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 | T0403.a2m | 2008 May 15 9:04:46 |
README file | README | 2008 May 15 12:47:05 |
Quick blastp of non-redundant PDB | T0403.pdb_blast.txt | 2008 May 15 12:47:22 |
Multiple alignment |
SAM_t04 multiple alignment in a2m format | T0403.t04.a2m.gz | 2008 May 15 13:29:17 |
SAM_t04 multiple alignment in pretty html format | T0403.t04.pa.html | 2008 May 15 13:32:28 |
SAM_t04 target hidden Markov model | T0403.t04.w0.5.mod | 2008 May 15 13:32:37 |
SAM_t04 multiple alignment---sequence logo (eps format) (pdf format) | T0403.t04.w0.5-logo | 2008 May 15 13:32:53 |
Script for highlighting in rasmol | conserved_t04 | 2008 May 15 13:32:55 |
SAM_t2k multiple alignment in a2m format | T0403.t2k.a2m.gz | 2008 May 15 13:56:18 |
SAM_t2k multiple alignment in pretty html format | T0403.t2k.pa.html | 2008 May 15 13:58:43 |
SAM_t2k target hidden Markov model | T0403.t2k.w0.5.mod | 2008 May 15 13:58:48 |
SAM_t2k multiple alignment---sequence logo (eps format) (pdf format) | T0403.t2k.w0.5-logo | 2008 May 15 13:59:02 |
Script for highlighting in rasmol | conserved_t2k | 2008 May 15 13:59:06 |
Secondary Structure Prediction (Explanation of secondary-structure predictions) |
str2 structure prediction (rdb format) (seq format) | T0403.t04.str2 | 2008 May 15 13:32:49 |
Script for T0403.t04.str2 coloring in rasmol | T0403.t04.str2-color.rasmol | 2008 May 15 13:59:11 |
str2---sequence logo (eps format) (pdf format) | T0403.t04.str2-logo | 2008 May 15 13:59:18 |
str2 structure prediction (rdb format) (seq format) | T0403.t2k.str2 | 2008 May 15 13:58:59 |
Script for T0403.t2k.str2 coloring in rasmol | T0403.t2k.str2-color.rasmol | 2008 May 15 13:59:20 |
str2---sequence logo (eps format) (pdf format) | T0403.t2k.str2-logo | 2008 May 15 13:59:28 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0403.t04.stride-ebghtl | 2008 May 15 13:59:34 |
Script for T0403.t04.stride-ebghtl coloring in rasmol | T0403.t04.stride-ebghtl-color.rasmol | 2008 May 15 13:59:35 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0403.t04.stride-ebghtl-logo | 2008 May 15 13:59:40 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0403.t2k.stride-ebghtl | 2008 May 15 13:59:43 |
Script for T0403.t2k.stride-ebghtl coloring in rasmol | T0403.t2k.stride-ebghtl-color.rasmol | 2008 May 15 13:59:47 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0403.t2k.stride-ebghtl-logo | 2008 May 15 13:59:52 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0403.t04.dssp-ebghstl | 2008 May 15 13:59:59 |
Script for T0403.t04.dssp-ebghstl coloring in rasmol | T0403.t04.dssp-ebghstl-color.rasmol | 2008 May 15 14:00:00 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0403.t04.dssp-ebghstl-logo | 2008 May 15 14:00:06 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0403.t2k.dssp-ebghstl | 2008 May 15 14:00:10 |
Script for T0403.t2k.dssp-ebghstl coloring in rasmol | T0403.t2k.dssp-ebghstl-color.rasmol | 2008 May 15 14:00:11 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0403.t2k.dssp-ebghstl-logo | 2008 May 15 14:00:18 |
alpha structure prediction (rdb format) (seq format) | T0403.t04.alpha | 2008 May 15 14:00:25 |
Script for T0403.t04.alpha coloring in rasmol | T0403.t04.alpha-color.rasmol | 2008 May 15 14:00:25 |
alpha---sequence logo (eps format) (pdf format) | T0403.t04.alpha-logo | 2008 May 15 14:00:31 |
alpha structure prediction (rdb format) (seq format) | T0403.t2k.alpha | 2008 May 15 14:00:37 |
Script for T0403.t2k.alpha coloring in rasmol | T0403.t2k.alpha-color.rasmol | 2008 May 15 14:00:38 |
alpha---sequence logo (eps format) (pdf format) | T0403.t2k.alpha-logo | 2008 May 15 14:00:43 |
bys structure prediction (rdb format) (seq format) | T0403.t04.bys | 2008 May 15 14:00:51 |
Script for T0403.t04.bys coloring in rasmol | T0403.t04.bys-color.rasmol | 2008 May 15 14:00:51 |
bys---sequence logo (eps format) (pdf format) | T0403.t04.bys-logo | 2008 May 15 14:00:57 |
bys structure prediction (rdb format) (seq format) | T0403.t2k.bys | 2008 May 15 14:01:01 |
Script for T0403.t2k.bys coloring in rasmol | T0403.t2k.bys-color.rasmol | 2008 May 15 14:01:02 |
bys---sequence logo (eps format) (pdf format) | T0403.t2k.bys-logo | 2008 May 15 14:01:09 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0403.t04.dssp-ehl2 | 2008 May 15 14:01:13 |
Script for T0403.t04.dssp-ehl2 coloring in rasmol | T0403.t04.dssp-ehl2-color.rasmol | 2008 May 15 14:01:13 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0403.t04.dssp-ehl2-logo | 2008 May 15 14:01:18 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0403.t2k.dssp-ehl2 | 2008 May 15 14:01:20 |
Script for T0403.t2k.dssp-ehl2 coloring in rasmol | T0403.t2k.dssp-ehl2-color.rasmol | 2008 May 15 14:01:21 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0403.t2k.dssp-ehl2-logo | 2008 May 15 14:01:27 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0403.dssp-ehl2 | 2008 May 15 14:01:32 |
Script for T0403.dssp-ehl2 coloring in rasmol | T0403.dssp-ehl2-color.rasmol | 2008 May 15 14:01:34 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0403.dssp-ehl2-logo | 2008 May 15 14:01:40 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0403.t04.CB_burial_14_7 | 2008 May 15 14:01:47 |
Script for T0403.t04.CB_burial_14_7 coloring in rasmol | T0403.t04.CB_burial_14_7-color.rasmol | 2008 May 15 14:01:47 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0403.t04.CB_burial_14_7-logo | 2008 May 15 14:01:54 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0403.t2k.CB_burial_14_7 | 2008 May 15 14:01:58 |
Script for T0403.t2k.CB_burial_14_7 coloring in rasmol | T0403.t2k.CB_burial_14_7-color.rasmol | 2008 May 15 14:01:59 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0403.t2k.CB_burial_14_7-logo | 2008 May 15 14:02:03 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0403.t04.near-backbone-11 | 2008 May 15 14:02:11 |
Script for T0403.t04.near-backbone-11 coloring in rasmol | T0403.t04.near-backbone-11-color.rasmol | 2008 May 15 14:02:12 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0403.t04.near-backbone-11-logo | 2008 May 15 14:02:17 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0403.t2k.near-backbone-11 | 2008 May 15 14:02:24 |
Script for T0403.t2k.near-backbone-11 coloring in rasmol | T0403.t2k.near-backbone-11-color.rasmol | 2008 May 15 14:02:25 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0403.t2k.near-backbone-11-logo | 2008 May 15 14:02:32 |
Target model scores |
amino acid single-track target model scores of PDB | T0403.t04-w0.5-scores.html | 2008 May 15 14:12:42 |
amino acid single-track target model scores of PDB | T0403.t2k-w0.5-scores.html | 2008 May 15 14:23:03 |
amino acid/100-30-str2 multi-track target model scores | T0403.t2k-100-30-str2-scores.html | 2008 May 15 14:27:26 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0403.t2k-100-30-stride-ebghtl-scores.html | 2008 May 15 14:31:50 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0403.t2k-100-30-dssp-ebghstl-scores.html | 2008 May 15 14:36:12 |
amino acid/100-30-alpha multi-track target model scores | T0403.t2k-100-30-alpha-scores.html | 2008 May 15 14:40:32 |
amino acid/100-30-bys multi-track target model scores | T0403.t2k-100-30-bys-scores.html | 2008 May 15 14:44:55 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0403.t2k-100-30-dssp-ehl2-scores.html | 2008 May 15 14:49:18 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0403.t2k-100-30-CB_burial_14_7-scores.html | 2008 May 15 14:53:39 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0403.t2k-100-30-near-backbone-11-scores.html | 2008 May 15 14:58:05 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0403.t2k-100-40-40-str2+CB_burial_14_7-scores.html | 2008 May 15 15:02:44 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0403.t2k-80-60-80-str2+near-backbone-11-scores.html | 2008 May 15 15:07:29 |
amino acid/100-30-str2 multi-track target model scores | T0403.t04-100-30-str2-scores.html | 2008 May 15 15:11:29 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0403.t04-100-30-stride-ebghtl-scores.html | 2008 May 15 15:15:29 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0403.t04-100-30-dssp-ebghstl-scores.html | 2008 May 15 15:19:29 |
amino acid/100-30-alpha multi-track target model scores | T0403.t04-100-30-alpha-scores.html | 2008 May 15 15:23:27 |
amino acid/100-30-bys multi-track target model scores | T0403.t04-100-30-bys-scores.html | 2008 May 15 15:27:31 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0403.t04-100-30-dssp-ehl2-scores.html | 2008 May 15 15:31:31 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0403.t04-100-30-CB_burial_14_7-scores.html | 2008 May 15 15:35:32 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0403.t04-100-30-near-backbone-11-scores.html | 2008 May 15 15:39:31 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0403.t04-100-40-40-str2+CB_burial_14_7-scores.html | 2008 May 15 15:43:46 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0403.t04-80-60-80-str2+near-backbone-11-scores.html | 2008 May 15 15:48:08 |
Template model scores |
Annotated t04 template model scores | T0403.t04-template-lib-scores.html | 2008 May 15 16:11:26 |
Annotated t2k template model scores | T0403.t2k-template-lib-scores.html | 2008 May 15 16:36:11 |
Top Hits |
Best scoring hits from t04 HMMs | T0403.t04.best-scores.html | 2008 May 15 16:36:23 |
Best scoring hits from t2k HMMs | T0403.t2k.best-scores.html | 2008 May 15 16:36:28 |
Best scoring hits from combining t04 t2k | T0403.best-scores.html | 2008 May 15 16:36:36 |
Alignments for Top Hits |
Top alignments from t04 hits | T0403.t04.top_reported_alignments.html | 2008 May 15 17:50:48 |
Top alignments from t2k hits | T0403.t2k.top_reported_alignments.html | 2008 May 15 17:51:40 |
Top alignments from combined hits | T0403.top_reported_alignments.html | 2008 May 15 17:53:00 |
multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2008 May 15 17:55:20 |
Undertaker (3d) files |
Undertaker input for top t04 alignments | T0403.t04.undertaker-align.under | 2008 May 15 17:55:24 |
Undertaker input for top t2k alignments | T0403.t2k.undertaker-align.under | 2008 May 15 17:55:26 |
Undertaker input for top combined alignments | T0403.undertaker-align.under | 2008 May 15 17:55:26 |
PDB file with model(s) for top alignments | T0403.undertaker-align.pdb.gz | 2008 May 15 18:00:28 |
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) | T0403.t04.many.frag.gz | 2008 May 15 18:10:19 |
Fragment list for undertaker (from fragfinder) | T0403.t2k.many.frag.gz | 2008 May 15 18:12:10 |
Contact predictions, based on |
contact predictions (rr format) (rr.constraints format) | T0403.449a_45 | 2008 May 15 18:18:55 |
First attempted model using undertaker | decoys/T0403.try1-opt2.pdb.gz | 2008 May 16 7:53:40 |
Images of complete model in decoys/T0403.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