Please cite the following papers:
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Description | Link to file | Date |
Inputs |
Submitted sequence | T0406.a2m | 2008 May 16 9:03:22 |
README file | README | 2008 May 16 9:03:29 |
Quick blastp of non-redundant PDB | T0406.pdb_blast.txt | 2008 May 16 9:03:33 |
Multiple alignment |
SAM_t04 multiple alignment in a2m format | T0406.t04.a2m.gz | 2008 May 16 9:09:09 |
SAM_t04 multiple alignment in pretty html format | T0406.t04.pa.html | 2008 May 16 9:10:34 |
SAM_t04 target hidden Markov model | T0406.t04.w0.5.mod | 2008 May 16 9:10:37 |
SAM_t04 multiple alignment---sequence logo (eps format) (pdf format) | T0406.t04.w0.5-logo | 2008 May 16 9:10:45 |
Script for highlighting in rasmol | conserved_t04 | 2008 May 16 9:10:47 |
SAM_t2k multiple alignment in a2m format | T0406.t2k.a2m.gz | 2008 May 16 9:13:00 |
SAM_t2k multiple alignment in pretty html format | T0406.t2k.pa.html | 2008 May 16 9:13:07 |
SAM_t2k target hidden Markov model | T0406.t2k.w0.5.mod | 2008 May 16 9:13:11 |
SAM_t2k multiple alignment---sequence logo (eps format) (pdf format) | T0406.t2k.w0.5-logo | 2008 May 16 9:13:21 |
Script for highlighting in rasmol | conserved_t2k | 2008 May 16 9:13:23 |
Secondary Structure Prediction (Explanation of secondary-structure predictions) |
str2 structure prediction (rdb format) (seq format) | T0406.t04.str2 | 2008 May 16 9:10:41 |
Script for T0406.t04.str2 coloring in rasmol | T0406.t04.str2-color.rasmol | 2008 May 16 9:13:26 |
str2---sequence logo (eps format) (pdf format) | T0406.t04.str2-logo | 2008 May 16 9:13:30 |
str2 structure prediction (rdb format) (seq format) | T0406.t2k.str2 | 2008 May 16 9:13:18 |
Script for T0406.t2k.str2 coloring in rasmol | T0406.t2k.str2-color.rasmol | 2008 May 16 9:13:32 |
str2---sequence logo (eps format) (pdf format) | T0406.t2k.str2-logo | 2008 May 16 9:13:38 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0406.t04.stride-ebghtl | 2008 May 16 9:13:44 |
Script for T0406.t04.stride-ebghtl coloring in rasmol | T0406.t04.stride-ebghtl-color.rasmol | 2008 May 16 9:13:45 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0406.t04.stride-ebghtl-logo | 2008 May 16 9:13:51 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0406.t2k.stride-ebghtl | 2008 May 16 9:13:54 |
Script for T0406.t2k.stride-ebghtl coloring in rasmol | T0406.t2k.stride-ebghtl-color.rasmol | 2008 May 16 9:13:55 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0406.t2k.stride-ebghtl-logo | 2008 May 16 9:14:00 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0406.t04.dssp-ebghstl | 2008 May 16 9:14:07 |
Script for T0406.t04.dssp-ebghstl coloring in rasmol | T0406.t04.dssp-ebghstl-color.rasmol | 2008 May 16 9:14:08 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0406.t04.dssp-ebghstl-logo | 2008 May 16 9:14:12 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0406.t2k.dssp-ebghstl | 2008 May 16 9:14:17 |
Script for T0406.t2k.dssp-ebghstl coloring in rasmol | T0406.t2k.dssp-ebghstl-color.rasmol | 2008 May 16 9:14:18 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0406.t2k.dssp-ebghstl-logo | 2008 May 16 9:14:22 |
alpha structure prediction (rdb format) (seq format) | T0406.t04.alpha | 2008 May 16 9:14:28 |
Script for T0406.t04.alpha coloring in rasmol | T0406.t04.alpha-color.rasmol | 2008 May 16 9:14:28 |
alpha---sequence logo (eps format) (pdf format) | T0406.t04.alpha-logo | 2008 May 16 9:14:32 |
alpha structure prediction (rdb format) (seq format) | T0406.t2k.alpha | 2008 May 16 9:14:35 |
Script for T0406.t2k.alpha coloring in rasmol | T0406.t2k.alpha-color.rasmol | 2008 May 16 9:14:36 |
alpha---sequence logo (eps format) (pdf format) | T0406.t2k.alpha-logo | 2008 May 16 9:14:42 |
bys structure prediction (rdb format) (seq format) | T0406.t04.bys | 2008 May 16 9:14:49 |
Script for T0406.t04.bys coloring in rasmol | T0406.t04.bys-color.rasmol | 2008 May 16 9:14:49 |
bys---sequence logo (eps format) (pdf format) | T0406.t04.bys-logo | 2008 May 16 9:14:52 |
bys structure prediction (rdb format) (seq format) | T0406.t2k.bys | 2008 May 16 9:14:55 |
Script for T0406.t2k.bys coloring in rasmol | T0406.t2k.bys-color.rasmol | 2008 May 16 9:14:56 |
bys---sequence logo (eps format) (pdf format) | T0406.t2k.bys-logo | 2008 May 16 9:15:01 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0406.t04.dssp-ehl2 | 2008 May 16 9:15:04 |
Script for T0406.t04.dssp-ehl2 coloring in rasmol | T0406.t04.dssp-ehl2-color.rasmol | 2008 May 16 9:15:04 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0406.t04.dssp-ehl2-logo | 2008 May 16 9:15:08 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0406.t2k.dssp-ehl2 | 2008 May 16 9:15:13 |
Script for T0406.t2k.dssp-ehl2 coloring in rasmol | T0406.t2k.dssp-ehl2-color.rasmol | 2008 May 16 9:15:13 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0406.t2k.dssp-ehl2-logo | 2008 May 16 9:15:17 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0406.dssp-ehl2 | 2008 May 16 9:15:20 |
Script for T0406.dssp-ehl2 coloring in rasmol | T0406.dssp-ehl2-color.rasmol | 2008 May 16 9:15:21 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0406.dssp-ehl2-logo | 2008 May 16 9:15:27 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0406.t04.CB_burial_14_7 | 2008 May 16 9:15:32 |
Script for T0406.t04.CB_burial_14_7 coloring in rasmol | T0406.t04.CB_burial_14_7-color.rasmol | 2008 May 16 9:15:32 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0406.t04.CB_burial_14_7-logo | 2008 May 16 9:15:38 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0406.t2k.CB_burial_14_7 | 2008 May 16 9:15:42 |
Script for T0406.t2k.CB_burial_14_7 coloring in rasmol | T0406.t2k.CB_burial_14_7-color.rasmol | 2008 May 16 9:15:43 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0406.t2k.CB_burial_14_7-logo | 2008 May 16 9:15:46 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0406.t04.near-backbone-11 | 2008 May 16 9:15:51 |
Script for T0406.t04.near-backbone-11 coloring in rasmol | T0406.t04.near-backbone-11-color.rasmol | 2008 May 16 9:15:52 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0406.t04.near-backbone-11-logo | 2008 May 16 9:15:57 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0406.t2k.near-backbone-11 | 2008 May 16 9:16:00 |
Script for T0406.t2k.near-backbone-11 coloring in rasmol | T0406.t2k.near-backbone-11-color.rasmol | 2008 May 16 9:16:01 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0406.t2k.near-backbone-11-logo | 2008 May 16 9:16:06 |
Target model scores |
amino acid single-track target model scores of PDB | T0406.t04-w0.5-scores.html | 2008 May 16 9:21:10 |
amino acid single-track target model scores of PDB | T0406.t2k-w0.5-scores.html | 2008 May 16 9:26:12 |
amino acid/100-30-str2 multi-track target model scores | T0406.t2k-100-30-str2-scores.html | 2008 May 16 9:28:21 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0406.t2k-100-30-stride-ebghtl-scores.html | 2008 May 16 9:30:30 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0406.t2k-100-30-dssp-ebghstl-scores.html | 2008 May 16 9:32:39 |
amino acid/100-30-alpha multi-track target model scores | T0406.t2k-100-30-alpha-scores.html | 2008 May 16 9:34:47 |
amino acid/100-30-bys multi-track target model scores | T0406.t2k-100-30-bys-scores.html | 2008 May 16 9:36:55 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0406.t2k-100-30-dssp-ehl2-scores.html | 2008 May 16 9:39:03 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0406.t2k-100-30-CB_burial_14_7-scores.html | 2008 May 16 9:41:14 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0406.t2k-100-30-near-backbone-11-scores.html | 2008 May 16 9:43:24 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0406.t2k-100-40-40-str2+CB_burial_14_7-scores.html | 2008 May 16 9:45:45 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0406.t2k-80-60-80-str2+near-backbone-11-scores.html | 2008 May 16 9:48:08 |
amino acid/100-30-str2 multi-track target model scores | T0406.t04-100-30-str2-scores.html | 2008 May 16 9:50:10 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0406.t04-100-30-stride-ebghtl-scores.html | 2008 May 16 9:52:12 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0406.t04-100-30-dssp-ebghstl-scores.html | 2008 May 16 9:54:14 |
amino acid/100-30-alpha multi-track target model scores | T0406.t04-100-30-alpha-scores.html | 2008 May 16 9:56:20 |
amino acid/100-30-bys multi-track target model scores | T0406.t04-100-30-bys-scores.html | 2008 May 16 9:58:20 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0406.t04-100-30-dssp-ehl2-scores.html | 2008 May 16 10:00:18 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0406.t04-100-30-CB_burial_14_7-scores.html | 2008 May 16 10:02:19 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0406.t04-100-30-near-backbone-11-scores.html | 2008 May 16 10:04:18 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0406.t04-100-40-40-str2+CB_burial_14_7-scores.html | 2008 May 16 10:06:28 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0406.t04-80-60-80-str2+near-backbone-11-scores.html | 2008 May 16 10:08:38 |
Template model scores |
Annotated t04 template model scores | T0406.t04-template-lib-scores.html | 2008 May 16 10:28:23 |
Annotated t2k template model scores | T0406.t2k-template-lib-scores.html | 2008 May 16 10:40:45 |
Top Hits |
Best scoring hits from t04 HMMs | T0406.t04.best-scores.html | 2008 May 16 10:40:49 |
Best scoring hits from t2k HMMs | T0406.t2k.best-scores.html | 2008 May 16 10:40:52 |
Best scoring hits from combining t04 t2k | T0406.best-scores.html | 2008 May 16 10:40:56 |
Alignments for Top Hits |
Top alignments from t04 hits | T0406.t04.top_reported_alignments.html | 2008 May 16 12:03:18 |
Top alignments from t2k hits | T0406.t2k.top_reported_alignments.html | 2008 May 16 12:03:42 |
Top alignments from combined hits | T0406.top_reported_alignments.html | 2008 May 16 12:03:56 |
multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2008 May 16 12:05:06 |
Undertaker (3d) files |
Undertaker input for top t04 alignments | T0406.t04.undertaker-align.under | 2008 May 16 12:05:08 |
Undertaker input for top t2k alignments | T0406.t2k.undertaker-align.under | 2008 May 16 12:05:08 |
Undertaker input for top combined alignments | T0406.undertaker-align.under | 2008 May 16 12:05:08 |
PDB file with model(s) for top alignments | T0406.undertaker-align.pdb.gz | 2008 May 16 12:06:18 |
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) | T0406.t04.many.frag.gz | 2008 May 16 12:08:33 |
Fragment list for undertaker (from fragfinder) | T0406.t2k.many.frag.gz | 2008 May 16 12:09:16 |
Contact predictions, based on |
contact predictions (rr format) (rr.constraints format) | T0406.449a_45 | 2008 May 16 12:11:54 |
First attempted model using undertaker | decoys/T0406.try1-opt2.pdb.gz | 2008 May 16 13:47:47 |
Images of complete model in decoys/T0406.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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based on prior design by Kevin Karplus and Rachel Karchin.
Maintained by Kevin Karplus: karplus@soe.ucsc.edu