Please cite the following papers:
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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 | T0588.a2m | 2010 Jun 14 9:09:30 |
README file | README | 2010 Jun 14 9:09:47 |
Quick blastp of non-redundant PDB | T0588.pdb_blast.txt | 2010 Jun 14 9:09:56 |
Multiple alignment |
SAM_t04 multiple alignment in a2m format | T0588.t04.a2m.gz | 2010 Jun 14 9:26:43 |
SAM_t04 multiple alignment in pretty html format | T0588.t04.pa.html | 2010 Jun 14 9:27:09 |
SAM_t04 target hidden Markov model | T0588.t04.w0.5.mod | 2010 Jun 14 9:27:14 |
SAM_t04 multiple alignment---sequence logo (eps format) (pdf format) | T0588.t04.w0.5-logo | 2010 Jun 14 9:27:24 |
Script for highlighting in rasmol | conserved_t04 | 2010 Jun 14 9:27:25 |
SAM_t2k multiple alignment in a2m format | T0588.t2k.a2m.gz | 2010 Jun 14 9:35:04 |
SAM_t2k multiple alignment in pretty html format | T0588.t2k.pa.html | 2010 Jun 14 9:35:14 |
SAM_t2k target hidden Markov model | T0588.t2k.w0.5.mod | 2010 Jun 14 9:35:17 |
SAM_t2k multiple alignment---sequence logo (eps format) (pdf format) | T0588.t2k.w0.5-logo | 2010 Jun 14 9:35:23 |
Script for highlighting in rasmol | conserved_t2k | 2010 Jun 14 9:35:25 |
Secondary Structure Prediction (Explanation of secondary-structure predictions) |
str2 structure prediction (rdb format) (seq format) | T0588.t04.str2 | 2010 Jun 14 9:27:20 |
Script for T0588.t04.str2 coloring in rasmol | T0588.t04.str2-color.rasmol | 2010 Jun 14 9:35:27 |
str2---sequence logo (eps format) (pdf format) | T0588.t04.str2-logo | 2010 Jun 14 9:35:31 |
str2 structure prediction (rdb format) (seq format) | T0588.t2k.str2 | 2010 Jun 14 9:35:20 |
Script for T0588.t2k.str2 coloring in rasmol | T0588.t2k.str2-color.rasmol | 2010 Jun 14 9:35:33 |
str2---sequence logo (eps format) (pdf format) | T0588.t2k.str2-logo | 2010 Jun 14 9:35:39 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0588.t04.stride-ebghtl | 2010 Jun 14 9:35:43 |
Script for T0588.t04.stride-ebghtl coloring in rasmol | T0588.t04.stride-ebghtl-color.rasmol | 2010 Jun 14 9:35:44 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0588.t04.stride-ebghtl-logo | 2010 Jun 14 9:35:47 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0588.t2k.stride-ebghtl | 2010 Jun 14 9:35:51 |
Script for T0588.t2k.stride-ebghtl coloring in rasmol | T0588.t2k.stride-ebghtl-color.rasmol | 2010 Jun 14 9:35:51 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0588.t2k.stride-ebghtl-logo | 2010 Jun 14 9:35:56 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0588.t04.dssp-ebghstl | 2010 Jun 14 9:36:00 |
Script for T0588.t04.dssp-ebghstl coloring in rasmol | T0588.t04.dssp-ebghstl-color.rasmol | 2010 Jun 14 9:36:00 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0588.t04.dssp-ebghstl-logo | 2010 Jun 14 9:36:04 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0588.t2k.dssp-ebghstl | 2010 Jun 14 9:36:07 |
Script for T0588.t2k.dssp-ebghstl coloring in rasmol | T0588.t2k.dssp-ebghstl-color.rasmol | 2010 Jun 14 9:36:08 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0588.t2k.dssp-ebghstl-logo | 2010 Jun 14 9:36:11 |
alpha structure prediction (rdb format) (seq format) | T0588.t04.alpha | 2010 Jun 14 9:36:15 |
Script for T0588.t04.alpha coloring in rasmol | T0588.t04.alpha-color.rasmol | 2010 Jun 14 9:36:15 |
alpha---sequence logo (eps format) (pdf format) | T0588.t04.alpha-logo | 2010 Jun 14 9:36:19 |
alpha structure prediction (rdb format) (seq format) | T0588.t2k.alpha | 2010 Jun 14 9:36:22 |
Script for T0588.t2k.alpha coloring in rasmol | T0588.t2k.alpha-color.rasmol | 2010 Jun 14 9:36:22 |
alpha---sequence logo (eps format) (pdf format) | T0588.t2k.alpha-logo | 2010 Jun 14 9:36:26 |
bys structure prediction (rdb format) (seq format) | T0588.t04.bys | 2010 Jun 14 9:36:31 |
Script for T0588.t04.bys coloring in rasmol | T0588.t04.bys-color.rasmol | 2010 Jun 14 9:36:31 |
bys---sequence logo (eps format) (pdf format) | T0588.t04.bys-logo | 2010 Jun 14 9:36:35 |
bys structure prediction (rdb format) (seq format) | T0588.t2k.bys | 2010 Jun 14 9:36:38 |
Script for T0588.t2k.bys coloring in rasmol | T0588.t2k.bys-color.rasmol | 2010 Jun 14 9:36:39 |
bys---sequence logo (eps format) (pdf format) | T0588.t2k.bys-logo | 2010 Jun 14 9:36:43 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0588.t04.dssp-ehl2 | 2010 Jun 14 9:36:46 |
Script for T0588.t04.dssp-ehl2 coloring in rasmol | T0588.t04.dssp-ehl2-color.rasmol | 2010 Jun 14 9:36:46 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0588.t04.dssp-ehl2-logo | 2010 Jun 14 9:36:50 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0588.t2k.dssp-ehl2 | 2010 Jun 14 9:36:51 |
Script for T0588.t2k.dssp-ehl2 coloring in rasmol | T0588.t2k.dssp-ehl2-color.rasmol | 2010 Jun 14 9:36:52 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0588.t2k.dssp-ehl2-logo | 2010 Jun 14 9:36:55 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0588.dssp-ehl2 | 2010 Jun 14 9:36:59 |
Script for T0588.dssp-ehl2 coloring in rasmol | T0588.dssp-ehl2-color.rasmol | 2010 Jun 14 9:36:59 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0588.dssp-ehl2-logo | 2010 Jun 14 9:37:02 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0588.t04.CB_burial_14_7 | 2010 Jun 14 9:37:08 |
Script for T0588.t04.CB_burial_14_7 coloring in rasmol | T0588.t04.CB_burial_14_7-color.rasmol | 2010 Jun 14 9:37:08 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0588.t04.CB_burial_14_7-logo | 2010 Jun 14 9:37:13 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0588.t2k.CB_burial_14_7 | 2010 Jun 14 9:37:15 |
Script for T0588.t2k.CB_burial_14_7 coloring in rasmol | T0588.t2k.CB_burial_14_7-color.rasmol | 2010 Jun 14 9:37:16 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0588.t2k.CB_burial_14_7-logo | 2010 Jun 14 9:37:20 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0588.t04.near-backbone-11 | 2010 Jun 14 9:37:24 |
Script for T0588.t04.near-backbone-11 coloring in rasmol | T0588.t04.near-backbone-11-color.rasmol | 2010 Jun 14 9:37:24 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0588.t04.near-backbone-11-logo | 2010 Jun 14 9:37:30 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0588.t2k.near-backbone-11 | 2010 Jun 14 9:37:33 |
Script for T0588.t2k.near-backbone-11 coloring in rasmol | T0588.t2k.near-backbone-11-color.rasmol | 2010 Jun 14 9:37:34 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0588.t2k.near-backbone-11-logo | 2010 Jun 14 9:37:38 |
Target model scores |
amino acid single-track target model scores of PDB | T0588.t04-w0.5-scores.html | 2010 Jun 14 9:54:10 |
amino acid single-track target model scores of PDB | T0588.t2k-w0.5-scores.html | 2010 Jun 14 10:10:33 |
amino acid/100-30-str2 multi-track target model scores | T0588.t2k-100-30-str2-scores.html | 2010 Jun 14 10:17:46 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0588.t2k-100-30-stride-ebghtl-scores.html | 2010 Jun 14 10:24:57 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0588.t2k-100-30-dssp-ebghstl-scores.html | 2010 Jun 14 10:32:11 |
amino acid/100-30-alpha multi-track target model scores | T0588.t2k-100-30-alpha-scores.html | 2010 Jun 14 10:39:31 |
amino acid/100-30-bys multi-track target model scores | T0588.t2k-100-30-bys-scores.html | 2010 Jun 14 10:46:52 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0588.t2k-100-30-dssp-ehl2-scores.html | 2010 Jun 14 10:54:06 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0588.t2k-100-30-CB_burial_14_7-scores.html | 2010 Jun 14 11:01:21 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0588.t2k-100-30-near-backbone-11-scores.html | 2010 Jun 14 11:08:37 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0588.t2k-100-40-40-str2+CB_burial_14_7-scores.html | 2010 Jun 14 11:16:16 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0588.t2k-80-60-80-str2+near-backbone-11-scores.html | 2010 Jun 14 11:23:56 |
amino acid/100-30-str2 multi-track target model scores | T0588.t04-100-30-str2-scores.html | 2010 Jun 14 11:30:51 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0588.t04-100-30-stride-ebghtl-scores.html | 2010 Jun 14 11:37:45 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0588.t04-100-30-dssp-ebghstl-scores.html | 2010 Jun 14 11:44:42 |
amino acid/100-30-alpha multi-track target model scores | T0588.t04-100-30-alpha-scores.html | 2010 Jun 14 11:51:37 |
amino acid/100-30-bys multi-track target model scores | T0588.t04-100-30-bys-scores.html | 2010 Jun 14 11:58:33 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0588.t04-100-30-dssp-ehl2-scores.html | 2010 Jun 14 12:05:28 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0588.t04-100-30-CB_burial_14_7-scores.html | 2010 Jun 14 12:12:21 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0588.t04-100-30-near-backbone-11-scores.html | 2010 Jun 14 12:19:15 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0588.t04-100-40-40-str2+CB_burial_14_7-scores.html | 2010 Jun 14 12:26:42 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0588.t04-80-60-80-str2+near-backbone-11-scores.html | 2010 Jun 14 12:34:07 |
Template model scores |
Annotated t04 template model scores | T0588.t04-template-lib-scores.html | 2010 Jun 14 13:11:14 |
Annotated t2k template model scores | T0588.t2k-template-lib-scores.html | 2010 Jun 14 13:38:56 |
Top Hits |
Best scoring hits from t04 HMMs | T0588.t04.best-scores.html | 2010 Jun 14 13:39:02 |
Best scoring hits from t2k HMMs | T0588.t2k.best-scores.html | 2010 Jun 14 13:39:05 |
Best scoring hits from combining t04 t2k | T0588.best-scores.html | 2010 Jun 14 13:39:09 |
Alignments for Top Hits |
Top alignments from t04 hits | T0588.t04.top_reported_alignments.html | 2010 Jun 14 15:02:42 |
Top alignments from t2k hits | T0588.t2k.top_reported_alignments.html | 2010 Jun 14 15:03:00 |
Top alignments from combined hits | T0588.top_reported_alignments.html | 2010 Jun 14 15:03:09 |
multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2010 Jun 14 15:04:03 |
Undertaker (3d) files |
Undertaker input for top t04 alignments | T0588.t04.undertaker-align.under | 2010 Jun 14 15:04:05 |
Undertaker input for top t2k alignments | T0588.t2k.undertaker-align.under | 2010 Jun 14 15:04:05 |
Undertaker input for top combined alignments | T0588.undertaker-align.under | 2010 Jun 14 15:04:05 |
PDB file with model(s) for top alignments | T0588.undertaker-align.pdb.gz | 2010 Jun 14 15:17:19 |
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) | T0588.t04.many.frag.gz | 2010 Jun 14 15:19:11 |
Fragment list for undertaker (from fragfinder) | T0588.t2k.many.frag.gz | 2010 Jun 14 15:20:49 |
Contact predictions, based on |
contact predictions (rr format) (rr.constraints format) | T0588.449a_45 | 2010 Jun 14 15:25:35 |
First attempted model using undertaker | decoys/T0588.try1-opt2.pdb.gz | 2010 Jun 15 6:58:23 |
Images of complete model in decoys/T0588.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