T0208 EFR41, E.faecalis
| Description | Link to file | Date |
| Inputs |
| Submitted sequence(s) | T0208.a2m | 2004 Jun 21 8:34:40 |
| README file | README | 2004 Jun 29 11:15:01 |
| Provided documentation | T0208.doc.html | 2004 Jun 21 8:34:40 |
| Multiple alignment |
| SAM_t04 multiple alignment in a2m format | T0208.t04.a2m.gz | 2004 Jun 21 8:45:46 |
| SAM_t04 multiple alignment in pretty html format | T0208.t04.pa.html | 2004 Jun 21 8:45:57 |
| SAM_t04 target hidden Markov model | T0208.t04.w0.5.mod | 2004 Jun 21 8:45:59 |
| SAM_t04 multiple alignment---sequence logo (eps format) (pdf format) | T0208.t04.w0.5-logo | 2004 Jun 21 8:46:07 |
| Script for highlighting in rasmol | conserved_t04 | 2004 Jun 21 8:46:08 |
| SAM_t2k multiple alignment in a2m format | T0208.t2k.a2m.gz | 2004 Jun 21 8:54:55 |
| SAM_t2k multiple alignment in pretty html format | T0208.t2k.pa.html | 2004 Jun 21 8:55:01 |
| SAM_t2k target hidden Markov model | T0208.t2k.w0.5.mod | 2004 Jun 21 8:55:02 |
| SAM_t2k multiple alignment---sequence logo (eps format) (pdf format) | T0208.t2k.w0.5-logo | 2004 Jun 21 8:55:07 |
| Script for highlighting in rasmol | conserved_t2k | 2004 Jun 21 8:55:07 |
| Secondary Structure Prediction (Explanation of secondary-structure predictions) |
| str2 structure prediction (rdb format) (seq format) | T0208.t2k.str2 | 2004 Jun 21 8:55:08 |
| Script for T0208.t2k.str2 coloring in rasmol | T0208.t2k.str2-color.rasmol | 2004 Jun 21 8:55:08 |
| str2---sequence logo (eps format) (pdf format) | T0208.t2k.str2-logo | 2004 Jun 21 8:55:14 |
| stride-ebghtl structure prediction (rdb format) (seq format) | T0208.t2k.stride-ebghtl | 2004 Jun 21 8:55:02 |
| Script for T0208.t2k.stride-ebghtl coloring in rasmol | T0208.t2k.stride-ebghtl-color.rasmol | 2004 Jun 21 8:55:14 |
| stride-ebghtl---sequence logo (eps format) (pdf format) | T0208.t2k.stride-ebghtl-logo | 2004 Jun 21 8:55:20 |
| dssp-ebghstl structure prediction (rdb format) (seq format) | T0208.t2k.dssp-ebghstl | 2004 Jun 21 8:55:21 |
| Script for T0208.t2k.dssp-ebghstl coloring in rasmol | T0208.t2k.dssp-ebghstl-color.rasmol | 2004 Jun 21 8:55:21 |
| dssp-ebghstl---sequence logo (eps format) (pdf format) | T0208.t2k.dssp-ebghstl-logo | 2004 Jun 21 8:55:26 |
| alpha structure prediction (rdb format) (seq format) | T0208.t2k.alpha | 2004 Jun 21 8:55:26 |
| Script for T0208.t2k.alpha coloring in rasmol | T0208.t2k.alpha-color.rasmol | 2004 Jun 21 8:55:26 |
| alpha---sequence logo (eps format) (pdf format) | T0208.t2k.alpha-logo | 2004 Jun 21 8:55:31 |
| bys structure prediction (rdb format) (seq format) | T0208.t2k.bys | 2004 Jun 21 8:55:31 |
| Script for T0208.t2k.bys coloring in rasmol | T0208.t2k.bys-color.rasmol | 2004 Jun 21 8:55:32 |
| dssp-ehl2 structure prediction (rdb format) (seq format) | T0208.t2k.dssp-ehl2 | 2004 Jun 21 8:55:33 |
| Script for T0208.t2k.dssp-ehl2 coloring in rasmol | T0208.t2k.dssp-ehl2-color.rasmol | 2004 Jun 21 8:55:33 |
| dssp-ehl2---sequence logo (eps format) (pdf format) | T0208.t2k.dssp-ehl2-logo | 2004 Jun 21 8:55:39 |
| CB_burial_14_7 structure prediction (rdb format) (seq format) | T0208.t2k.CB_burial_14_7 | 2004 Jun 21 8:55:40 |
| Script for T0208.t2k.CB_burial_14_7 coloring in rasmol | T0208.t2k.CB_burial_14_7-color.rasmol | 2004 Jun 21 8:55:40 |
| CB_burial_14_7---sequence logo (eps format) (pdf format) | T0208.t2k.CB_burial_14_7-logo | 2004 Jun 21 8:55:45 |
| near-backbone-11 structure prediction (rdb format) (seq format) | T0208.t2k.near-backbone-11 | 2004 Jul 3 22:10:53 |
| Script for T0208.t2k.near-backbone-11 coloring in rasmol | T0208.t2k.near-backbone-11-color.rasmol | 2004 Jul 3 22:10:53 |
| str2 structure prediction (rdb format) (seq format) | T0208.t04.str2 | 2004 Jun 21 8:55:47 |
| Script for T0208.t04.str2 coloring in rasmol | T0208.t04.str2-color.rasmol | 2004 Jun 21 8:55:47 |
| str2---sequence logo (eps format) (pdf format) | T0208.t04.str2-logo | 2004 Jun 21 8:55:53 |
| stride-ebghtl structure prediction (rdb format) (seq format) | T0208.t04.stride-ebghtl | 2004 Jun 21 8:46:02 |
| Script for T0208.t04.stride-ebghtl coloring in rasmol | T0208.t04.stride-ebghtl-color.rasmol | 2004 Jun 21 8:55:53 |
| stride-ebghtl---sequence logo (eps format) (pdf format) | T0208.t04.stride-ebghtl-logo | 2004 Jun 21 8:55:58 |
| dssp-ebghstl structure prediction (rdb format) (seq format) | T0208.t04.dssp-ebghstl | 2004 Jun 21 8:55:59 |
| Script for T0208.t04.dssp-ebghstl coloring in rasmol | T0208.t04.dssp-ebghstl-color.rasmol | 2004 Jun 21 8:56:00 |
| dssp-ebghstl---sequence logo (eps format) (pdf format) | T0208.t04.dssp-ebghstl-logo | 2004 Jun 21 8:56:05 |
| alpha structure prediction (rdb format) (seq format) | T0208.t04.alpha | 2004 Jun 21 8:56:05 |
| Script for T0208.t04.alpha coloring in rasmol | T0208.t04.alpha-color.rasmol | 2004 Jun 21 8:56:06 |
| alpha---sequence logo (eps format) (pdf format) | T0208.t04.alpha-logo | 2004 Jun 21 8:56:11 |
| bys structure prediction (rdb format) (seq format) | T0208.t04.bys | 2004 Jun 21 8:56:15 |
| Script for T0208.t04.bys coloring in rasmol | T0208.t04.bys-color.rasmol | 2004 Jun 21 8:56:16 |
| dssp-ehl2 structure prediction (rdb format) (seq format) | T0208.t04.dssp-ehl2 | 2004 Jun 21 8:56:19 |
| Script for T0208.t04.dssp-ehl2 coloring in rasmol | T0208.t04.dssp-ehl2-color.rasmol | 2004 Jun 21 8:56:20 |
| dssp-ehl2---sequence logo (eps format) (pdf format) | T0208.t04.dssp-ehl2-logo | 2004 Jun 21 8:56:26 |
| CB_burial_14_7 structure prediction (rdb format) (seq format) | T0208.t04.CB_burial_14_7 | 2004 Jun 21 8:56:31 |
| Script for T0208.t04.CB_burial_14_7 coloring in rasmol | T0208.t04.CB_burial_14_7-color.rasmol | 2004 Jun 21 8:56:32 |
| CB_burial_14_7---sequence logo (eps format) (pdf format) | T0208.t04.CB_burial_14_7-logo | 2004 Jun 21 8:56:37 |
| near-backbone-11 structure prediction (rdb format) (seq format) | T0208.t04.near-backbone-11 | 2004 Jul 3 22:11:08 |
| Script for T0208.t04.near-backbone-11 coloring in rasmol | T0208.t04.near-backbone-11-color.rasmol | 2004 Jul 3 22:11:09 |
| Target model scores |
| amino acid single-track target model scores of PDB | T0208.t2k-w0.5-scores.html | 2004 Jun 21 9:03:12 |
| amino acid single-track target model scores of PDB | T0208.t04-w0.5-scores.html | 2004 Jun 21 9:09:13 |
| amino acid/100-30-str2 two-track target model scores | T0208.t2k-100-30-str2-scores.html | 2004 Jun 21 9:15:43 |
| amino acid/100-30-stride-ebghtl two-track target model scores | T0208.t2k-100-30-stride-ebghtl-scores.html | 2004 Jun 21 9:22:20 |
| amino acid/100-30-dssp-ebghstl two-track target model scores | T0208.t2k-100-30-dssp-ebghstl-scores.html | 2004 Jun 21 9:28:56 |
| amino acid/100-30-alpha two-track target model scores | T0208.t2k-100-30-alpha-scores.html | 2004 Jun 21 9:35:32 |
| amino acid/100-30-dssp-ehl2 two-track target model scores | T0208.t2k-100-30-dssp-ehl2-scores.html | 2004 Jun 21 9:41:52 |
| amino acid/100-30-CB_burial_14_7 two-track target model scores | T0208.t2k-100-30-CB_burial_14_7-scores.html | 2004 Jun 21 9:48:21 |
| amino acid/100-40-40-str2+CB_burial_14_7 two-track target model scores | T0208.t2k-100-40-40-str2+CB_burial_14_7-scores.html | 2004 Jun 21 9:55:54 |
| amino acid/100-30-str2 two-track target model scores | T0208.t04-100-30-str2-scores.html | 2004 Jun 21 9:59:55 |
| amino acid/100-30-stride-ebghtl two-track target model scores | T0208.t04-100-30-stride-ebghtl-scores.html | 2004 Jun 21 10:03:17 |
| amino acid/100-30-dssp-ebghstl two-track target model scores | T0208.t04-100-30-dssp-ebghstl-scores.html | 2004 Jun 21 10:05:39 |
| amino acid/100-30-alpha two-track target model scores | T0208.t04-100-30-alpha-scores.html | 2004 Jun 21 10:08:03 |
| amino acid/100-30-dssp-ehl2 two-track target model scores | T0208.t04-100-30-dssp-ehl2-scores.html | 2004 Jun 21 10:12:12 |
| amino acid/100-30-CB_burial_14_7 two-track target model scores | T0208.t04-100-30-CB_burial_14_7-scores.html | 2004 Jun 21 10:15:36 |
| amino acid/100-40-40-str2+CB_burial_14_7 two-track target model scores | T0208.t04-100-40-40-str2+CB_burial_14_7-scores.html | 2004 Jun 21 10:18:43 |
| Template model scores |
| Annotated template model scores | T0208.template-lib-scores.html | 2004 Jun 21 10:24:14 |
| Top Hits |
| Alignments for Top Hits |
| multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2004 Jul 5 10:05:23 |
| Undertaker (3d) files |
| Multiple alignment for undertaker templates | T0208.t04-2track-undertaker.a2m | 2004 Jul 5 10:07:38 |
| Fragment list for undertaker (from fragfinder) | T0208.t04.many.frag.gz | 2004 Jul 5 10:09:26 |
| First attempted model using undertaker | decoys/T0208.try1-opt2.pdb.gz | 2004 Jun 21 15:12:28 |
| Significant mutual information between column pairs |
| Mutual information table (align thinned to 30% ID) | T0208.t2k-thin30.mi.rdb | 2004 Jul 5 9:09:58 |
| Mutual information table (align thinned to 35% ID) | T0208.t2k-thin35.mi.rdb | 2004 Jul 5 9:17:43 |
| Mutual information table (align thinned to 40% ID) | T0208.t2k-thin40.mi.rdb | 2004 Jul 5 9:26:06 |
| Mutual information table (align thinned to 50% ID) | T0208.t2k-thin50.mi.rdb | 2004 Jul 5 9:29:29 |
| Mutual information table (align thinned to 62% ID) | T0208.t2k-thin62.mi.rdb | 2004 Jul 5 9:33:00 |
| Mutual information table (align thinned to 30% ID) | T0208.t04-thin30.mi.rdb | 2004 Jul 5 9:33:39 |
| Mutual information table (align thinned to 35% ID) | T0208.t04-thin35.mi.rdb | 2004 Jul 5 9:34:24 |
| Mutual information table (align thinned to 40% ID) | T0208.t04-thin40.mi.rdb | 2004 Jul 5 9:35:14 |
| Mutual information table (align thinned to 50% ID) | T0208.t04-thin50.mi.rdb | 2004 Jul 5 9:36:35 |
| Mutual information table (align thinned to 62% ID) | T0208.t04-thin62.mi.rdb | 2004 Jul 5 9:42:36 |
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