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 | T0582.a2m | 2010 Jun 9 9:14:41 |
README file | README | 2010 Jun 9 10:15:54 |
Quick blastp of non-redundant PDB | T0582.pdb_blast.txt | 2010 Jun 9 10:16:17 |
Multiple alignment |
SAM_t04 multiple alignment in a2m format | T0582.t04.a2m.gz | 2010 Jun 9 10:42:57 |
SAM_t04 multiple alignment in pretty html format | T0582.t04.pa.html | 2010 Jun 9 10:44:52 |
SAM_t04 target hidden Markov model | T0582.t04.w0.5.mod | 2010 Jun 9 10:45:01 |
SAM_t04 multiple alignment---sequence logo (eps format) (pdf format) | T0582.t04.w0.5-logo | 2010 Jun 9 10:45:18 |
Script for highlighting in rasmol | conserved_t04 | 2010 Jun 9 10:45:19 |
SAM_t2k multiple alignment in a2m format | T0582.t2k.a2m.gz | 2010 Jun 9 10:51:38 |
SAM_t2k multiple alignment in pretty html format | T0582.t2k.pa.html | 2010 Jun 9 10:52:02 |
SAM_t2k target hidden Markov model | T0582.t2k.w0.5.mod | 2010 Jun 9 10:52:06 |
SAM_t2k multiple alignment---sequence logo (eps format) (pdf format) | T0582.t2k.w0.5-logo | 2010 Jun 9 10:52:18 |
Script for highlighting in rasmol | conserved_t2k | 2010 Jun 9 10:52:20 |
Secondary Structure Prediction (Explanation of secondary-structure predictions) |
str2 structure prediction (rdb format) (seq format) | T0582.t04.str2 | 2010 Jun 9 10:45:09 |
Script for T0582.t04.str2 coloring in rasmol | T0582.t04.str2-color.rasmol | 2010 Jun 9 10:52:24 |
str2---sequence logo (eps format) (pdf format) | T0582.t04.str2-logo | 2010 Jun 9 10:52:39 |
str2 structure prediction (rdb format) (seq format) | T0582.t2k.str2 | 2010 Jun 9 10:52:11 |
Script for T0582.t2k.str2 coloring in rasmol | T0582.t2k.str2-color.rasmol | 2010 Jun 9 10:52:41 |
str2---sequence logo (eps format) (pdf format) | T0582.t2k.str2-logo | 2010 Jun 9 10:52:49 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0582.t04.stride-ebghtl | 2010 Jun 9 10:52:54 |
Script for T0582.t04.stride-ebghtl coloring in rasmol | T0582.t04.stride-ebghtl-color.rasmol | 2010 Jun 9 10:52:55 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0582.t04.stride-ebghtl-logo | 2010 Jun 9 10:53:06 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0582.t2k.stride-ebghtl | 2010 Jun 9 10:53:10 |
Script for T0582.t2k.stride-ebghtl coloring in rasmol | T0582.t2k.stride-ebghtl-color.rasmol | 2010 Jun 9 10:53:10 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0582.t2k.stride-ebghtl-logo | 2010 Jun 9 10:53:17 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0582.t04.dssp-ebghstl | 2010 Jun 9 10:53:23 |
Script for T0582.t04.dssp-ebghstl coloring in rasmol | T0582.t04.dssp-ebghstl-color.rasmol | 2010 Jun 9 10:53:23 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0582.t04.dssp-ebghstl-logo | 2010 Jun 9 10:53:32 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0582.t2k.dssp-ebghstl | 2010 Jun 9 10:53:36 |
Script for T0582.t2k.dssp-ebghstl coloring in rasmol | T0582.t2k.dssp-ebghstl-color.rasmol | 2010 Jun 9 10:53:36 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0582.t2k.dssp-ebghstl-logo | 2010 Jun 9 10:53:45 |
alpha structure prediction (rdb format) (seq format) | T0582.t04.alpha | 2010 Jun 9 10:53:51 |
Script for T0582.t04.alpha coloring in rasmol | T0582.t04.alpha-color.rasmol | 2010 Jun 9 10:53:52 |
alpha---sequence logo (eps format) (pdf format) | T0582.t04.alpha-logo | 2010 Jun 9 10:53:59 |
alpha structure prediction (rdb format) (seq format) | T0582.t2k.alpha | 2010 Jun 9 10:54:02 |
Script for T0582.t2k.alpha coloring in rasmol | T0582.t2k.alpha-color.rasmol | 2010 Jun 9 10:54:03 |
alpha---sequence logo (eps format) (pdf format) | T0582.t2k.alpha-logo | 2010 Jun 9 10:54:08 |
bys structure prediction (rdb format) (seq format) | T0582.t04.bys | 2010 Jun 9 10:54:13 |
Script for T0582.t04.bys coloring in rasmol | T0582.t04.bys-color.rasmol | 2010 Jun 9 10:54:14 |
bys---sequence logo (eps format) (pdf format) | T0582.t04.bys-logo | 2010 Jun 9 10:54:22 |
bys structure prediction (rdb format) (seq format) | T0582.t2k.bys | 2010 Jun 9 10:54:26 |
Script for T0582.t2k.bys coloring in rasmol | T0582.t2k.bys-color.rasmol | 2010 Jun 9 10:54:27 |
bys---sequence logo (eps format) (pdf format) | T0582.t2k.bys-logo | 2010 Jun 9 10:54:35 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0582.t04.dssp-ehl2 | 2010 Jun 9 10:54:40 |
Script for T0582.t04.dssp-ehl2 coloring in rasmol | T0582.t04.dssp-ehl2-color.rasmol | 2010 Jun 9 10:54:41 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0582.t04.dssp-ehl2-logo | 2010 Jun 9 10:54:48 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0582.t2k.dssp-ehl2 | 2010 Jun 9 10:54:51 |
Script for T0582.t2k.dssp-ehl2 coloring in rasmol | T0582.t2k.dssp-ehl2-color.rasmol | 2010 Jun 9 10:54:52 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0582.t2k.dssp-ehl2-logo | 2010 Jun 9 10:54:58 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0582.dssp-ehl2 | 2010 Jun 9 10:55:03 |
Script for T0582.dssp-ehl2 coloring in rasmol | T0582.dssp-ehl2-color.rasmol | 2010 Jun 9 10:55:03 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0582.dssp-ehl2-logo | 2010 Jun 9 10:55:13 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0582.t04.CB_burial_14_7 | 2010 Jun 9 10:55:20 |
Script for T0582.t04.CB_burial_14_7 coloring in rasmol | T0582.t04.CB_burial_14_7-color.rasmol | 2010 Jun 9 10:55:21 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0582.t04.CB_burial_14_7-logo | 2010 Jun 9 10:55:29 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0582.t2k.CB_burial_14_7 | 2010 Jun 9 10:55:32 |
Script for T0582.t2k.CB_burial_14_7 coloring in rasmol | T0582.t2k.CB_burial_14_7-color.rasmol | 2010 Jun 9 10:55:33 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0582.t2k.CB_burial_14_7-logo | 2010 Jun 9 10:55:40 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0582.t04.near-backbone-11 | 2010 Jun 9 10:55:47 |
Script for T0582.t04.near-backbone-11 coloring in rasmol | T0582.t04.near-backbone-11-color.rasmol | 2010 Jun 9 10:55:47 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0582.t04.near-backbone-11-logo | 2010 Jun 9 10:55:53 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0582.t2k.near-backbone-11 | 2010 Jun 9 10:55:56 |
Script for T0582.t2k.near-backbone-11 coloring in rasmol | T0582.t2k.near-backbone-11-color.rasmol | 2010 Jun 9 10:55:57 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0582.t2k.near-backbone-11-logo | 2010 Jun 9 10:56:01 |
Target model scores |
amino acid single-track target model scores of PDB | T0582.t04-w0.5-scores.html | 2010 Jun 9 11:05:27 |
amino acid single-track target model scores of PDB | T0582.t2k-w0.5-scores.html | 2010 Jun 9 11:14:41 |
amino acid/100-30-str2 multi-track target model scores | T0582.t2k-100-30-str2-scores.html | 2010 Jun 9 11:18:54 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0582.t2k-100-30-stride-ebghtl-scores.html | 2010 Jun 9 11:22:58 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0582.t2k-100-30-dssp-ebghstl-scores.html | 2010 Jun 9 11:27:02 |
amino acid/100-30-alpha multi-track target model scores | T0582.t2k-100-30-alpha-scores.html | 2010 Jun 9 11:31:06 |
amino acid/100-30-bys multi-track target model scores | T0582.t2k-100-30-bys-scores.html | 2010 Jun 9 11:35:12 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0582.t2k-100-30-dssp-ehl2-scores.html | 2010 Jun 9 11:39:15 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0582.t2k-100-30-CB_burial_14_7-scores.html | 2010 Jun 9 11:43:20 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0582.t2k-100-30-near-backbone-11-scores.html | 2010 Jun 9 11:47:23 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0582.t2k-100-40-40-str2+CB_burial_14_7-scores.html | 2010 Jun 9 11:51:44 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0582.t2k-80-60-80-str2+near-backbone-11-scores.html | 2010 Jun 9 11:56:09 |
amino acid/100-30-str2 multi-track target model scores | T0582.t04-100-30-str2-scores.html | 2010 Jun 9 12:00:06 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0582.t04-100-30-stride-ebghtl-scores.html | 2010 Jun 9 12:04:00 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0582.t04-100-30-dssp-ebghstl-scores.html | 2010 Jun 9 12:07:54 |
amino acid/100-30-alpha multi-track target model scores | T0582.t04-100-30-alpha-scores.html | 2010 Jun 9 12:11:45 |
amino acid/100-30-bys multi-track target model scores | T0582.t04-100-30-bys-scores.html | 2010 Jun 9 12:15:37 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0582.t04-100-30-dssp-ehl2-scores.html | 2010 Jun 9 12:19:30 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0582.t04-100-30-CB_burial_14_7-scores.html | 2010 Jun 9 12:23:23 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0582.t04-100-30-near-backbone-11-scores.html | 2010 Jun 9 12:27:16 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0582.t04-100-40-40-str2+CB_burial_14_7-scores.html | 2010 Jun 9 12:31:24 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0582.t04-80-60-80-str2+near-backbone-11-scores.html | 2010 Jun 9 12:35:33 |
Template model scores |
Annotated t04 template model scores | T0582.t04-template-lib-scores.html | 2010 Jun 9 15:11:27 |
Annotated t2k template model scores | T0582.t2k-template-lib-scores.html | 2010 Jun 9 18:32:22 |
Top Hits |
Best scoring hits from t04 HMMs | T0582.t04.best-scores.html | 2010 Jun 9 18:32:32 |
Best scoring hits from t2k HMMs | T0582.t2k.best-scores.html | 2010 Jun 9 18:32:36 |
Best scoring hits from combining t04 t2k | T0582.best-scores.html | 2010 Jun 9 18:32:40 |
Alignments for Top Hits |
Top alignments from t04 hits | T0582.t04.top_reported_alignments.html | 2010 Jun 9 21:22:46 |
Top alignments from t2k hits | T0582.t2k.top_reported_alignments.html | 2010 Jun 9 21:23:54 |
Top alignments from combined hits | T0582.top_reported_alignments.html | 2010 Jun 9 21:25:24 |
multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2010 Jun 9 21:29:33 |
Undertaker (3d) files |
Undertaker input for top t04 alignments | T0582.t04.undertaker-align.under | 2010 Jun 9 21:29:36 |
Undertaker input for top t2k alignments | T0582.t2k.undertaker-align.under | 2010 Jun 9 21:29:37 |
Undertaker input for top combined alignments | T0582.undertaker-align.under | 2010 Jun 9 21:29:39 |
PDB file with model(s) for top alignments | T0582.undertaker-align.pdb.gz | 2010 Jun 9 21:33:51 |
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) | T0582.t04.many.frag.gz | 2010 Jun 9 21:35:26 |
Fragment list for undertaker (from fragfinder) | T0582.t2k.many.frag.gz | 2010 Jun 9 21:36:30 |
Contact predictions, based on |
contact predictions (rr format) (rr.constraints format) | T0582.449a_45 | 2010 Jun 9 21:38:42 |
First attempted model using undertaker | decoys/T0582.try1-opt2.pdb.gz | 2010 Jun 10 8:48:11 |
Images of complete model in decoys/T0582.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:
This page has finished loading, and your query has now been completely processed.
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