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) | T0301.a2m | 2006 May 25 18:49:00 |
README file | README | 2006 May 25 18:50:29 |
Quick blastp of non-redundant PDB | T0301.pdb.blast | 2006 May 25 18:50:32 |
Multiple alignment |
SAM_t06 multiple alignment in a2m format | T0301.t06.a2m.gz | 2006 May 25 18:59:15 |
SAM_t06 multiple alignment in pretty html format | T0301.t06.pa.html | 2006 May 25 18:59:22 |
SAM_t06 target hidden Markov model | T0301.t06.w0.5.mod | 2006 May 25 18:59:24 |
SAM_t06 multiple alignment---sequence logo (eps format) (pdf format) | T0301.t06.w0.5-logo | 2006 May 25 18:59:36 |
Script for highlighting in rasmol | conserved_t06 | 2006 May 25 18:59:37 |
SAM_t04 multiple alignment in a2m format | T0301.t04.a2m.gz | 2006 May 25 19:06:34 |
SAM_t04 multiple alignment in pretty html format | T0301.t04.pa.html | 2006 May 25 19:06:41 |
SAM_t04 target hidden Markov model | T0301.t04.w0.5.mod | 2006 May 25 19:06:43 |
SAM_t04 multiple alignment---sequence logo (eps format) (pdf format) | T0301.t04.w0.5-logo | 2006 May 25 19:06:55 |
Script for highlighting in rasmol | conserved_t04 | 2006 May 25 19:06:56 |
SAM_t2k multiple alignment in a2m format | T0301.t2k.a2m.gz | 2006 May 25 19:09:34 |
SAM_t2k multiple alignment in pretty html format | T0301.t2k.pa.html | 2006 May 25 19:09:42 |
SAM_t2k target hidden Markov model | T0301.t2k.w0.5.mod | 2006 May 25 19:09:43 |
SAM_t2k multiple alignment---sequence logo (eps format) (pdf format) | T0301.t2k.w0.5-logo | 2006 May 25 19:09:54 |
Script for highlighting in rasmol | conserved_t2k | 2006 May 25 19:09:55 |
Secondary Structure Prediction (Explanation of secondary-structure predictions) |
str2 structure prediction (rdb format) (seq format) | T0301.t06.str2 | 2006 May 25 18:59:27 |
Script for T0301.t06.str2 coloring in rasmol | T0301.t06.str2-color.rasmol | 2006 May 25 19:09:57 |
str2---sequence logo (eps format) (pdf format) | T0301.t06.str2-logo | 2006 May 25 19:10:06 |
str2 structure prediction (rdb format) (seq format) | T0301.t04.str2 | 2006 May 25 19:06:46 |
Script for T0301.t04.str2 coloring in rasmol | T0301.t04.str2-color.rasmol | 2006 May 25 19:10:07 |
str2---sequence logo (eps format) (pdf format) | T0301.t04.str2-logo | 2006 May 25 19:10:16 |
str2 structure prediction (rdb format) (seq format) | T0301.t2k.str2 | 2006 May 25 19:09:46 |
Script for T0301.t2k.str2 coloring in rasmol | T0301.t2k.str2-color.rasmol | 2006 May 25 19:10:16 |
str2---sequence logo (eps format) (pdf format) | T0301.t2k.str2-logo | 2006 May 25 19:10:26 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0301.t06.stride-ebghtl | 2006 May 25 19:10:28 |
Script for T0301.t06.stride-ebghtl coloring in rasmol | T0301.t06.stride-ebghtl-color.rasmol | 2006 May 25 19:10:29 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0301.t06.stride-ebghtl-logo | 2006 May 25 19:10:38 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0301.t04.stride-ebghtl | 2006 May 25 19:10:40 |
Script for T0301.t04.stride-ebghtl coloring in rasmol | T0301.t04.stride-ebghtl-color.rasmol | 2006 May 25 19:10:40 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0301.t04.stride-ebghtl-logo | 2006 May 25 19:10:50 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0301.t2k.stride-ebghtl | 2006 May 25 19:10:51 |
Script for T0301.t2k.stride-ebghtl coloring in rasmol | T0301.t2k.stride-ebghtl-color.rasmol | 2006 May 25 19:10:52 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0301.t2k.stride-ebghtl-logo | 2006 May 25 19:11:01 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0301.t06.dssp-ebghstl | 2006 May 25 19:11:03 |
Script for T0301.t06.dssp-ebghstl coloring in rasmol | T0301.t06.dssp-ebghstl-color.rasmol | 2006 May 25 19:11:03 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0301.t06.dssp-ebghstl-logo | 2006 May 25 19:11:13 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0301.t04.dssp-ebghstl | 2006 May 25 19:11:15 |
Script for T0301.t04.dssp-ebghstl coloring in rasmol | T0301.t04.dssp-ebghstl-color.rasmol | 2006 May 25 19:11:15 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0301.t04.dssp-ebghstl-logo | 2006 May 25 19:11:25 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0301.t2k.dssp-ebghstl | 2006 May 25 19:11:27 |
Script for T0301.t2k.dssp-ebghstl coloring in rasmol | T0301.t2k.dssp-ebghstl-color.rasmol | 2006 May 25 19:11:27 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0301.t2k.dssp-ebghstl-logo | 2006 May 25 19:11:36 |
alpha structure prediction (rdb format) (seq format) | T0301.t06.alpha | 2006 May 25 19:11:38 |
Script for T0301.t06.alpha coloring in rasmol | T0301.t06.alpha-color.rasmol | 2006 May 25 19:11:39 |
alpha---sequence logo (eps format) (pdf format) | T0301.t06.alpha-logo | 2006 May 25 19:11:48 |
alpha structure prediction (rdb format) (seq format) | T0301.t04.alpha | 2006 May 25 19:11:50 |
Script for T0301.t04.alpha coloring in rasmol | T0301.t04.alpha-color.rasmol | 2006 May 25 19:11:50 |
alpha---sequence logo (eps format) (pdf format) | T0301.t04.alpha-logo | 2006 May 25 19:12:00 |
alpha structure prediction (rdb format) (seq format) | T0301.t2k.alpha | 2006 May 25 19:12:02 |
Script for T0301.t2k.alpha coloring in rasmol | T0301.t2k.alpha-color.rasmol | 2006 May 25 19:12:02 |
alpha---sequence logo (eps format) (pdf format) | T0301.t2k.alpha-logo | 2006 May 25 19:12:10 |
bys structure prediction (rdb format) (seq format) | T0301.t06.bys | 2006 May 25 19:12:12 |
Script for T0301.t06.bys coloring in rasmol | T0301.t06.bys-color.rasmol | 2006 May 25 19:12:12 |
bys---sequence logo (eps format) (pdf format) | T0301.t06.bys-logo | 2006 May 25 19:12:22 |
bys structure prediction (rdb format) (seq format) | T0301.t04.bys | 2006 May 25 19:12:24 |
Script for T0301.t04.bys coloring in rasmol | T0301.t04.bys-color.rasmol | 2006 May 25 19:12:24 |
bys---sequence logo (eps format) (pdf format) | T0301.t04.bys-logo | 2006 May 25 19:12:34 |
bys structure prediction (rdb format) (seq format) | T0301.t2k.bys | 2006 May 25 19:12:36 |
Script for T0301.t2k.bys coloring in rasmol | T0301.t2k.bys-color.rasmol | 2006 May 25 19:12:36 |
bys---sequence logo (eps format) (pdf format) | T0301.t2k.bys-logo | 2006 May 25 19:12:46 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0301.t06.dssp-ehl2 | 2006 May 25 19:12:47 |
Script for T0301.t06.dssp-ehl2 coloring in rasmol | T0301.t06.dssp-ehl2-color.rasmol | 2006 May 25 19:12:47 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0301.t06.dssp-ehl2-logo | 2006 May 25 19:12:56 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0301.t04.dssp-ehl2 | 2006 May 25 19:12:57 |
Script for T0301.t04.dssp-ehl2 coloring in rasmol | T0301.t04.dssp-ehl2-color.rasmol | 2006 May 25 19:12:58 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0301.t04.dssp-ehl2-logo | 2006 May 25 19:13:07 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0301.t2k.dssp-ehl2 | 2006 May 25 19:13:08 |
Script for T0301.t2k.dssp-ehl2 coloring in rasmol | T0301.t2k.dssp-ehl2-color.rasmol | 2006 May 25 19:13:08 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0301.t2k.dssp-ehl2-logo | 2006 May 25 19:13:17 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0301.dssp-ehl2 | 2006 May 25 19:13:19 |
Script for T0301.dssp-ehl2 coloring in rasmol | T0301.dssp-ehl2-color.rasmol | 2006 May 25 19:13:19 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0301.dssp-ehl2-logo | 2006 May 25 19:13:28 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0301.t06.CB_burial_14_7 | 2006 May 25 19:13:30 |
Script for T0301.t06.CB_burial_14_7 coloring in rasmol | T0301.t06.CB_burial_14_7-color.rasmol | 2006 May 25 19:13:30 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0301.t06.CB_burial_14_7-logo | 2006 May 25 19:13:39 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0301.t04.CB_burial_14_7 | 2006 May 25 19:13:41 |
Script for T0301.t04.CB_burial_14_7 coloring in rasmol | T0301.t04.CB_burial_14_7-color.rasmol | 2006 May 25 19:13:42 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0301.t04.CB_burial_14_7-logo | 2006 May 25 19:13:50 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0301.t2k.CB_burial_14_7 | 2006 May 25 19:13:52 |
Script for T0301.t2k.CB_burial_14_7 coloring in rasmol | T0301.t2k.CB_burial_14_7-color.rasmol | 2006 May 25 19:13:52 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0301.t2k.CB_burial_14_7-logo | 2006 May 25 19:14:01 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0301.t06.near-backbone-11 | 2006 May 25 19:14:04 |
Script for T0301.t06.near-backbone-11 coloring in rasmol | T0301.t06.near-backbone-11-color.rasmol | 2006 May 25 19:14:04 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0301.t06.near-backbone-11-logo | 2006 May 25 19:14:13 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0301.t04.near-backbone-11 | 2006 May 25 19:14:15 |
Script for T0301.t04.near-backbone-11 coloring in rasmol | T0301.t04.near-backbone-11-color.rasmol | 2006 May 25 19:14:15 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0301.t04.near-backbone-11-logo | 2006 May 25 19:14:25 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0301.t2k.near-backbone-11 | 2006 May 25 19:14:27 |
Script for T0301.t2k.near-backbone-11 coloring in rasmol | T0301.t2k.near-backbone-11-color.rasmol | 2006 May 25 19:14:27 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0301.t2k.near-backbone-11-logo | 2006 May 25 19:14:36 |
Target model scores |
amino acid single-track target model scores of PDB | T0301.t06-w0.5-scores.html | 2006 May 25 19:18:04 |
amino acid single-track target model scores of PDB | T0301.t04-w0.5-scores.html | 2006 May 25 19:22:13 |
amino acid single-track target model scores of PDB | T0301.t2k-w0.5-scores.html | 2006 May 25 19:26:49 |
amino acid/100-30-str2 multi-track target model scores | T0301.t06-100-30-str2-scores.html | 2006 May 25 19:27:37 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0301.t06-100-30-stride-ebghtl-scores.html | 2006 May 25 19:28:24 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0301.t06-100-30-dssp-ebghstl-scores.html | 2006 May 25 19:29:11 |
amino acid/100-30-alpha multi-track target model scores | T0301.t06-100-30-alpha-scores.html | 2006 May 25 19:29:56 |
amino acid/100-30-bys multi-track target model scores | T0301.t06-100-30-bys-scores.html | 2006 May 25 19:30:42 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0301.t06-100-30-dssp-ehl2-scores.html | 2006 May 25 19:31:29 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0301.t06-100-30-CB_burial_14_7-scores.html | 2006 May 25 19:32:15 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0301.t06-100-30-near-backbone-11-scores.html | 2006 May 25 19:33:00 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0301.t06-100-40-40-str2+CB_burial_14_7-scores.html | 2006 May 25 19:33:53 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0301.t06-80-60-80-str2+near-backbone-11-scores.html | 2006 May 25 19:34:47 |
amino acid/100-30-str2 multi-track target model scores | T0301.t04-100-30-str2-scores.html | 2006 May 25 19:36:28 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0301.t04-100-30-stride-ebghtl-scores.html | 2006 May 25 19:38:08 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0301.t04-100-30-dssp-ebghstl-scores.html | 2006 May 25 19:39:49 |
amino acid/100-30-alpha multi-track target model scores | T0301.t04-100-30-alpha-scores.html | 2006 May 25 19:41:27 |
amino acid/100-30-bys multi-track target model scores | T0301.t04-100-30-bys-scores.html | 2006 May 25 19:43:07 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0301.t04-100-30-dssp-ehl2-scores.html | 2006 May 25 19:44:46 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0301.t04-100-30-CB_burial_14_7-scores.html | 2006 May 25 19:46:26 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0301.t04-100-30-near-backbone-11-scores.html | 2006 May 25 19:48:03 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0301.t04-100-40-40-str2+CB_burial_14_7-scores.html | 2006 May 25 19:49:56 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0301.t04-80-60-80-str2+near-backbone-11-scores.html | 2006 May 25 19:51:54 |
amino acid/100-30-str2 multi-track target model scores | T0301.t2k-100-30-str2-scores.html | 2006 May 25 19:54:11 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0301.t2k-100-30-stride-ebghtl-scores.html | 2006 May 25 19:56:28 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0301.t2k-100-30-dssp-ebghstl-scores.html | 2006 May 25 19:58:45 |
amino acid/100-30-alpha multi-track target model scores | T0301.t2k-100-30-alpha-scores.html | 2006 May 25 20:01:01 |
amino acid/100-30-bys multi-track target model scores | T0301.t2k-100-30-bys-scores.html | 2006 May 25 20:03:15 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0301.t2k-100-30-dssp-ehl2-scores.html | 2006 May 25 20:05:30 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0301.t2k-100-30-CB_burial_14_7-scores.html | 2006 May 25 20:07:43 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0301.t2k-100-30-near-backbone-11-scores.html | 2006 May 25 20:09:55 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0301.t2k-100-40-40-str2+CB_burial_14_7-scores.html | 2006 May 25 20:12:28 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0301.t2k-80-60-80-str2+near-backbone-11-scores.html | 2006 May 25 20:15:08 |
Template model scores |
Annotated t06 template model scores | T0301.t06-template-lib-scores.html | 2006 May 25 20:34:46 |
Annotated t04 template model scores | T0301.t04-template-lib-scores.html | 2006 May 25 21:17:35 |
Annotated t2k template model scores | T0301.t2k-template-lib-scores.html | 2006 May 25 22:14:55 |
Top Hits |
Best scoring hits from t06 HMMs | T0301.t06.best-scores.html | 2006 May 25 22:15:00 |
Best scoring hits from t04 HMMs | T0301.t04.best-scores.html | 2006 May 25 22:15:02 |
Best scoring hits from t2k HMMs | T0301.t2k.best-scores.html | 2006 May 25 22:15:05 |
Best scoring hits from combining t06 t04 t2k | T0301.best-scores.html | 2006 May 25 22:15:08 |
Alignments for Top Hits |
Top alignments from t06 hits | T0301.t06.top_reported_alignments.html | 2006 May 25 22:40:45 |
Top alignments from t04 hits | T0301.t04.top_reported_alignments.html | 2006 May 25 22:40:56 |
Top alignments from t2k hits | T0301.t2k.top_reported_alignments.html | 2006 May 25 22:41:07 |
Top alignments from combined hits | T0301.top_reported_alignments.html | 2006 May 25 22:41:11 |
multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2006 May 25 22:41:29 |
Undertaker (3d) files |
Undertaker input for top t06 alignments | T0301.t06.undertaker-align.under | 2006 May 25 22:41:30 |
Undertaker input for top t04 alignments | T0301.t04.undertaker-align.under | 2006 May 25 22:41:30 |
Undertaker input for top t2k alignments | T0301.t2k.undertaker-align.under | 2006 May 25 22:41:30 |
Undertaker input for top combined alignments | T0301.undertaker-align.under | 2006 May 25 22:41:31 |
PDB file with model(s) for top alignments | T0301.undertaker-align.pdb.gz | 2006 May 25 22:42:31 |
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) | T0301.t06.many.frag.gz | 2006 May 25 22:44:36 |
Fragment list for undertaker (from fragfinder) | T0301.t04.many.frag.gz | 2006 May 25 22:45:29 |
Fragment list for undertaker (from fragfinder) | T0301.t2k.many.frag.gz | 2006 May 25 22:46:23 |
Contact predictions, based on |
contact predictions (rr format) (rr.constraints format) | T0301.449a_45 | 2006 May 25 22:47:08 |
First attempted model using undertaker | decoys/T0301.try1-opt2.pdb.gz | 2006 May 26 0:53:18 |
Images of complete model in decoys/T0301.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