:31:59 |
First attempted model using undertaker | decoys/T0294.try1-opt2.pdb.gz | 2006 May 19 0:19:02 |
Images of complete model in decoys/T0294.try1-opt2.pdb.gz
Coloring is defined by the dssp rasmol script, to show predicted secondary structure (red for helix, yellow for strand, blue for turn, grey for other).
Front | Top | Side |
500x500 | 500x500 | 500x500 |
Please cite the following papers:
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SAM web system designed by Kevin Karplus and Alex Williams,
based on prior design by Kevin Karplus and Rachel Karchin.
Maintained by Kevin Karplus: karplus@soe.ucsc.edu