T0255 AAG06109, Pseudomonas aeruginosa PAO1
Description | Link to file | Date |
Inputs |
Submitted sequence(s) | T0255.a2m | 2004 Jul 28 8:55:52 |
README file | README | 2004 Jul 30 0:23:12 |
Provided documentation | T0255.doc.html | 2004 Jul 28 8:55:52 |
Multiple alignment |
SAM_t04 multiple alignment in a2m format | T0255.t04.a2m.gz | 2004 Jul 30 0:26:37 |
SAM_t04 multiple alignment in pretty html format | T0255.t04.pa.html | 2004 Jul 30 0:26:49 |
SAM_t04 target hidden Markov model | T0255.t04.w0.5.mod | 2004 Jul 30 0:26:49 |
SAM_t04 multiple alignment---sequence logo (eps format) (pdf format) | T0255.t04.w0.5-logo | 2004 Jul 30 0:26:55 |
Script for highlighting in rasmol | conserved_t04 | 2004 Jul 30 0:26:54 |
SAM_t2k multiple alignment in a2m format | T0255.t2k.a2m.gz | 2004 Jul 30 0:31:58 |
SAM_t2k multiple alignment in pretty html format | T0255.t2k.pa.html | 2004 Jul 30 0:32:04 |
SAM_t2k target hidden Markov model | T0255.t2k.w0.5.mod | 2004 Jul 30 0:32:04 |
SAM_t2k multiple alignment---sequence logo (eps format) (pdf format) | T0255.t2k.w0.5-logo | 2004 Jul 30 0:32:09 |
Script for highlighting in rasmol | conserved_t2k | 2004 Jul 30 0:32:07 |
Secondary Structure Prediction (Explanation of secondary-structure predictions) |
str2 structure prediction (rdb format) (seq format) | T0255.t2k.str2 | 2004 Jul 30 0:32:08 |
Script for T0255.t2k.str2 coloring in rasmol | T0255.t2k.str2-color.rasmol | 2004 Jul 30 0:32:08 |
str2---sequence logo (eps format) (pdf format) | T0255.t2k.str2-logo | 2004 Jul 30 0:32:13 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0255.t2k.stride-ebghtl | 2004 Jul 30 0:32:04 |
Script for T0255.t2k.stride-ebghtl coloring in rasmol | T0255.t2k.stride-ebghtl-color.rasmol | 2004 Jul 30 0:32:12 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0255.t2k.stride-ebghtl-logo | 2004 Jul 30 0:32:16 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0255.t2k.dssp-ebghstl | 2004 Jul 30 0:32:15 |
Script for T0255.t2k.dssp-ebghstl coloring in rasmol | T0255.t2k.dssp-ebghstl-color.rasmol | 2004 Jul 30 0:32:15 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0255.t2k.dssp-ebghstl-logo | 2004 Jul 30 0:32:20 |
alpha structure prediction (rdb format) (seq format) | T0255.t2k.alpha | 2004 Jul 30 0:32:19 |
Script for T0255.t2k.alpha coloring in rasmol | T0255.t2k.alpha-color.rasmol | 2004 Jul 30 0:32:19 |
alpha---sequence logo (eps format) (pdf format) | T0255.t2k.alpha-logo | 2004 Jul 30 0:32:24 |
bys structure prediction (rdb format) (seq format) | T0255.t2k.bys | 2004 Jul 30 0:32:23 |
Script for T0255.t2k.bys coloring in rasmol | T0255.t2k.bys-color.rasmol | 2004 Jul 30 0:32:23 |
bys---sequence logo (eps format) (pdf format) | T0255.t2k.bys-logo | 2004 Jul 30 0:32:27 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0255.t2k.dssp-ehl2 | 2004 Jul 30 0:32:26 |
Script for T0255.t2k.dssp-ehl2 coloring in rasmol | T0255.t2k.dssp-ehl2-color.rasmol | 2004 Jul 30 0:32:26 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0255.t2k.dssp-ehl2-logo | 2004 Jul 30 0:32:31 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0255.t2k.CB_burial_14_7 | 2004 Jul 30 0:32:30 |
Script for T0255.t2k.CB_burial_14_7 coloring in rasmol | T0255.t2k.CB_burial_14_7-color.rasmol | 2004 Jul 30 0:32:30 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0255.t2k.CB_burial_14_7-logo | 2004 Jul 30 0:32:34 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0255.t2k.near-backbone-11 | 2004 Jul 30 0:32:33 |
Script for T0255.t2k.near-backbone-11 coloring in rasmol | T0255.t2k.near-backbone-11-color.rasmol | 2004 Jul 30 0:32:34 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0255.t2k.near-backbone-11-logo | 2004 Jul 30 0:32:38 |
str2 structure prediction (rdb format) (seq format) | T0255.t04.str2 | 2004 Jul 30 0:32:37 |
Script for T0255.t04.str2 coloring in rasmol | T0255.t04.str2-color.rasmol | 2004 Jul 30 0:32:38 |
str2---sequence logo (eps format) (pdf format) | T0255.t04.str2-logo | 2004 Jul 30 0:32:42 |
stride-ebghtl structure prediction (rdb format) (seq format) | T0255.t04.stride-ebghtl | 2004 Jul 30 0:26:50 |
Script for T0255.t04.stride-ebghtl coloring in rasmol | T0255.t04.stride-ebghtl-color.rasmol | 2004 Jul 30 0:32:41 |
stride-ebghtl---sequence logo (eps format) (pdf format) | T0255.t04.stride-ebghtl-logo | 2004 Jul 30 0:32:46 |
dssp-ebghstl structure prediction (rdb format) (seq format) | T0255.t04.dssp-ebghstl | 2004 Jul 30 0:32:45 |
Script for T0255.t04.dssp-ebghstl coloring in rasmol | T0255.t04.dssp-ebghstl-color.rasmol | 2004 Jul 30 0:32:45 |
dssp-ebghstl---sequence logo (eps format) (pdf format) | T0255.t04.dssp-ebghstl-logo | 2004 Jul 30 0:32:49 |
alpha structure prediction (rdb format) (seq format) | T0255.t04.alpha | 2004 Jul 30 0:32:48 |
Script for T0255.t04.alpha coloring in rasmol | T0255.t04.alpha-color.rasmol | 2004 Jul 30 0:32:48 |
alpha---sequence logo (eps format) (pdf format) | T0255.t04.alpha-logo | 2004 Jul 30 0:32:53 |
bys structure prediction (rdb format) (seq format) | T0255.t04.bys | 2004 Jul 30 0:32:52 |
Script for T0255.t04.bys coloring in rasmol | T0255.t04.bys-color.rasmol | 2004 Jul 30 0:32:52 |
bys---sequence logo (eps format) (pdf format) | T0255.t04.bys-logo | 2004 Jul 30 0:32:57 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0255.t04.dssp-ehl2 | 2004 Jul 30 0:32:56 |
Script for T0255.t04.dssp-ehl2 coloring in rasmol | T0255.t04.dssp-ehl2-color.rasmol | 2004 Jul 30 0:32:56 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0255.t04.dssp-ehl2-logo | 2004 Jul 30 0:33:00 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0255.t04.CB_burial_14_7 | 2004 Jul 30 0:33:00 |
Script for T0255.t04.CB_burial_14_7 coloring in rasmol | T0255.t04.CB_burial_14_7-color.rasmol | 2004 Jul 30 0:33:00 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0255.t04.CB_burial_14_7-logo | 2004 Jul 30 0:33:04 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0255.t04.near-backbone-11 | 2004 Jul 30 0:33:03 |
Script for T0255.t04.near-backbone-11 coloring in rasmol | T0255.t04.near-backbone-11-color.rasmol | 2004 Jul 30 0:33:03 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0255.t04.near-backbone-11-logo | 2004 Jul 30 0:33:08 |
Target model scores |
amino acid single-track target model scores of PDB | T0255.t2k-w0.5-scores.html | 2004 Jul 30 0:34:37 |
amino acid single-track target model scores of PDB | T0255.t04-w0.5-scores.html | 2004 Jul 30 0:36:02 |
amino acid/100-30-str2 two-track target model scores | T0255.t2k-100-30-str2-scores.html | 2004 Jul 30 0:37:40 |
amino acid/100-30-stride-ebghtl two-track target model scores | T0255.t2k-100-30-stride-ebghtl-scores.html | 2004 Jul 30 0:39:13 |
amino acid/100-30-dssp-ebghstl two-track target model scores | T0255.t2k-100-30-dssp-ebghstl-scores.html | 2004 Jul 30 0:40:50 |
amino acid/100-30-alpha two-track target model scores | T0255.t2k-100-30-alpha-scores.html | 2004 Jul 30 0:42:24 |
amino acid/100-30-bys two-track target model scores | T0255.t2k-100-30-bys-scores.html | 2004 Jul 30 0:43:58 |
amino acid/100-30-dssp-ehl2 two-track target model scores | T0255.t2k-100-30-dssp-ehl2-scores.html | 2004 Jul 30 0:45:28 |
amino acid/100-30-CB_burial_14_7 two-track target model scores | T0255.t2k-100-30-CB_burial_14_7-scores.html | 2004 Jul 30 0:47:10 |
amino acid/100-30-near-backbone-11 two-track target model scores | T0255.t2k-100-30-near-backbone-11-scores.html | 2004 Jul 30 0:48:44 |
amino acid/100-40-40-str2+CB_burial_14_7 two-track target model scores | T0255.t2k-100-40-40-str2+CB_burial_14_7-scores.html | 2004 Jul 30 0:50:25 |
amino acid/100-30-str2 two-track target model scores | T0255.t04-100-30-str2-scores.html | 2004 Jul 30 0:51:27 |
amino acid/100-30-stride-ebghtl two-track target model scores | T0255.t04-100-30-stride-ebghtl-scores.html | 2004 Jul 30 0:52:32 |
amino acid/100-30-dssp-ebghstl two-track target model scores | T0255.t04-100-30-dssp-ebghstl-scores.html | 2004 Jul 30 0:53:37 |
amino acid/100-30-alpha two-track target model scores | T0255.t04-100-30-alpha-scores.html | 2004 Jul 30 0:54:40 |
amino acid/100-30-bys two-track target model scores | T0255.t04-100-30-bys-scores.html | 2004 Jul 30 0:55:44 |
amino acid/100-30-dssp-ehl2 two-track target model scores | T0255.t04-100-30-dssp-ehl2-scores.html | 2004 Jul 30 0:56:48 |
amino acid/100-30-CB_burial_14_7 two-track target model scores | T0255.t04-100-30-CB_burial_14_7-scores.html | 2004 Jul 30 0:57:57 |
amino acid/100-30-near-backbone-11 two-track target model scores | T0255.t04-100-30-near-backbone-11-scores.html | 2004 Jul 30 0:59:01 |
amino acid/100-40-40-str2+CB_burial_14_7 two-track target model scores | T0255.t04-100-40-40-str2+CB_burial_14_7-scores.html | 2004 Jul 30 1:00:12 |
Template model scores |
Annotated template model scores | T0255.template-lib-scores.html | 2004 Jul 29 2:07:35 |
Top Hits |
Best scoring hits from all models | T0255.t2k.best-scores.html | 2004 Jul 30 1:00:13 |
Alignments for Top Hits |
T02 Many Alignments Summary | T0255.t2k.many_alignments.html | 2004 Jul 30 1:02:57 |
T02 Top Models Summary | T0255.t2k.top_reported_alignments.html | 2004 Jul 30 1:03:02 |
multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2004 Jul 30 1:03:10 |
Undertaker (3d) files |
Multiple alignment for undertaker templates | T0255.t2k-2track-undertaker.a2m | 2004 Jul 30 1:03:56 |
Undertaker input for top alignments | T0255.t2k.undertaker-align.under | 2004 Jul 30 1:03:54 |
PDB file with model(s) for top alignments | T0255.t2k.undertaker-align.pdb.gz | 2004 Jul 30 1:04:32 |
Fragment list for undertaker (from fragfinder) | T0255.t2k.many.frag.gz | 2004 Jul 30 1:04:59 |
First attempted model using undertaker | decoys/T0255.try1-opt2.pdb.gz | 2004 Jul 30 2:28:45 |
Significant mutual information between column pairs |
Mutual information table (align thinned to 30% ID) | T0255.t2k-thin30.mi.rdb | 2004 Jul 30 2:29:37 |
Mutual information table (align thinned to 35% ID) | T0255.t2k-thin35.mi.rdb | 2004 Jul 30 2:30:17 |
Mutual information table (align thinned to 40% ID) | T0255.t2k-thin40.mi.rdb | 2004 Jul 30 2:30:47 |
Mutual information table (align thinned to 50% ID) | T0255.t2k-thin50.mi.rdb | 2004 Jul 30 2:31:00 |
Mutual information table (align thinned to 62% ID) | T0255.t2k-thin62.mi.rdb | 2004 Jul 30 2:31:15 |
Mutual information table (align thinned to 30% ID) | T0255.t04-thin30.mi.rdb | 2004 Jul 30 2:32:03 |
Mutual information table (align thinned to 35% ID) | T0255.t04-thin35.mi.rdb | 2004 Jul 30 2:32:22 |
Mutual information table (align thinned to 40% ID) | T0255.t04-thin40.mi.rdb | 2004 Jul 30 2:32:33 |
Mutual information table (align thinned to 50% ID) | T0255.t04-thin50.mi.rdb | 2004 Jul 30 2:32:53 |
Mutual information table (align thinned to 62% ID) | T0255.t04-thin62.mi.rdb | 2004 Jul 30 2:33:55 |
contact predictions (rr format) (rr.constraints format) | T0255.280 | 2004 Jul 30 2:33:58 |
Please cite: Karplus, K. and Karchin, R. and Barrett, C. and Tu, S. and Cline, M. and Diekhans, M. and Grate, L. and Casper, J. and Hughey, R. ``What is the value added by human intervention in protein structure prediction?'' Proteins: Structure Function and Genetics 45(S5):86-91,2001
SAM_T02 web system designed by Rachel Karchin and Kevin Karplus rachelk@soe.ucsc.edu karplus@soe.ucsc.edu