Please cite the following papers:
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Description | Link to file | Date |
Inputs |
Submitted sequence | T0389.a2m | 2008 May 6 9:20:39 |
README file | README | 2008 May 6 9:20:52 |
Quick blastp of non-redundant PDB | T0389.pdb_blast.txt | 2008 May 6 9:20:58 |
Multiple alignment |
SAM_t04 multiple alignment in a2m format | T0389.t04.a2m.gz | 2008 May 6 9:31:32 |
SAM_t04 multiple alignment in pretty html format | T0389.t04.pa.html | 2008 May 6 9:34:16 |
SAM_t04 target hidden Markov model | T0389.t04.w0.5.mod | 2008 May 6 9:34:23 |
SAM_t04 multiple alignment---sequence logo (eps format) (pdf format) | T0389.t04.w0.5-logo | 2008 May 6 9:34:43 |
Script for highlighting in rasmol | conserved_t04 | 2008 May 6 9:34:48 |
SAM_t2k multiple alignment in a2m format | T0389.t2k.a2m.gz | 2008 May 6 9:38:55 |
SAM_t2k multiple alignment in pretty html format | T0389.t2k.pa.html | 2008 May 6 9:39:23 |
SAM_t2k target hidden Markov model | T0389.t2k.w0.5.mod | 2008 May 6 9:39:30 |
SAM_t2k multiple alignment---sequence logo (eps format) (pdf format) | T0389.t2k.w0.5-logo | 2008 May 6 9:39:41 |
Script for highlighting in rasmol | conserved_t2k | 2008 May 6 9:39:46 |
Secondary Structure Prediction (Explanation of secondary-structure predictions) |
str2 structure prediction (rdb format) (seq format) | T0389.t04.str2 | 2008 May 6 9:34:39 |
Script for T0389.t04.str2 coloring in rasmol | T0389.t04.str2-color.rasmol | 2008 May 6 9:39:51 |
str2---sequence logo (eps format) (pdf format) | T0389.t04.str2-logo | 2008 May 6 9:39:59 |
str2 structure prediction (rdb format) (seq format) | T0389.t2k.str2 | 2008 May 6 9:39:37 |
Script for T0389.t2k.str2 coloring in rasmol | T0389.t2k.str2-color.rasmol | 2008 May 6 9:40:04 |
str2---sequence logo (eps format) (pdf format) | T0389.t2k.str2-logo | 2008 May 6 9:40:12 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0389.t04.stride-ebghtl | 2008 May 6 9:40:23 |
Script for T0389.t04.stride-ebghtl coloring in rasmol | T0389.t04.stride-ebghtl-color.rasmol | 2008 May 6 9:40:25 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0389.t04.stride-ebghtl-logo | 2008 May 6 9:40:30 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0389.t2k.stride-ebghtl | 2008 May 6 9:40:40 |
Script for T0389.t2k.stride-ebghtl coloring in rasmol | T0389.t2k.stride-ebghtl-color.rasmol | 2008 May 6 9:40:41 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0389.t2k.stride-ebghtl-logo | 2008 May 6 9:40:46 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0389.t04.dssp-ebghstl | 2008 May 6 9:41:00 |
Script for T0389.t04.dssp-ebghstl coloring in rasmol | T0389.t04.dssp-ebghstl-color.rasmol | 2008 May 6 9:41:01 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0389.t04.dssp-ebghstl-logo | 2008 May 6 9:41:07 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0389.t2k.dssp-ebghstl | 2008 May 6 9:41:16 |
Script for T0389.t2k.dssp-ebghstl coloring in rasmol | T0389.t2k.dssp-ebghstl-color.rasmol | 2008 May 6 9:41:17 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0389.t2k.dssp-ebghstl-logo | 2008 May 6 9:41:25 |
alpha structure prediction (rdb format) (seq format) | T0389.t04.alpha | 2008 May 6 9:41:37 |
Script for T0389.t04.alpha coloring in rasmol | T0389.t04.alpha-color.rasmol | 2008 May 6 9:41:38 |
alpha---sequence logo (eps format) (pdf format) | T0389.t04.alpha-logo | 2008 May 6 9:41:47 |
alpha structure prediction (rdb format) (seq format) | T0389.t2k.alpha | 2008 May 6 9:41:54 |
Script for T0389.t2k.alpha coloring in rasmol | T0389.t2k.alpha-color.rasmol | 2008 May 6 9:41:55 |
alpha---sequence logo (eps format) (pdf format) | T0389.t2k.alpha-logo | 2008 May 6 9:42:03 |
bys structure prediction (rdb format) (seq format) | T0389.t04.bys | 2008 May 6 9:42:19 |
Script for T0389.t04.bys coloring in rasmol | T0389.t04.bys-color.rasmol | 2008 May 6 9:42:21 |
bys---sequence logo (eps format) (pdf format) | T0389.t04.bys-logo | 2008 May 6 9:42:27 |
bys structure prediction (rdb format) (seq format) | T0389.t2k.bys | 2008 May 6 9:42:37 |
Script for T0389.t2k.bys coloring in rasmol | T0389.t2k.bys-color.rasmol | 2008 May 6 9:42:39 |
bys---sequence logo (eps format) (pdf format) | T0389.t2k.bys-logo | 2008 May 6 9:42:48 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0389.t04.dssp-ehl2 | 2008 May 6 9:42:57 |
Script for T0389.t04.dssp-ehl2 coloring in rasmol | T0389.t04.dssp-ehl2-color.rasmol | 2008 May 6 9:42:58 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0389.t04.dssp-ehl2-logo | 2008 May 6 9:43:06 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0389.t2k.dssp-ehl2 | 2008 May 6 9:43:10 |
Script for T0389.t2k.dssp-ehl2 coloring in rasmol | T0389.t2k.dssp-ehl2-color.rasmol | 2008 May 6 9:43:11 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0389.t2k.dssp-ehl2-logo | 2008 May 6 9:43:18 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0389.dssp-ehl2 | 2008 May 6 9:43:24 |
Script for T0389.dssp-ehl2 coloring in rasmol | T0389.dssp-ehl2-color.rasmol | 2008 May 6 9:43:25 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0389.dssp-ehl2-logo | 2008 May 6 9:43:34 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0389.t04.CB_burial_14_7 | 2008 May 6 9:43:45 |
Script for T0389.t04.CB_burial_14_7 coloring in rasmol | T0389.t04.CB_burial_14_7-color.rasmol | 2008 May 6 9:43:46 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0389.t04.CB_burial_14_7-logo | 2008 May 6 9:43:51 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0389.t2k.CB_burial_14_7 | 2008 May 6 9:43:56 |
Script for T0389.t2k.CB_burial_14_7 coloring in rasmol | T0389.t2k.CB_burial_14_7-color.rasmol | 2008 May 6 9:44:00 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0389.t2k.CB_burial_14_7-logo | 2008 May 6 9:44:04 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0389.t04.near-backbone-11 | 2008 May 6 9:44:12 |
Script for T0389.t04.near-backbone-11 coloring in rasmol | T0389.t04.near-backbone-11-color.rasmol | 2008 May 6 9:44:13 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0389.t04.near-backbone-11-logo | 2008 May 6 9:44:20 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0389.t2k.near-backbone-11 | 2008 May 6 9:44:24 |
Script for T0389.t2k.near-backbone-11 coloring in rasmol | T0389.t2k.near-backbone-11-color.rasmol | 2008 May 6 9:44:25 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0389.t2k.near-backbone-11-logo | 2008 May 6 9:44:30 |
Target model scores |
amino acid single-track target model scores of PDB | T0389.t04-w0.5-scores.html | 2008 May 6 9:49:13 |
amino acid single-track target model scores of PDB | T0389.t2k-w0.5-scores.html | 2008 May 6 9:53:53 |
amino acid/100-30-str2 multi-track target model scores | T0389.t2k-100-30-str2-scores.html | 2008 May 6 9:55:56 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0389.t2k-100-30-stride-ebghtl-scores.html | 2008 May 6 9:58:00 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0389.t2k-100-30-dssp-ebghstl-scores.html | 2008 May 6 10:00:04 |
amino acid/100-30-alpha multi-track target model scores | T0389.t2k-100-30-alpha-scores.html | 2008 May 6 10:02:06 |
amino acid/100-30-bys multi-track target model scores | T0389.t2k-100-30-bys-scores.html | 2008 May 6 10:04:09 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0389.t2k-100-30-dssp-ehl2-scores.html | 2008 May 6 10:06:11 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0389.t2k-100-30-CB_burial_14_7-scores.html | 2008 May 6 10:08:16 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0389.t2k-100-30-near-backbone-11-scores.html | 2008 May 6 10:10:16 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0389.t2k-100-40-40-str2+CB_burial_14_7-scores.html | 2008 May 6 10:12:25 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0389.t2k-80-60-80-str2+near-backbone-11-scores.html | 2008 May 6 10:14:39 |
amino acid/100-30-str2 multi-track target model scores | T0389.t04-100-30-str2-scores.html | 2008 May 6 10:16:33 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0389.t04-100-30-stride-ebghtl-scores.html | 2008 May 6 10:18:26 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0389.t04-100-30-dssp-ebghstl-scores.html | 2008 May 6 10:20:20 |
amino acid/100-30-alpha multi-track target model scores | T0389.t04-100-30-alpha-scores.html | 2008 May 6 10:22:12 |
amino acid/100-30-bys multi-track target model scores | T0389.t04-100-30-bys-scores.html | 2008 May 6 10:24:07 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0389.t04-100-30-dssp-ehl2-scores.html | 2008 May 6 10:25:59 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0389.t04-100-30-CB_burial_14_7-scores.html | 2008 May 6 10:27:55 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0389.t04-100-30-near-backbone-11-scores.html | 2008 May 6 10:29:45 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0389.t04-100-40-40-str2+CB_burial_14_7-scores.html | 2008 May 6 10:31:47 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0389.t04-80-60-80-str2+near-backbone-11-scores.html | 2008 May 6 10:33:51 |
Template model scores |
Annotated t04 template model scores | T0389.t04-template-lib-scores.html | 2008 May 6 10:58:46 |
Annotated t2k template model scores | T0389.t2k-template-lib-scores.html | 2008 May 6 11:23:33 |
Top Hits |
Best scoring hits from t04 HMMs | T0389.t04.best-scores.html | 2008 May 6 11:23:42 |
Best scoring hits from t2k HMMs | T0389.t2k.best-scores.html | 2008 May 6 11:23:47 |
Best scoring hits from combining t04 t2k | T0389.best-scores.html | 2008 May 6 11:23:59 |
Alignments for Top Hits |
Top alignments from t04 hits | T0389.t04.top_reported_alignments.html | 2008 May 6 13:45:01 |
Top alignments from t2k hits | T0389.t2k.top_reported_alignments.html | 2008 May 6 13:46:39 |
Top alignments from combined hits | T0389.top_reported_alignments.html | 2008 May 6 13:49:30 |
multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2008 May 6 13:53:32 |
Undertaker (3d) files |
Undertaker input for top t04 alignments | T0389.t04.undertaker-align.under | 2008 May 6 13:53:34 |
Undertaker input for top t2k alignments | T0389.t2k.undertaker-align.under | 2008 May 6 13:53:37 |
Undertaker input for top combined alignments | T0389.undertaker-align.under | 2008 May 6 13:53:37 |
PDB file with model(s) for top alignments | T0389.undertaker-align.pdb.gz | 2008 May 6 13:55:14 |
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) | T0389.t04.many.frag.gz | 2008 May 6 14:00:03 |
Fragment list for undertaker (from fragfinder) | T0389.t2k.many.frag.gz | 2008 May 6 14:00:52 |
Contact predictions, based on |
contact predictions (rr format) (rr.constraints format) | T0389.449a_45 | 2008 May 6 14:04:30 |
First attempted model using undertaker | decoys/T0389.try1-opt2.pdb.gz | 2008 May 6 15:46:49 |
Images of complete model in decoys/T0389.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