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 | T0398.a2m | 2008 May 12 9:20:00 |
README file | README | 2008 May 12 9:20:04 |
Quick blastp of non-redundant PDB | T0398.pdb_blast.txt | 2008 May 12 9:20:10 |
Multiple alignment |
SAM_t04 multiple alignment in a2m format | T0398.t04.a2m.gz | 2008 May 12 9:42:55 |
SAM_t04 multiple alignment in pretty html format | T0398.t04.pa.html | 2008 May 12 9:44:38 |
SAM_t04 target hidden Markov model | T0398.t04.w0.5.mod | 2008 May 12 9:44:43 |
SAM_t04 multiple alignment---sequence logo (eps format) (pdf format) | T0398.t04.w0.5-logo | 2008 May 12 9:44:54 |
Script for highlighting in rasmol | conserved_t04 | 2008 May 12 9:44:55 |
SAM_t2k multiple alignment in a2m format | T0398.t2k.a2m.gz | 2008 May 12 9:57:12 |
SAM_t2k multiple alignment in pretty html format | T0398.t2k.pa.html | 2008 May 12 9:59:50 |
SAM_t2k target hidden Markov model | T0398.t2k.w0.5.mod | 2008 May 12 9:59:56 |
SAM_t2k multiple alignment---sequence logo (eps format) (pdf format) | T0398.t2k.w0.5-logo | 2008 May 12 10:00:07 |
Script for highlighting in rasmol | conserved_t2k | 2008 May 12 10:00:08 |
Secondary Structure Prediction (Explanation of secondary-structure predictions) |
str2 structure prediction (rdb format) (seq format) | T0398.t04.str2 | 2008 May 12 9:44:51 |
Script for T0398.t04.str2 coloring in rasmol | T0398.t04.str2-color.rasmol | 2008 May 12 10:00:09 |
str2---sequence logo (eps format) (pdf format) | T0398.t04.str2-logo | 2008 May 12 10:00:12 |
str2 structure prediction (rdb format) (seq format) | T0398.t2k.str2 | 2008 May 12 10:00:04 |
Script for T0398.t2k.str2 coloring in rasmol | T0398.t2k.str2-color.rasmol | 2008 May 12 10:00:13 |
str2---sequence logo (eps format) (pdf format) | T0398.t2k.str2-logo | 2008 May 12 10:00:18 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0398.t04.stride-ebghtl | 2008 May 12 10:00:22 |
Script for T0398.t04.stride-ebghtl coloring in rasmol | T0398.t04.stride-ebghtl-color.rasmol | 2008 May 12 10:00:22 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0398.t04.stride-ebghtl-logo | 2008 May 12 10:00:26 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0398.t2k.stride-ebghtl | 2008 May 12 10:00:30 |
Script for T0398.t2k.stride-ebghtl coloring in rasmol | T0398.t2k.stride-ebghtl-color.rasmol | 2008 May 12 10:00:31 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0398.t2k.stride-ebghtl-logo | 2008 May 12 10:00:34 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0398.t04.dssp-ebghstl | 2008 May 12 10:00:39 |
Script for T0398.t04.dssp-ebghstl coloring in rasmol | T0398.t04.dssp-ebghstl-color.rasmol | 2008 May 12 10:00:39 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0398.t04.dssp-ebghstl-logo | 2008 May 12 10:00:42 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0398.t2k.dssp-ebghstl | 2008 May 12 10:00:44 |
Script for T0398.t2k.dssp-ebghstl coloring in rasmol | T0398.t2k.dssp-ebghstl-color.rasmol | 2008 May 12 10:00:44 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0398.t2k.dssp-ebghstl-logo | 2008 May 12 10:00:48 |
alpha structure prediction (rdb format) (seq format) | T0398.t04.alpha | 2008 May 12 10:00:52 |
Script for T0398.t04.alpha coloring in rasmol | T0398.t04.alpha-color.rasmol | 2008 May 12 10:00:53 |
alpha---sequence logo (eps format) (pdf format) | T0398.t04.alpha-logo | 2008 May 12 10:00:56 |
alpha structure prediction (rdb format) (seq format) | T0398.t2k.alpha | 2008 May 12 10:00:58 |
Script for T0398.t2k.alpha coloring in rasmol | T0398.t2k.alpha-color.rasmol | 2008 May 12 10:00:58 |
alpha---sequence logo (eps format) (pdf format) | T0398.t2k.alpha-logo | 2008 May 12 10:01:02 |
bys structure prediction (rdb format) (seq format) | T0398.t04.bys | 2008 May 12 10:01:07 |
Script for T0398.t04.bys coloring in rasmol | T0398.t04.bys-color.rasmol | 2008 May 12 10:01:07 |
bys---sequence logo (eps format) (pdf format) | T0398.t04.bys-logo | 2008 May 12 10:01:10 |
bys structure prediction (rdb format) (seq format) | T0398.t2k.bys | 2008 May 12 10:01:14 |
Script for T0398.t2k.bys coloring in rasmol | T0398.t2k.bys-color.rasmol | 2008 May 12 10:01:14 |
bys---sequence logo (eps format) (pdf format) | T0398.t2k.bys-logo | 2008 May 12 10:01:17 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0398.t04.dssp-ehl2 | 2008 May 12 10:01:19 |
Script for T0398.t04.dssp-ehl2 coloring in rasmol | T0398.t04.dssp-ehl2-color.rasmol | 2008 May 12 10:01:19 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0398.t04.dssp-ehl2-logo | 2008 May 12 10:01:24 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0398.t2k.dssp-ehl2 | 2008 May 12 10:01:25 |
Script for T0398.t2k.dssp-ehl2 coloring in rasmol | T0398.t2k.dssp-ehl2-color.rasmol | 2008 May 12 10:01:25 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0398.t2k.dssp-ehl2-logo | 2008 May 12 10:01:28 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0398.dssp-ehl2 | 2008 May 12 10:01:30 |
Script for T0398.dssp-ehl2 coloring in rasmol | T0398.dssp-ehl2-color.rasmol | 2008 May 12 10:01:32 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0398.dssp-ehl2-logo | 2008 May 12 10:01:36 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0398.t04.CB_burial_14_7 | 2008 May 12 10:01:42 |
Script for T0398.t04.CB_burial_14_7 coloring in rasmol | T0398.t04.CB_burial_14_7-color.rasmol | 2008 May 12 10:01:42 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0398.t04.CB_burial_14_7-logo | 2008 May 12 10:01:45 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0398.t2k.CB_burial_14_7 | 2008 May 12 10:01:47 |
Script for T0398.t2k.CB_burial_14_7 coloring in rasmol | T0398.t2k.CB_burial_14_7-color.rasmol | 2008 May 12 10:01:47 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0398.t2k.CB_burial_14_7-logo | 2008 May 12 10:01:50 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0398.t04.near-backbone-11 | 2008 May 12 10:01:56 |
Script for T0398.t04.near-backbone-11 coloring in rasmol | T0398.t04.near-backbone-11-color.rasmol | 2008 May 12 10:01:57 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0398.t04.near-backbone-11-logo | 2008 May 12 10:02:00 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0398.t2k.near-backbone-11 | 2008 May 12 10:02:05 |
Script for T0398.t2k.near-backbone-11 coloring in rasmol | T0398.t2k.near-backbone-11-color.rasmol | 2008 May 12 10:02:05 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0398.t2k.near-backbone-11-logo | 2008 May 12 10:02:08 |
Target model scores |
amino acid single-track target model scores of PDB | T0398.t04-w0.5-scores.html | 2008 May 12 10:10:56 |
amino acid single-track target model scores of PDB | T0398.t2k-w0.5-scores.html | 2008 May 12 10:19:52 |
amino acid/100-30-str2 multi-track target model scores | T0398.t2k-100-30-str2-scores.html | 2008 May 12 10:23:34 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0398.t2k-100-30-stride-ebghtl-scores.html | 2008 May 12 10:27:16 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0398.t2k-100-30-dssp-ebghstl-scores.html | 2008 May 12 10:31:02 |
amino acid/100-30-alpha multi-track target model scores | T0398.t2k-100-30-alpha-scores.html | 2008 May 12 10:34:47 |
amino acid/100-30-bys multi-track target model scores | T0398.t2k-100-30-bys-scores.html | 2008 May 12 10:38:33 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0398.t2k-100-30-dssp-ehl2-scores.html | 2008 May 12 10:42:16 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0398.t2k-100-30-CB_burial_14_7-scores.html | 2008 May 12 10:46:01 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0398.t2k-100-30-near-backbone-11-scores.html | 2008 May 12 10:49:47 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0398.t2k-100-40-40-str2+CB_burial_14_7-scores.html | 2008 May 12 10:53:49 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0398.t2k-80-60-80-str2+near-backbone-11-scores.html | 2008 May 12 10:57:53 |
amino acid/100-30-str2 multi-track target model scores | T0398.t04-100-30-str2-scores.html | 2008 May 12 11:01:17 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0398.t04-100-30-stride-ebghtl-scores.html | 2008 May 12 11:04:40 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0398.t04-100-30-dssp-ebghstl-scores.html | 2008 May 12 11:08:04 |
amino acid/100-30-alpha multi-track target model scores | T0398.t04-100-30-alpha-scores.html | 2008 May 12 11:11:30 |
amino acid/100-30-bys multi-track target model scores | T0398.t04-100-30-bys-scores.html | 2008 May 12 11:14:54 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0398.t04-100-30-dssp-ehl2-scores.html | 2008 May 12 11:18:20 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0398.t04-100-30-CB_burial_14_7-scores.html | 2008 May 12 11:21:46 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0398.t04-100-30-near-backbone-11-scores.html | 2008 May 12 11:25:09 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0398.t04-100-40-40-str2+CB_burial_14_7-scores.html | 2008 May 12 11:28:49 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0398.t04-80-60-80-str2+near-backbone-11-scores.html | 2008 May 12 11:32:33 |
Template model scores |
Annotated t04 template model scores | T0398.t04-template-lib-scores.html | 2008 May 12 11:38:31 |
Annotated t2k template model scores | T0398.t2k-template-lib-scores.html | 2008 May 12 11:45:13 |
Top Hits |
Best scoring hits from t04 HMMs | T0398.t04.best-scores.html | 2008 May 12 11:45:19 |
Best scoring hits from t2k HMMs | T0398.t2k.best-scores.html | 2008 May 12 11:45:22 |
Best scoring hits from combining t04 t2k | T0398.best-scores.html | 2008 May 12 11:45:25 |
Alignments for Top Hits |
Top alignments from t04 hits | T0398.t04.top_reported_alignments.html | 2008 May 12 13:43:05 |
Top alignments from t2k hits | T0398.t2k.top_reported_alignments.html | 2008 May 12 13:43:23 |
Top alignments from combined hits | T0398.top_reported_alignments.html | 2008 May 12 13:43:34 |
multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2008 May 12 13:44:35 |
Undertaker (3d) files |
Undertaker input for top t04 alignments | T0398.t04.undertaker-align.under | 2008 May 12 13:44:36 |
Undertaker input for top t2k alignments | T0398.t2k.undertaker-align.under | 2008 May 12 13:44:36 |
Undertaker input for top combined alignments | T0398.undertaker-align.under | 2008 May 12 13:44:36 |
PDB file with model(s) for top alignments | T0398.undertaker-align.pdb.gz | 2008 May 12 13:46:50 |
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) | T0398.t04.many.frag.gz | 2008 May 12 13:49:44 |
Fragment list for undertaker (from fragfinder) | T0398.t2k.many.frag.gz | 2008 May 12 13:50:57 |
Contact predictions, based on |
contact predictions (rr format) (rr.constraints format) | T0398.449a_45 | 2008 May 12 13:54:35 |
First attempted model using undertaker | decoys/T0398.try1-opt2.pdb.gz | 2008 May 12 17:47:39 |
Images of complete model in decoys/T0398.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