Please cite the following papers:
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Description | Link to file | Date |
Inputs |
Submitted sequence(s) | T0342.a2m | 2006 Jul 10 17:15:53 |
README file | README | 2006 Jul 10 17:17:24 |
Quick blastp of non-redundant PDB | T0342.pdb.blast | 2006 Jul 10 17:17:27 |
Multiple alignment |
SAM_t06 multiple alignment in a2m format | T0342.t06.a2m.gz | 2006 Jul 10 17:20:15 |
SAM_t06 multiple alignment in pretty html format | T0342.t06.pa.html | 2006 Jul 10 17:20:24 |
SAM_t06 target hidden Markov model | T0342.t06.w0.5.mod | 2006 Jul 10 17:20:26 |
Script for highlighting in rasmol | conserved_t06 | 2006 Jul 10 17:20:33 |
SAM_t04 multiple alignment in a2m format | T0342.t04.a2m.gz | 2006 Jul 10 17:22:30 |
SAM_t04 multiple alignment in pretty html format | T0342.t04.pa.html | 2006 Jul 10 17:22:35 |
SAM_t04 target hidden Markov model | T0342.t04.w0.5.mod | 2006 Jul 10 17:22:37 |
Script for highlighting in rasmol | conserved_t04 | 2006 Jul 10 17:22:42 |
SAM_t2k multiple alignment in a2m format | T0342.t2k.a2m.gz | 2006 Jul 10 17:23:16 |
SAM_t2k multiple alignment in pretty html format | T0342.t2k.pa.html | 2006 Jul 10 17:23:22 |
SAM_t2k target hidden Markov model | T0342.t2k.w0.5.mod | 2006 Jul 10 17:23:23 |
Script for highlighting in rasmol | conserved_t2k | 2006 Jul 10 17:23:28 |
Secondary Structure Prediction (Explanation of secondary-structure predictions) |
str2 structure prediction (rdb format) (seq format) | T0342.t06.str2 | 2006 Jul 10 17:20:30 |
Script for T0342.t06.str2 coloring in rasmol | T0342.t06.str2-color.rasmol | 2006 Jul 10 17:23:30 |
str2 structure prediction (rdb format) (seq format) | T0342.t04.str2 | 2006 Jul 10 17:22:40 |
Script for T0342.t04.str2 coloring in rasmol | T0342.t04.str2-color.rasmol | 2006 Jul 10 17:23:33 |
str2 structure prediction (rdb format) (seq format) | T0342.t2k.str2 | 2006 Jul 10 17:23:26 |
Script for T0342.t2k.str2 coloring in rasmol | T0342.t2k.str2-color.rasmol | 2006 Jul 10 17:23:35 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0342.t06.stride-ebghtl | 2006 Jul 10 17:23:39 |
Script for T0342.t06.stride-ebghtl coloring in rasmol | T0342.t06.stride-ebghtl-color.rasmol | 2006 Jul 10 17:23:40 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0342.t04.stride-ebghtl | 2006 Jul 10 17:23:43 |
Script for T0342.t04.stride-ebghtl coloring in rasmol | T0342.t04.stride-ebghtl-color.rasmol | 2006 Jul 10 17:23:44 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0342.t2k.stride-ebghtl | 2006 Jul 10 17:23:48 |
Script for T0342.t2k.stride-ebghtl coloring in rasmol | T0342.t2k.stride-ebghtl-color.rasmol | 2006 Jul 10 17:23:48 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0342.t06.dssp-ebghstl | 2006 Jul 10 17:23:52 |
Script for T0342.t06.dssp-ebghstl coloring in rasmol | T0342.t06.dssp-ebghstl-color.rasmol | 2006 Jul 10 17:23:53 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0342.t04.dssp-ebghstl | 2006 Jul 10 17:23:57 |
Script for T0342.t04.dssp-ebghstl coloring in rasmol | T0342.t04.dssp-ebghstl-color.rasmol | 2006 Jul 10 17:23:57 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0342.t2k.dssp-ebghstl | 2006 Jul 10 17:24:01 |
Script for T0342.t2k.dssp-ebghstl coloring in rasmol | T0342.t2k.dssp-ebghstl-color.rasmol | 2006 Jul 10 17:24:02 |
alpha structure prediction (rdb format) (seq format) | T0342.t06.alpha | 2006 Jul 10 17:24:06 |
Script for T0342.t06.alpha coloring in rasmol | T0342.t06.alpha-color.rasmol | 2006 Jul 10 17:24:06 |
alpha structure prediction (rdb format) (seq format) | T0342.t04.alpha | 2006 Jul 10 17:24:10 |
Script for T0342.t04.alpha coloring in rasmol | T0342.t04.alpha-color.rasmol | 2006 Jul 10 17:24:11 |
alpha structure prediction (rdb format) (seq format) | T0342.t2k.alpha | 2006 Jul 10 17:24:14 |
Script for T0342.t2k.alpha coloring in rasmol | T0342.t2k.alpha-color.rasmol | 2006 Jul 10 17:24:15 |
bys structure prediction (rdb format) (seq format) | T0342.t06.bys | 2006 Jul 10 17:24:19 |
Script for T0342.t06.bys coloring in rasmol | T0342.t06.bys-color.rasmol | 2006 Jul 10 17:24:19 |
bys structure prediction (rdb format) (seq format) | T0342.t04.bys | 2006 Jul 10 17:24:23 |
Script for T0342.t04.bys coloring in rasmol | T0342.t04.bys-color.rasmol | 2006 Jul 10 17:24:24 |
bys structure prediction (rdb format) (seq format) | T0342.t2k.bys | 2006 Jul 10 17:24:28 |
Script for T0342.t2k.bys coloring in rasmol | T0342.t2k.bys-color.rasmol | 2006 Jul 10 17:24:28 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0342.t06.dssp-ehl2 | 2006 Jul 10 17:24:32 |
Script for T0342.t06.dssp-ehl2 coloring in rasmol | T0342.t06.dssp-ehl2-color.rasmol | 2006 Jul 10 17:24:32 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0342.t04.dssp-ehl2 | 2006 Jul 10 17:24:35 |
Script for T0342.t04.dssp-ehl2 coloring in rasmol | T0342.t04.dssp-ehl2-color.rasmol | 2006 Jul 10 17:24:35 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0342.t2k.dssp-ehl2 | 2006 Jul 10 17:24:38 |
Script for T0342.t2k.dssp-ehl2 coloring in rasmol | T0342.t2k.dssp-ehl2-color.rasmol | 2006 Jul 10 17:24:38 |
n_notor2 structure prediction (rdb format) (seq format) | T0342.t06.n_notor2 | 2006 Jul 10 17:24:43 |
Script for T0342.t06.n_notor2 coloring in rasmol | T0342.t06.n_notor2-color.rasmol | 2006 Jul 10 17:24:43 |
n_notor2 structure prediction (rdb format) (seq format) | T0342.t04.n_notor2 | 2006 Jul 10 17:24:47 |
Script for T0342.t04.n_notor2 coloring in rasmol | T0342.t04.n_notor2-color.rasmol | 2006 Jul 10 17:24:48 |
n_notor2 structure prediction (rdb format) (seq format) | T0342.t2k.n_notor2 | 2006 Jul 10 17:24:51 |
Script for T0342.t2k.n_notor2 coloring in rasmol | T0342.t2k.n_notor2-color.rasmol | 2006 Jul 10 17:24:52 |
o_notor2 structure prediction (rdb format) (seq format) | T0342.t06.o_notor2 | 2006 Jul 10 17:24:56 |
Script for T0342.t06.o_notor2 coloring in rasmol | T0342.t06.o_notor2-color.rasmol | 2006 Jul 10 17:24:57 |
o_notor2 structure prediction (rdb format) (seq format) | T0342.t04.o_notor2 | 2006 Jul 10 17:25:00 |
Script for T0342.t04.o_notor2 coloring in rasmol | T0342.t04.o_notor2-color.rasmol | 2006 Jul 10 17:25:01 |
o_notor2 structure prediction (rdb format) (seq format) | T0342.t2k.o_notor2 | 2006 Jul 10 17:25:04 |
Script for T0342.t2k.o_notor2 coloring in rasmol | T0342.t2k.o_notor2-color.rasmol | 2006 Jul 10 17:25:04 |
n_sep structure prediction (rdb format) (seq format) | T0342.t06.n_sep | 2006 Jul 10 17:25:09 |
Script for T0342.t06.n_sep coloring in rasmol | T0342.t06.n_sep-color.rasmol | 2006 Jul 10 17:25:09 |
n_sep structure prediction (rdb format) (seq format) | T0342.t04.n_sep | 2006 Jul 10 17:25:13 |
Script for T0342.t04.n_sep coloring in rasmol | T0342.t04.n_sep-color.rasmol | 2006 Jul 10 17:25:13 |
n_sep structure prediction (rdb format) (seq format) | T0342.t2k.n_sep | 2006 Jul 10 17:25:17 |
Script for T0342.t2k.n_sep coloring in rasmol | T0342.t2k.n_sep-color.rasmol | 2006 Jul 10 17:25:18 |
o_sep structure prediction (rdb format) (seq format) | T0342.t06.o_sep | 2006 Jul 10 17:25:22 |
Script for T0342.t06.o_sep coloring in rasmol | T0342.t06.o_sep-color.rasmol | 2006 Jul 10 17:25:22 |
o_sep structure prediction (rdb format) (seq format) | T0342.t04.o_sep | 2006 Jul 10 17:25:26 |
Script for T0342.t04.o_sep coloring in rasmol | T0342.t04.o_sep-color.rasmol | 2006 Jul 10 17:25:26 |
o_sep structure prediction (rdb format) (seq format) | T0342.t2k.o_sep | 2006 Jul 10 17:25:30 |
Script for T0342.t2k.o_sep coloring in rasmol | T0342.t2k.o_sep-color.rasmol | 2006 Jul 10 17:25:30 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0342.dssp-ehl2 | 2006 Jul 10 17:25:33 |
Script for T0342.dssp-ehl2 coloring in rasmol | T0342.dssp-ehl2-color.rasmol | 2006 Jul 10 17:25:33 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0342.t06.CB_burial_14_7 | 2006 Jul 10 17:25:37 |
Script for T0342.t06.CB_burial_14_7 coloring in rasmol | T0342.t06.CB_burial_14_7-color.rasmol | 2006 Jul 10 17:25:38 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0342.t04.CB_burial_14_7 | 2006 Jul 10 17:25:41 |
Script for T0342.t04.CB_burial_14_7 coloring in rasmol | T0342.t04.CB_burial_14_7-color.rasmol | 2006 Jul 10 17:25:42 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0342.t2k.CB_burial_14_7 | 2006 Jul 10 17:25:45 |
Script for T0342.t2k.CB_burial_14_7 coloring in rasmol | T0342.t2k.CB_burial_14_7-color.rasmol | 2006 Jul 10 17:25:46 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0342.t06.near-backbone-11 | 2006 Jul 10 17:25:50 |
Script for T0342.t06.near-backbone-11 coloring in rasmol | T0342.t06.near-backbone-11-color.rasmol | 2006 Jul 10 17:25:50 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0342.t04.near-backbone-11 | 2006 Jul 10 17:25:54 |
Script for T0342.t04.near-backbone-11 coloring in rasmol | T0342.t04.near-backbone-11-color.rasmol | 2006 Jul 10 17:25:55 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0342.t2k.near-backbone-11 | 2006 Jul 10 17:25:58 |
Script for T0342.t2k.near-backbone-11 coloring in rasmol | T0342.t2k.near-backbone-11-color.rasmol | 2006 Jul 10 17:25:59 |
Target model scores |
amino acid single-track target model scores of PDB | T0342.t06-w0.5-scores.html | 2006 Jul 10 17:26:48 |
amino acid single-track target model scores of PDB | T0342.t04-w0.5-scores.html | 2006 Jul 10 17:27:40 |
amino acid single-track target model scores of PDB | T0342.t2k-w0.5-scores.html | 2006 Jul 10 17:28:38 |
amino acid/100-30-str2 multi-track target model scores | T0342.t06-100-30-str2-scores.html | 2006 Jul 10 17:28:56 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0342.t06-100-30-stride-ebghtl-scores.html | 2006 Jul 10 17:29:13 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0342.t06-100-30-dssp-ebghstl-scores.html | 2006 Jul 10 17:29:29 |
amino acid/100-30-alpha multi-track target model scores | T0342.t06-100-30-alpha-scores.html | 2006 Jul 10 17:29:47 |
amino acid/100-30-bys multi-track target model scores | T0342.t06-100-30-bys-scores.html | 2006 Jul 10 17:30:05 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0342.t06-100-30-dssp-ehl2-scores.html | 2006 Jul 10 17:30:22 |
amino acid/100-30-n_notor2 multi-track target model scores | T0342.t06-100-30-n_notor2-scores.html | 2006 Jul 10 17:30:39 |
amino acid/100-30-o_notor2 multi-track target model scores | T0342.t06-100-30-o_notor2-scores.html | 2006 Jul 10 17:30:57 |
amino acid/100-30-n_sep multi-track target model scores | T0342.t06-100-30-n_sep-scores.html | 2006 Jul 10 17:31:16 |
amino acid/100-30-o_sep multi-track target model scores | T0342.t06-100-30-o_sep-scores.html | 2006 Jul 10 17:31:33 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0342.t06-100-30-CB_burial_14_7-scores.html | 2006 Jul 10 17:31:51 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0342.t06-100-30-near-backbone-11-scores.html | 2006 Jul 10 17:32:08 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0342.t06-100-40-40-str2+CB_burial_14_7-scores.html | 2006 Jul 10 17:32:28 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0342.t06-80-60-80-str2+near-backbone-11-scores.html | 2006 Jul 10 17:32:49 |
amino acid/100-30-str2 multi-track target model scores | T0342.t04-100-30-str2-scores.html | 2006 Jul 10 17:33:14 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0342.t04-100-30-stride-ebghtl-scores.html | 2006 Jul 10 17:33:37 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0342.t04-100-30-dssp-ebghstl-scores.html | 2006 Jul 10 17:34:04 |
amino acid/100-30-alpha multi-track target model scores | T0342.t04-100-30-alpha-scores.html | 2006 Jul 10 17:34:29 |
amino acid/100-30-bys multi-track target model scores | T0342.t04-100-30-bys-scores.html | 2006 Jul 10 17:34:52 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0342.t04-100-30-dssp-ehl2-scores.html | 2006 Jul 10 17:35:14 |
amino acid/100-30-n_notor2 multi-track target model scores | T0342.t04-100-30-n_notor2-scores.html | 2006 Jul 10 17:35:37 |
amino acid/100-30-o_notor2 multi-track target model scores | T0342.t04-100-30-o_notor2-scores.html | 2006 Jul 10 17:36:00 |
amino acid/100-30-n_sep multi-track target model scores | T0342.t04-100-30-n_sep-scores.html | 2006 Jul 10 17:36:23 |
amino acid/100-30-o_sep multi-track target model scores | T0342.t04-100-30-o_sep-scores.html | 2006 Jul 10 17:36:44 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0342.t04-100-30-CB_burial_14_7-scores.html | 2006 Jul 10 17:37:12 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0342.t04-100-30-near-backbone-11-scores.html | 2006 Jul 10 17:37:35 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0342.t04-100-40-40-str2+CB_burial_14_7-scores.html | 2006 Jul 10 17:38:00 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0342.t04-80-60-80-str2+near-backbone-11-scores.html | 2006 Jul 10 17:38:27 |
amino acid/100-30-str2 multi-track target model scores | T0342.t2k-100-30-str2-scores.html | 2006 Jul 10 17:38:57 |
amino acid/100-30-stride-ebghtl multi-track target model scores | T0342.t2k-100-30-stride-ebghtl-scores.html | 2006 Jul 10 17:39:27 |
amino acid/100-30-dssp-ebghstl multi-track target model scores | T0342.t2k-100-30-dssp-ebghstl-scores.html | 2006 Jul 10 17:39:56 |
amino acid/100-30-alpha multi-track target model scores | T0342.t2k-100-30-alpha-scores.html | 2006 Jul 10 17:40:25 |
amino acid/100-30-bys multi-track target model scores | T0342.t2k-100-30-bys-scores.html | 2006 Jul 10 17:41:01 |
amino acid/100-30-dssp-ehl2 multi-track target model scores | T0342.t2k-100-30-dssp-ehl2-scores.html | 2006 Jul 10 17:41:30 |
amino acid/100-30-n_notor2 multi-track target model scores | T0342.t2k-100-30-n_notor2-scores.html | 2006 Jul 10 17:41:59 |
amino acid/100-30-o_notor2 multi-track target model scores | T0342.t2k-100-30-o_notor2-scores.html | 2006 Jul 10 17:42:28 |
amino acid/100-30-n_sep multi-track target model scores | T0342.t2k-100-30-n_sep-scores.html | 2006 Jul 10 17:42:59 |
amino acid/100-30-o_sep multi-track target model scores | T0342.t2k-100-30-o_sep-scores.html | 2006 Jul 10 17:43:33 |
amino acid/100-30-CB_burial_14_7 multi-track target model scores | T0342.t2k-100-30-CB_burial_14_7-scores.html | 2006 Jul 10 17:44:04 |
amino acid/100-30-near-backbone-11 multi-track target model scores | T0342.t2k-100-30-near-backbone-11-scores.html | 2006 Jul 10 17:44:33 |
amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores | T0342.t2k-100-40-40-str2+CB_burial_14_7-scores.html | 2006 Jul 10 17:45:06 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0342.t2k-80-60-80-str2+near-backbone-11-scores.html | 2006 Jul 10 17:45:40 |
Template model scores |
Annotated t06 template model scores | T0342.t06-template-lib-scores.html | 2006 Jul 10 18:18:58 |
Annotated t04 template model scores | T0342.t04-template-lib-scores.html | 2006 Jul 10 19:08:16 |
Annotated t2k template model scores | T0342.t2k-template-lib-scores.html | 2006 Jul 10 19:57:36 |
Top Hits |
Best scoring hits from t06 HMMs | T0342.t06.best-scores.html | 2006 Jul 10 19:57:39 |
Best scoring hits from t04 HMMs | T0342.t04.best-scores.html | 2006 Jul 10 19:57:41 |
Best scoring hits from t2k HMMs | T0342.t2k.best-scores.html | 2006 Jul 10 19:57:43 |
Best scoring hits from combining t06 t04 t2k | T0342.best-scores.html | 2006 Jul 10 19:57:46 |
Alignments for Top Hits |
Top alignments from t06 hits | T0342.t06.top_reported_alignments.html | 2006 Jul 10 20:31:24 |
Top alignments from t04 hits | T0342.t04.top_reported_alignments.html | 2006 Jul 10 20:31:40 |
Top alignments from t2k hits | T0342.t2k.top_reported_alignments.html | 2006 Jul 10 20:31:52 |
Top alignments from combined hits | T0342.top_reported_alignments.html | 2006 Jul 10 20:31:55 |
multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2006 Jul 10 20:32:19 |
Undertaker (3d) files |
Undertaker input for top t06 alignments | T0342.t06.undertaker-align.under | 2006 Jul 10 20:32:20 |
Undertaker input for top t04 alignments | T0342.t04.undertaker-align.under | 2006 Jul 10 20:32:20 |
Undertaker input for top t2k alignments | T0342.t2k.undertaker-align.under | 2006 Jul 10 20:32:20 |
Undertaker input for top combined alignments | T0342.undertaker-align.under | 2006 Jul 10 20:32:20 |
PDB file with model(s) for top alignments | T0342.undertaker-align.pdb.gz | 2006 Jul 10 20:33:41 |
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) | T0342.t06.many.frag.gz | 2006 Jul 10 20:35:13 |
Fragment list for undertaker (from fragfinder) | T0342.t04.many.frag.gz | 2006 Jul 10 20:35:26 |
Fragment list for undertaker (from fragfinder) | T0342.t2k.many.frag.gz | 2006 Jul 10 20:35:40 |
Contact predictions, based on |
contact predictions (rr format) (rr.constraints format) | T0342.449a_45 | 2006 Jul 10 20:35:47 |
First attempted model using undertaker | decoys/T0342.try1-opt2.pdb.gz | 2006 Jul 10 21:07:48 |
Images of complete model in decoys/T0342.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