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 | T0545.a2m | 2010 May 18 9:08:40 |
README file | README | 2010 May 18 9:09:08 |
Quick blastp of non-redundant PDB | T0545.pdb_blast.txt | 2010 May 18 9:09:15 |
Multiple alignment |
SAM_t04 multiple alignment in a2m format | T0545.t04.a2m.gz | 2010 May 18 9:19:54 |
SAM_t04 multiple alignment in pretty html format | T0545.t04.pa.html | 2010 May 18 9:20:53 |
SAM_t04 target hidden Markov model | T0545.t04.w0.5.mod | 2010 May 18 9:20:57 |
SAM_t04 multiple alignment---sequence logo (eps format) (pdf format) | T0545.t04.w0.5-logo | 2010 May 18 9:21:09 |
Script for highlighting in rasmol | conserved_t04 | 2010 May 18 9:21:11 |
SAM_t2k multiple alignment in a2m format | T0545.t2k.a2m.gz | 2010 May 18 9:26:23 |
SAM_t2k multiple alignment in pretty html format | T0545.t2k.pa.html | 2010 May 18 9:26:40 |
SAM_t2k target hidden Markov model | T0545.t2k.w0.5.mod | 2010 May 18 9:26:44 |
SAM_t2k multiple alignment---sequence logo (eps format) (pdf format) | T0545.t2k.w0.5-logo | 2010 May 18 9:26:55 |
Script for highlighting in rasmol | conserved_t2k | 2010 May 18 9:26:57 |
Secondary Structure Prediction (Explanation of secondary-structure predictions) |
str2 structure prediction (rdb format) (seq format) | T0545.t04.str2 | 2010 May 18 9:21:05 |
Script for T0545.t04.str2 coloring in rasmol | T0545.t04.str2-color.rasmol | 2010 May 18 9:27:02 |
str2---sequence logo (eps format) (pdf format) | T0545.t04.str2-logo | 2010 May 18 9:27:08 |
str2 structure prediction (rdb format) (seq format) | T0545.t2k.str2 | 2010 May 18 9:26:51 |
Script for T0545.t2k.str2 coloring in rasmol | T0545.t2k.str2-color.rasmol | 2010 May 18 9:27:11 |
str2---sequence logo (eps format) (pdf format) | T0545.t2k.str2-logo | 2010 May 18 9:27:17 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0545.t04.stride-ebghtl | 2010 May 18 9:27:24 |
Script for T0545.t04.stride-ebghtl coloring in rasmol | T0545.t04.stride-ebghtl-color.rasmol | 2010 May 18 9:27:25 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0545.t04.stride-ebghtl-logo | 2010 May 18 9:27:31 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0545.t2k.stride-ebghtl | 2010 May 18 9:27:37 |
Script for T0545.t2k.stride-ebghtl coloring in rasmol | T0545.t2k.stride-ebghtl-color.rasmol | 2010 May 18 9:27:38 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0545.t2k.stride-ebghtl-logo | 2010 May 18 9:27:44 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0545.t04.dssp-ebghstl | 2010 May 18 9:27:53 |
Script for T0545.t04.dssp-ebghstl coloring in rasmol | T0545.t04.dssp-ebghstl-color.rasmol | 2010 May 18 9:27:54 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0545.t04.dssp-ebghstl-logo | 2010 May 18 9:28:00 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0545.t2k.dssp-ebghstl | 2010 May 18 9:28:07 |
Script for T0545.t2k.dssp-ebghstl coloring in rasmol | T0545.t2k.dssp-ebghstl-color.rasmol | 2010 May 18 9:28:08 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0545.t2k.dssp-ebghstl-logo | 2010 May 18 9:28:15 |
alpha structure prediction (rdb format) (seq format) | T0545.t04.alpha | 2010 May 18 9:28:23 |
Script for T0545.t04.alpha coloring in rasmol | T0545.t04.alpha-color.rasmol | 2010 May 18 9:28:24 |
alpha---sequence logo (eps format) (pdf format) | T0545.t04.alpha-logo | 2010 May 18 9:28:31 |
alpha structure prediction (rdb format) (seq format) | T0545.t2k.alpha | 2010 May 18 9:28:37 |
Script for T0545.t2k.alpha coloring in rasmol | T0545.t2k.alpha-color.rasmol | 2010 May 18 9:28:38 |
alpha---sequence logo (eps format) (pdf format) | T0545.t2k.alpha-logo | 2010 May 18 9:28:44 |
bys structure prediction (rdb format) (seq format) | T0545.t04.bys | 2010 May 18 9:28:52 |
Script for T0545.t04.bys coloring in rasmol | T0545.t04.bys-color.rasmol | 2010 May 18 9:28:53 |
bys---sequence logo (eps format) (pdf format) | T0545.t04.bys-logo | 2010 May 18 9:28:59 |
bys structure prediction (rdb format) (seq format) | T0545.t2k.bys | 2010 May 18 9:29:03 |
Script for T0545.t2k.bys coloring in rasmol | T0545.t2k.bys-color.rasmol | 2010 May 18 9:29:04 |
bys---sequence logo (eps format) (pdf format) | T0545.t2k.bys-logo | 2010 May 18 9:29:09 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0545.t04.dssp-ehl2 | 2010 May 18 9:29:14 |
Script for T0545.t04.dssp-ehl2 coloring in rasmol | T0545.t04.dssp-ehl2-color.rasmol | 2010 May 18 9:29:14 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0545.t04.dssp-ehl2-logo | 2010 May 18 9:29:20 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0545.t2k.dssp-ehl2 | 2010 May 18 9:29:23 |
Script for T0545.t2k.dssp-ehl2 coloring in rasmol | T0545.t2k.dssp-ehl2-color.rasmol | 2010 May 18 9:29:23 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0545.t2k.dssp-ehl2-logo | 2010 May 18 9:29:28 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0545.dssp-ehl2 | 2010 May 18 9:29:34 |
Script for T0545.dssp-ehl2 coloring in rasmol | T0545.dssp-ehl2-color.rasmol | 2010 May 18 9:29:35 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0545.dssp-ehl2-logo | 2010 May 18 9:29:40 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0545.t04.CB_burial_14_7 | 2010 May 18 9:29:47 |
Script for T0545.t04.CB_burial_14_7 coloring in rasmol | T0545.t04.CB_burial_14_7-color.rasmol | 2010 May 18 9:29:48 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0545.t04.CB_burial_14_7-logo | 2010 May 18 9:29:53 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0545.t2k.CB_burial_14_7 | 2010 May 18 9:29:58 |
Script for T0545.t2k.CB_burial_14_7 coloring in rasmol | T0545.t2k.CB_burial_14_7-color.rasmol | 2010 May 18 9:29:58 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0545.t2k.CB_burial_14_7-logo | 2010 May 18 9:30:04 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0545.t04.near-backbone-11 | 2010 May 18 9:30:11 |
Script for T0545.t04.near-backbone-11 coloring in rasmol | T0545.t04.near-backbone-11-color.rasmol | 2010 May 18 9:30:12 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0545.t04.near-backbone-11-logo | 2010 May 18 9:30:18 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0545.t2k.near-backbone-11 | 2010 May 18 9:30:24 |
Script for T0545.t2k.near-backbone-11 coloring in rasmol | T0545.t2k.near-backbone-11-color.rasmol | 2010 May 18 9:30:25 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0545.t2k.near-backbone-11-logo | 2010 May 18 9:30:30 |
Target model scores |
amino acid single-track target model scores of PDB | T0545.t04-w0.5-scores.html | 2010 May 18 9:36:57 |
amino acid single-track target model scores of PDB | T0545.t2k-w0.5-scores.html | 2010 May 18 9:43:21 |
amino acid/100-30-str2 multi-track target model scores | T0545.t2k-100-30-str2-scores.html | 2010 May 18 9:46:15 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0545.t2k-100-30-stride-ebghtl-scores.html | 2010 May 18 9:49:08 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0545.t2k-100-30-dssp-ebghstl-scores.html | 2010 May 18 9:52:01 |
amino acid/100-30-alpha multi-track target model scores | T0545.t2k-100-30-alpha-scores.html | 2010 May 18 9:54:52 |
amino acid/100-30-bys multi-track target model scores | T0545.t2k-100-30-bys-scores.html | 2010 May 18 9:57:45 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0545.t2k-100-30-dssp-ehl2-scores.html | 2010 May 18 10:00:36 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0545.t2k-100-30-CB_burial_14_7-scores.html | 2010 May 18 10:03:29 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0545.t2k-100-30-near-backbone-11-scores.html | 2010 May 18 10:06:19 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0545.t2k-100-40-40-str2+CB_burial_14_7-scores.html | 2010 May 18 10:09:24 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0545.t2k-80-60-80-str2+near-backbone-11-scores.html | 2010 May 18 10:12:36 |
amino acid/100-30-str2 multi-track target model scores | T0545.t04-100-30-str2-scores.html | 2010 May 18 10:15:21 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0545.t04-100-30-stride-ebghtl-scores.html | 2010 May 18 10:18:04 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0545.t04-100-30-dssp-ebghstl-scores.html | 2010 May 18 10:20:48 |
amino acid/100-30-alpha multi-track target model scores | T0545.t04-100-30-alpha-scores.html | 2010 May 18 10:23:31 |
amino acid/100-30-bys multi-track target model scores | T0545.t04-100-30-bys-scores.html | 2010 May 18 10:26:15 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0545.t04-100-30-dssp-ehl2-scores.html | 2010 May 18 10:28:57 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0545.t04-100-30-CB_burial_14_7-scores.html | 2010 May 18 10:31:41 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0545.t04-100-30-near-backbone-11-scores.html | 2010 May 18 10:34:24 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0545.t04-100-40-40-str2+CB_burial_14_7-scores.html | 2010 May 18 10:37:18 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0545.t04-80-60-80-str2+near-backbone-11-scores.html | 2010 May 18 10:40:18 |
Template model scores |
Annotated t04 template model scores | T0545.t04-template-lib-scores.html | 2010 May 18 11:08:25 |
Annotated t2k template model scores | T0545.t2k-template-lib-scores.html | 2010 May 18 11:27:54 |
Top Hits |
Best scoring hits from t04 HMMs | T0545.t04.best-scores.html | 2010 May 18 11:27:58 |
Best scoring hits from t2k HMMs | T0545.t2k.best-scores.html | 2010 May 18 11:28:00 |
Best scoring hits from combining t04 t2k | T0545.best-scores.html | 2010 May 18 11:28:02 |
Alignments for Top Hits |
Top alignments from t04 hits | T0545.t04.top_reported_alignments.html | 2010 May 18 12:45:20 |
Top alignments from t2k hits | T0545.t2k.top_reported_alignments.html | 2010 May 18 12:45:47 |
Top alignments from combined hits | T0545.top_reported_alignments.html | 2010 May 18 12:46:04 |
multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2010 May 18 12:47:22 |
Undertaker (3d) files |
Undertaker input for top t04 alignments | T0545.t04.undertaker-align.under | 2010 May 18 12:47:26 |
Undertaker input for top t2k alignments | T0545.t2k.undertaker-align.under | 2010 May 18 12:47:27 |
Undertaker input for top combined alignments | T0545.undertaker-align.under | 2010 May 18 12:47:27 |
PDB file with model(s) for top alignments | T0545.undertaker-align.pdb.gz | 2010 May 18 12:50:03 |
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) | T0545.t04.many.frag.gz | 2010 May 18 12:50:54 |
Fragment list for undertaker (from fragfinder) | T0545.t2k.many.frag.gz | 2010 May 18 12:51:34 |
Contact predictions, based on |
contact predictions (rr format) (rr.constraints format) | T0545.449a_45 | 2010 May 18 12:52:46 |
First attempted model using undertaker | decoys/T0545.try1-opt2.pdb.gz | 2010 May 18 18:39:52 |
Images of complete model in decoys/T0545.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