Please cite the following papers:
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Description | Link to file | Date |
Inputs |
Submitted sequence | T0538.a2m | 2010 May 13 9:19:17 |
README file | README | 2010 May 13 12:56:33 |
Quick blastp of non-redundant PDB | T0538.pdb_blast.txt | 2010 May 13 12:56:47 |
Multiple alignment |
SAM_t04 multiple alignment in a2m format | T0538.t04.a2m.gz | 2010 May 13 13:04:03 |
SAM_t04 multiple alignment in pretty html format | T0538.t04.pa.html | 2010 May 13 13:04:22 |
SAM_t04 target hidden Markov model | T0538.t04.w0.5.mod | 2010 May 13 13:04:27 |
SAM_t04 multiple alignment---sequence logo (eps format) (pdf format) | T0538.t04.w0.5-logo | 2010 May 13 13:04:38 |
Script for highlighting in rasmol | conserved_t04 | 2010 May 13 13:04:40 |
SAM_t2k multiple alignment in a2m format | T0538.t2k.a2m.gz | 2010 May 13 13:06:05 |
SAM_t2k multiple alignment in pretty html format | T0538.t2k.pa.html | 2010 May 13 13:06:14 |
SAM_t2k target hidden Markov model | T0538.t2k.w0.5.mod | 2010 May 13 13:06:17 |
SAM_t2k multiple alignment---sequence logo (eps format) (pdf format) | T0538.t2k.w0.5-logo | 2010 May 13 13:06:28 |
Script for highlighting in rasmol | conserved_t2k | 2010 May 13 13:06:29 |
Secondary Structure Prediction (Explanation of secondary-structure predictions) |
str2 structure prediction (rdb format) (seq format) | T0538.t04.str2 | 2010 May 13 13:04:33 |
Script for T0538.t04.str2 coloring in rasmol | T0538.t04.str2-color.rasmol | 2010 May 13 13:06:34 |
str2---sequence logo (eps format) (pdf format) | T0538.t04.str2-logo | 2010 May 13 13:06:44 |
str2 structure prediction (rdb format) (seq format) | T0538.t2k.str2 | 2010 May 13 13:06:23 |
Script for T0538.t2k.str2 coloring in rasmol | T0538.t2k.str2-color.rasmol | 2010 May 13 13:06:46 |
str2---sequence logo (eps format) (pdf format) | T0538.t2k.str2-logo | 2010 May 13 13:06:54 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0538.t04.stride-ebghtl | 2010 May 13 13:07:00 |
Script for T0538.t04.stride-ebghtl coloring in rasmol | T0538.t04.stride-ebghtl-color.rasmol | 2010 May 13 13:07:01 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0538.t04.stride-ebghtl-logo | 2010 May 13 13:07:06 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0538.t2k.stride-ebghtl | 2010 May 13 13:07:10 |
Script for T0538.t2k.stride-ebghtl coloring in rasmol | T0538.t2k.stride-ebghtl-color.rasmol | 2010 May 13 13:07:11 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0538.t2k.stride-ebghtl-logo | 2010 May 13 13:07:16 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0538.t04.dssp-ebghstl | 2010 May 13 13:07:23 |
Script for T0538.t04.dssp-ebghstl coloring in rasmol | T0538.t04.dssp-ebghstl-color.rasmol | 2010 May 13 13:07:24 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0538.t04.dssp-ebghstl-logo | 2010 May 13 13:07:30 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0538.t2k.dssp-ebghstl | 2010 May 13 13:07:35 |
Script for T0538.t2k.dssp-ebghstl coloring in rasmol | T0538.t2k.dssp-ebghstl-color.rasmol | 2010 May 13 13:07:36 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0538.t2k.dssp-ebghstl-logo | 2010 May 13 13:07:44 |
alpha structure prediction (rdb format) (seq format) | T0538.t04.alpha | 2010 May 13 13:07:50 |
Script for T0538.t04.alpha coloring in rasmol | T0538.t04.alpha-color.rasmol | 2010 May 13 13:07:50 |
alpha---sequence logo (eps format) (pdf format) | T0538.t04.alpha-logo | 2010 May 13 13:07:56 |
alpha structure prediction (rdb format) (seq format) | T0538.t2k.alpha | 2010 May 13 13:08:01 |
Script for T0538.t2k.alpha coloring in rasmol | T0538.t2k.alpha-color.rasmol | 2010 May 13 13:08:02 |
alpha---sequence logo (eps format) (pdf format) | T0538.t2k.alpha-logo | 2010 May 13 13:08:07 |
bys structure prediction (rdb format) (seq format) | T0538.t04.bys | 2010 May 13 13:08:13 |
Script for T0538.t04.bys coloring in rasmol | T0538.t04.bys-color.rasmol | 2010 May 13 13:08:14 |
bys---sequence logo (eps format) (pdf format) | T0538.t04.bys-logo | 2010 May 13 13:08:20 |
bys structure prediction (rdb format) (seq format) | T0538.t2k.bys | 2010 May 13 13:08:25 |
Script for T0538.t2k.bys coloring in rasmol | T0538.t2k.bys-color.rasmol | 2010 May 13 13:08:26 |
bys---sequence logo (eps format) (pdf format) | T0538.t2k.bys-logo | 2010 May 13 13:08:31 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0538.t04.dssp-ehl2 | 2010 May 13 13:08:37 |
Script for T0538.t04.dssp-ehl2 coloring in rasmol | T0538.t04.dssp-ehl2-color.rasmol | 2010 May 13 13:08:38 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0538.t04.dssp-ehl2-logo | 2010 May 13 13:08:46 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0538.t2k.dssp-ehl2 | 2010 May 13 13:08:50 |
Script for T0538.t2k.dssp-ehl2 coloring in rasmol | T0538.t2k.dssp-ehl2-color.rasmol | 2010 May 13 13:08:50 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0538.t2k.dssp-ehl2-logo | 2010 May 13 13:08:58 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0538.dssp-ehl2 | 2010 May 13 13:09:03 |
Script for T0538.dssp-ehl2 coloring in rasmol | T0538.dssp-ehl2-color.rasmol | 2010 May 13 13:09:03 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0538.dssp-ehl2-logo | 2010 May 13 13:09:09 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0538.t04.CB_burial_14_7 | 2010 May 13 13:09:15 |
Script for T0538.t04.CB_burial_14_7 coloring in rasmol | T0538.t04.CB_burial_14_7-color.rasmol | 2010 May 13 13:09:15 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0538.t04.CB_burial_14_7-logo | 2010 May 13 13:09:22 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0538.t2k.CB_burial_14_7 | 2010 May 13 13:09:26 |
Script for T0538.t2k.CB_burial_14_7 coloring in rasmol | T0538.t2k.CB_burial_14_7-color.rasmol | 2010 May 13 13:09:28 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0538.t2k.CB_burial_14_7-logo | 2010 May 13 13:09:34 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0538.t04.near-backbone-11 | 2010 May 13 13:09:40 |
Script for T0538.t04.near-backbone-11 coloring in rasmol | T0538.t04.near-backbone-11-color.rasmol | 2010 May 13 13:09:41 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0538.t04.near-backbone-11-logo | 2010 May 13 13:09:48 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0538.t2k.near-backbone-11 | 2010 May 13 13:09:53 |
Script for T0538.t2k.near-backbone-11 coloring in rasmol | T0538.t2k.near-backbone-11-color.rasmol | 2010 May 13 13:09:54 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0538.t2k.near-backbone-11-logo | 2010 May 13 13:10:00 |
Target model scores |
amino acid single-track target model scores of PDB | T0538.t04-w0.5-scores.html | 2010 May 13 13:12:15 |
amino acid single-track target model scores of PDB | T0538.t2k-w0.5-scores.html | 2010 May 13 13:14:31 |
amino acid/100-30-str2 multi-track target model scores | T0538.t2k-100-30-str2-scores.html | 2010 May 13 13:15:37 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0538.t2k-100-30-stride-ebghtl-scores.html | 2010 May 13 13:16:41 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0538.t2k-100-30-dssp-ebghstl-scores.html | 2010 May 13 13:17:43 |
amino acid/100-30-alpha multi-track target model scores | T0538.t2k-100-30-alpha-scores.html | 2010 May 13 13:18:48 |
amino acid/100-30-bys multi-track target model scores | T0538.t2k-100-30-bys-scores.html | 2010 May 13 13:19:53 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0538.t2k-100-30-dssp-ehl2-scores.html | 2010 May 13 13:20:57 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0538.t2k-100-30-CB_burial_14_7-scores.html | 2010 May 13 13:22:01 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0538.t2k-100-30-near-backbone-11-scores.html | 2010 May 13 13:23:04 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0538.t2k-100-40-40-str2+CB_burial_14_7-scores.html | 2010 May 13 13:24:15 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0538.t2k-80-60-80-str2+near-backbone-11-scores.html | 2010 May 13 13:25:27 |
amino acid/100-30-str2 multi-track target model scores | T0538.t04-100-30-str2-scores.html | 2010 May 13 13:26:30 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0538.t04-100-30-stride-ebghtl-scores.html | 2010 May 13 13:27:30 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0538.t04-100-30-dssp-ebghstl-scores.html | 2010 May 13 13:28:30 |
amino acid/100-30-alpha multi-track target model scores | T0538.t04-100-30-alpha-scores.html | 2010 May 13 13:29:30 |
amino acid/100-30-bys multi-track target model scores | T0538.t04-100-30-bys-scores.html | 2010 May 13 13:30:30 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0538.t04-100-30-dssp-ehl2-scores.html | 2010 May 13 13:31:29 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0538.t04-100-30-CB_burial_14_7-scores.html | 2010 May 13 13:32:28 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0538.t04-100-30-near-backbone-11-scores.html | 2010 May 13 13:33:28 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0538.t04-100-40-40-str2+CB_burial_14_7-scores.html | 2010 May 13 13:34:32 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0538.t04-80-60-80-str2+near-backbone-11-scores.html | 2010 May 13 13:35:40 |
Template model scores |
Annotated t04 template model scores | T0538.t04-template-lib-scores.html | 2010 May 13 14:45:13 |
Annotated t2k template model scores | T0538.t2k-template-lib-scores.html | 2010 May 13 16:08:49 |
Top Hits |
Best scoring hits from t04 HMMs | T0538.t04.best-scores.html | 2010 May 13 16:08:59 |
Best scoring hits from t2k HMMs | T0538.t2k.best-scores.html | 2010 May 13 16:09:03 |
Best scoring hits from combining t04 t2k | T0538.best-scores.html | 2010 May 13 16:09:08 |
Alignments for Top Hits |
Top alignments from t04 hits | T0538.t04.top_reported_alignments.html | 2010 May 13 19:12:51 |
Top alignments from t2k hits | T0538.t2k.top_reported_alignments.html | 2010 May 13 19:16:11 |
Top alignments from combined hits | T0538.top_reported_alignments.html | 2010 May 13 19:24:31 |
multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2010 May 13 19:35:36 |
Undertaker (3d) files |
Undertaker input for top t04 alignments | T0538.t04.undertaker-align.under | 2010 May 13 19:35:41 |
Undertaker input for top t2k alignments | T0538.t2k.undertaker-align.under | 2010 May 13 19:35:41 |
Undertaker input for top combined alignments | T0538.undertaker-align.under | 2010 May 13 19:35:42 |
PDB file with model(s) for top alignments | T0538.undertaker-align.pdb.gz | 2010 May 13 19:37:12 |
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) | T0538.t04.many.frag.gz | 2010 May 13 19:38:06 |
Fragment list for undertaker (from fragfinder) | T0538.t2k.many.frag.gz | 2010 May 13 19:38:30 |
Contact predictions, based on |
contact predictions (rr format) (rr.constraints format) | T0538.449a_45 | 2010 May 13 19:39:00 |
First attempted model using undertaker | decoys/T0538.try1-opt2.pdb.gz | 2010 May 13 21:07:41 |
Images of complete model in decoys/T0538.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