Please cite the following papers:
When SAM_T08 finishes loading, you should see links to
You may also view the list of files created so far. This link gives access to the full directory of file produced, including query progress logs, and this html file (summary.html). When the process is finished, you may want to download the entire directory to your computer, using a tool such as "wget".
Description | Link to file | Date |
Inputs |
Submitted sequence(s) | T0558.a2m | 2010 May 25 9:10:56 |
README file | README | 2010 May 25 9:11:06 |
Quick blastp of non-redundant PDB | T0558.pdb_blast.txt | 2010 May 25 9:11:10 |
Multiple alignment |
SAM_t06 multiple alignment in a2m format | T0558.t06.a2m.gz | 2010 May 25 10:49:41 |
SAM_t06 multiple alignment in pretty html format | T0558.t06.pa.html | 2010 May 25 10:53:10 |
SAM_t06 target hidden Markov model | T0558.t06.w0.5.mod | 2010 May 25 10:53:43 |
SAM_t06 multiple alignment---sequence logo (eps format) (pdf format) | T0558.t06.w0.5-logo | 2010 May 25 10:54:27 |
SAM_t06 consensus sequence | T0558.t06.w0.5.maxp | 2010 May 25 10:54:28 |
Script for highlighting in rasmol | conserved_t06 | 2010 May 25 10:54:29 |
SAM_t04 multiple alignment in a2m format | T0558.t04.a2m.gz | 2010 May 25 11:32:05 |
SAM_t04 multiple alignment in pretty html format | T0558.t04.pa.html | 2010 May 25 11:35:13 |
SAM_t04 target hidden Markov model | T0558.t04.w0.5.mod | 2010 May 25 11:35:27 |
SAM_t04 multiple alignment---sequence logo (eps format) (pdf format) | T0558.t04.w0.5-logo | 2010 May 25 11:35:45 |
SAM_t04 consensus sequence | T0558.t04.w0.5.maxp | 2010 May 25 11:35:46 |
Script for highlighting in rasmol | conserved_t04 | 2010 May 25 11:35:48 |
SAM_t2k multiple alignment in a2m format | T0558.t2k.a2m.gz | 2010 May 25 11:41:04 |
SAM_t2k multiple alignment in pretty html format | T0558.t2k.pa.html | 2010 May 25 11:41:13 |
SAM_t2k target hidden Markov model | T0558.t2k.w0.5.mod | 2010 May 25 11:41:15 |
SAM_t2k multiple alignment---sequence logo (eps format) (pdf format) | T0558.t2k.w0.5-logo | 2010 May 25 11:41:22 |
SAM_t2k consensus sequence | T0558.t2k.w0.5.maxp | 2010 May 25 11:41:23 |
Script for highlighting in rasmol | conserved_t2k | 2010 May 25 11:41:23 |
Secondary Structure Prediction (Explanation of secondary-structure predictions) |
str4 structure prediction (rdb format) (seq format) | T0558.t06.str4 | 2010 May 25 11:41:40 |
Script for T0558.t06.str4 coloring in rasmol | T0558.t06.str4-color.rasmol | 2010 May 25 11:41:42 |
str4---sequence logo (eps format) (pdf format) | T0558.t06.str4-logo | 2010 May 25 11:41:45 |
str4 structure prediction (rdb format) (seq format) | T0558.t04.str4 | 2010 May 25 11:41:50 |
Script for T0558.t04.str4 coloring in rasmol | T0558.t04.str4-color.rasmol | 2010 May 25 11:41:51 |
str4---sequence logo (eps format) (pdf format) | T0558.t04.str4-logo | 2010 May 25 11:41:55 |
str4 structure prediction (rdb format) (seq format) | T0558.t2k.str4 | 2010 May 25 11:41:58 |
Script for T0558.t2k.str4 coloring in rasmol | T0558.t2k.str4-color.rasmol | 2010 May 25 11:41:58 |
str4---sequence logo (eps format) (pdf format) | T0558.t2k.str4-logo | 2010 May 25 11:42:02 |
str2 structure prediction (rdb format) (seq format) | T0558.t06.str2 | 2010 May 25 10:54:24 |
Script for T0558.t06.str2 coloring in rasmol | T0558.t06.str2-color.rasmol | 2010 May 25 11:42:04 |
str2---sequence logo (eps format) (pdf format) | T0558.t06.str2-logo | 2010 May 25 11:42:08 |
str2 structure prediction (rdb format) (seq format) | T0558.t04.str2 | 2010 May 25 11:35:42 |
Script for T0558.t04.str2 coloring in rasmol | T0558.t04.str2-color.rasmol | 2010 May 25 11:42:10 |
str2---sequence logo (eps format) (pdf format) | T0558.t04.str2-logo | 2010 May 25 11:42:13 |
str2 structure prediction (rdb format) (seq format) | T0558.t2k.str2 | 2010 May 25 11:41:19 |
Script for T0558.t2k.str2 coloring in rasmol | T0558.t2k.str2-color.rasmol | 2010 May 25 11:42:15 |
str2---sequence logo (eps format) (pdf format) | T0558.t2k.str2-logo | 2010 May 25 11:42:18 |
alpha structure prediction (rdb format) (seq format) | T0558.t06.alpha | 2010 May 25 11:42:26 |
Script for T0558.t06.alpha coloring in rasmol | T0558.t06.alpha-color.rasmol | 2010 May 25 11:42:26 |
alpha---sequence logo (eps format) (pdf format) | T0558.t06.alpha-logo | 2010 May 25 11:42:30 |
alpha structure prediction (rdb format) (seq format) | T0558.t04.alpha | 2010 May 25 11:42:35 |
Script for T0558.t04.alpha coloring in rasmol | T0558.t04.alpha-color.rasmol | 2010 May 25 11:42:36 |
alpha---sequence logo (eps format) (pdf format) | T0558.t04.alpha-logo | 2010 May 25 11:42:39 |
alpha structure prediction (rdb format) (seq format) | T0558.t2k.alpha | 2010 May 25 11:42:42 |
Script for T0558.t2k.alpha coloring in rasmol | T0558.t2k.alpha-color.rasmol | 2010 May 25 11:42:42 |
alpha---sequence logo (eps format) (pdf format) | T0558.t2k.alpha-logo | 2010 May 25 11:42:46 |
bys structure prediction (rdb format) (seq format) | T0558.t06.bys | 2010 May 25 11:42:54 |
Script for T0558.t06.bys coloring in rasmol | T0558.t06.bys-color.rasmol | 2010 May 25 11:42:54 |
bys---sequence logo (eps format) (pdf format) | T0558.t06.bys-logo | 2010 May 25 11:42:57 |
bys structure prediction (rdb format) (seq format) | T0558.t04.bys | 2010 May 25 11:43:02 |
Script for T0558.t04.bys coloring in rasmol | T0558.t04.bys-color.rasmol | 2010 May 25 11:43:03 |
bys---sequence logo (eps format) (pdf format) | T0558.t04.bys-logo | 2010 May 25 11:43:06 |
bys structure prediction (rdb format) (seq format) | T0558.t2k.bys | 2010 May 25 11:43:09 |
Script for T0558.t2k.bys coloring in rasmol | T0558.t2k.bys-color.rasmol | 2010 May 25 11:43:09 |
bys---sequence logo (eps format) (pdf format) | T0558.t2k.bys-logo | 2010 May 25 11:43:13 |
pb structure prediction (rdb format) (seq format) | T0558.t06.pb | 2010 May 25 11:43:21 |
Script for T0558.t06.pb coloring in rasmol | T0558.t06.pb-color.rasmol | 2010 May 25 11:43:21 |
pb---sequence logo (eps format) (pdf format) | T0558.t06.pb-logo | 2010 May 25 11:43:25 |
pb structure prediction (rdb format) (seq format) | T0558.t04.pb | 2010 May 25 11:43:30 |
Script for T0558.t04.pb coloring in rasmol | T0558.t04.pb-color.rasmol | 2010 May 25 11:43:30 |
pb---sequence logo (eps format) (pdf format) | T0558.t04.pb-logo | 2010 May 25 11:43:33 |
pb structure prediction (rdb format) (seq format) | T0558.t2k.pb | 2010 May 25 11:43:36 |
Script for T0558.t2k.pb coloring in rasmol | T0558.t2k.pb-color.rasmol | 2010 May 25 11:43:36 |
pb---sequence logo (eps format) (pdf format) | T0558.t2k.pb-logo | 2010 May 25 11:43:39 |
n_notor2 structure prediction (rdb format) (seq format) | T0558.t06.n_notor2 | 2010 May 25 11:43:47 |
Script for T0558.t06.n_notor2 coloring in rasmol | T0558.t06.n_notor2-color.rasmol | 2010 May 25 11:43:48 |
n_notor2---sequence logo (eps format) (pdf format) | T0558.t06.n_notor2-logo | 2010 May 25 11:43:51 |
n_notor2 structure prediction (rdb format) (seq format) | T0558.t04.n_notor2 | 2010 May 25 11:43:56 |
Script for T0558.t04.n_notor2 coloring in rasmol | T0558.t04.n_notor2-color.rasmol | 2010 May 25 11:43:57 |
n_notor2---sequence logo (eps format) (pdf format) | T0558.t04.n_notor2-logo | 2010 May 25 11:44:00 |
n_notor2 structure prediction (rdb format) (seq format) | T0558.t2k.n_notor2 | 2010 May 25 11:44:03 |
Script for T0558.t2k.n_notor2 coloring in rasmol | T0558.t2k.n_notor2-color.rasmol | 2010 May 25 11:44:03 |
n_notor2---sequence logo (eps format) (pdf format) | T0558.t2k.n_notor2-logo | 2010 May 25 11:44:06 |
n_notor structure prediction (rdb format) (seq format) | T0558.t06.n_notor | 2010 May 25 11:44:14 |
Script for T0558.t06.n_notor coloring in rasmol | T0558.t06.n_notor-color.rasmol | 2010 May 25 11:44:16 |
n_notor---sequence logo (eps format) (pdf format) | T0558.t06.n_notor-logo | 2010 May 25 11:44:20 |
n_notor structure prediction (rdb format) (seq format) | T0558.t04.n_notor | 2010 May 25 11:44:25 |
Script for T0558.t04.n_notor coloring in rasmol | T0558.t04.n_notor-color.rasmol | 2010 May 25 11:44:25 |
n_notor---sequence logo (eps format) (pdf format) | T0558.t04.n_notor-logo | 2010 May 25 11:44:28 |
n_notor structure prediction (rdb format) (seq format) | T0558.t2k.n_notor | 2010 May 25 11:44:31 |
Script for T0558.t2k.n_notor coloring in rasmol | T0558.t2k.n_notor-color.rasmol | 2010 May 25 11:44:32 |
n_notor---sequence logo (eps format) (pdf format) | T0558.t2k.n_notor-logo | 2010 May 25 11:44:36 |
n_sep structure prediction (rdb format) (seq format) | T0558.t06.n_sep | 2010 May 25 11:44:44 |
Script for T0558.t06.n_sep coloring in rasmol | T0558.t06.n_sep-color.rasmol | 2010 May 25 11:44:44 |
n_sep---sequence logo (eps format) (pdf format) | T0558.t06.n_sep-logo | 2010 May 25 11:44:47 |
n_sep structure prediction (rdb format) (seq format) | T0558.t04.n_sep | 2010 May 25 11:44:52 |
Script for T0558.t04.n_sep coloring in rasmol | T0558.t04.n_sep-color.rasmol | 2010 May 25 11:44:53 |
n_sep---sequence logo (eps format) (pdf format) | T0558.t04.n_sep-logo | 2010 May 25 11:44:57 |
n_sep structure prediction (rdb format) (seq format) | T0558.t2k.n_sep | 2010 May 25 11:45:00 |
Script for T0558.t2k.n_sep coloring in rasmol | T0558.t2k.n_sep-color.rasmol | 2010 May 25 11:45:00 |
n_sep---sequence logo (eps format) (pdf format) | T0558.t2k.n_sep-logo | 2010 May 25 11:45:03 |
o_notor2 structure prediction (rdb format) (seq format) | T0558.t06.o_notor2 | 2010 May 25 11:45:12 |
Script for T0558.t06.o_notor2 coloring in rasmol | T0558.t06.o_notor2-color.rasmol | 2010 May 25 11:45:13 |
o_notor2---sequence logo (eps format) (pdf format) | T0558.t06.o_notor2-logo | 2010 May 25 11:45:17 |
o_notor2 structure prediction (rdb format) (seq format) | T0558.t04.o_notor2 | 2010 May 25 11:45:22 |
Script for T0558.t04.o_notor2 coloring in rasmol | T0558.t04.o_notor2-color.rasmol | 2010 May 25 11:45:23 |
o_notor2---sequence logo (eps format) (pdf format) | T0558.t04.o_notor2-logo | 2010 May 25 11:45:27 |
o_notor2 structure prediction (rdb format) (seq format) | T0558.t2k.o_notor2 | 2010 May 25 11:45:30 |
Script for T0558.t2k.o_notor2 coloring in rasmol | T0558.t2k.o_notor2-color.rasmol | 2010 May 25 11:45:30 |
o_notor2---sequence logo (eps format) (pdf format) | T0558.t2k.o_notor2-logo | 2010 May 25 11:45:34 |
o_notor structure prediction (rdb format) (seq format) | T0558.t06.o_notor | 2010 May 25 11:45:42 |
Script for T0558.t06.o_notor coloring in rasmol | T0558.t06.o_notor-color.rasmol | 2010 May 25 11:45:42 |
o_notor---sequence logo (eps format) (pdf format) | T0558.t06.o_notor-logo | 2010 May 25 11:45:45 |
o_notor structure prediction (rdb format) (seq format) | T0558.t04.o_notor | 2010 May 25 11:45:50 |
Script for T0558.t04.o_notor coloring in rasmol | T0558.t04.o_notor-color.rasmol | 2010 May 25 11:45:50 |
o_notor---sequence logo (eps format) (pdf format) | T0558.t04.o_notor-logo | 2010 May 25 11:45:53 |
o_notor structure prediction (rdb format) (seq format) | T0558.t2k.o_notor | 2010 May 25 11:45:56 |
Script for T0558.t2k.o_notor coloring in rasmol | T0558.t2k.o_notor-color.rasmol | 2010 May 25 11:45:56 |
o_notor---sequence logo (eps format) (pdf format) | T0558.t2k.o_notor-logo | 2010 May 25 11:45:59 |
o_sep structure prediction (rdb format) (seq format) | T0558.t06.o_sep | 2010 May 25 11:46:07 |
Script for T0558.t06.o_sep coloring in rasmol | T0558.t06.o_sep-color.rasmol | 2010 May 25 11:46:07 |
o_sep---sequence logo (eps format) (pdf format) | T0558.t06.o_sep-logo | 2010 May 25 11:46:12 |
o_sep structure prediction (rdb format) (seq format) | T0558.t04.o_sep | 2010 May 25 11:46:18 |
Script for T0558.t04.o_sep coloring in rasmol | T0558.t04.o_sep-color.rasmol | 2010 May 25 11:46:18 |
o_sep---sequence logo (eps format) (pdf format) | T0558.t04.o_sep-logo | 2010 May 25 11:46:21 |
o_sep structure prediction (rdb format) (seq format) | T0558.t2k.o_sep | 2010 May 25 11:46:26 |
Script for T0558.t2k.o_sep coloring in rasmol | T0558.t2k.o_sep-color.rasmol | 2010 May 25 11:46:26 |
o_sep---sequence logo (eps format) (pdf format) | T0558.t2k.o_sep-logo | 2010 May 25 11:46:29 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0558.t06.dssp-ehl2 | 2010 May 25 11:46:32 |
Script for T0558.t06.dssp-ehl2 coloring in rasmol | T0558.t06.dssp-ehl2-color.rasmol | 2010 May 25 11:46:32 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0558.t06.dssp-ehl2-logo | 2010 May 25 11:46:35 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0558.t04.dssp-ehl2 | 2010 May 25 11:46:36 |
Script for T0558.t04.dssp-ehl2 coloring in rasmol | T0558.t04.dssp-ehl2-color.rasmol | 2010 May 25 11:46:37 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0558.t04.dssp-ehl2-logo | 2010 May 25 11:46:39 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0558.t2k.dssp-ehl2 | 2010 May 25 11:46:41 |
Script for T0558.t2k.dssp-ehl2 coloring in rasmol | T0558.t2k.dssp-ehl2-color.rasmol | 2010 May 25 11:46:41 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0558.t2k.dssp-ehl2-logo | 2010 May 25 11:46:44 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0558.dssp-ehl2 | 2010 May 25 11:46:46 |
Script for T0558.dssp-ehl2 coloring in rasmol | T0558.dssp-ehl2-color.rasmol | 2010 May 25 11:46:47 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0558.dssp-ehl2-logo | 2010 May 25 11:46:49 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0558.t06.CB_burial_14_7 | 2010 May 25 11:46:57 |
Script for T0558.t06.CB_burial_14_7 coloring in rasmol | T0558.t06.CB_burial_14_7-color.rasmol | 2010 May 25 11:46:57 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0558.t06.CB_burial_14_7-logo | 2010 May 25 11:47:01 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0558.t04.CB_burial_14_7 | 2010 May 25 11:47:05 |
Script for T0558.t04.CB_burial_14_7 coloring in rasmol | T0558.t04.CB_burial_14_7-color.rasmol | 2010 May 25 11:47:06 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0558.t04.CB_burial_14_7-logo | 2010 May 25 11:47:08 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0558.t2k.CB_burial_14_7 | 2010 May 25 11:47:11 |
Script for T0558.t2k.CB_burial_14_7 coloring in rasmol | T0558.t2k.CB_burial_14_7-color.rasmol | 2010 May 25 11:47:12 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0558.t2k.CB_burial_14_7-logo | 2010 May 25 11:47:15 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0558.t06.near-backbone-11 | 2010 May 25 11:47:24 |
Script for T0558.t06.near-backbone-11 coloring in rasmol | T0558.t06.near-backbone-11-color.rasmol | 2010 May 25 11:47:25 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0558.t06.near-backbone-11-logo | 2010 May 25 11:47:29 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0558.t04.near-backbone-11 | 2010 May 25 11:47:34 |
Script for T0558.t04.near-backbone-11 coloring in rasmol | T0558.t04.near-backbone-11-color.rasmol | 2010 May 25 11:47:35 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0558.t04.near-backbone-11-logo | 2010 May 25 11:47:38 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0558.t2k.near-backbone-11 | 2010 May 25 11:47:41 |
Script for T0558.t2k.near-backbone-11 coloring in rasmol | T0558.t2k.near-backbone-11-color.rasmol | 2010 May 25 11:47:41 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0558.t2k.near-backbone-11-logo | 2010 May 25 11:47:44 |
CB8-sep9 structure prediction (rdb format) (seq format) | T0558.t06.CB8-sep9 | 2010 May 25 11:47:52 |
Script for T0558.t06.CB8-sep9 coloring in rasmol | T0558.t06.CB8-sep9-color.rasmol | 2010 May 25 11:47:53 |
CB8-sep9---sequence logo (eps format) (pdf format) | T0558.t06.CB8-sep9-logo | 2010 May 25 11:47:56 |
CB8-sep9 structure prediction (rdb format) (seq format) | T0558.t04.CB8-sep9 | 2010 May 25 11:48:00 |
Script for T0558.t04.CB8-sep9 coloring in rasmol | T0558.t04.CB8-sep9-color.rasmol | 2010 May 25 11:48:01 |
CB8-sep9---sequence logo (eps format) (pdf format) | T0558.t04.CB8-sep9-logo | 2010 May 25 11:48:03 |
CB8-sep9 structure prediction (rdb format) (seq format) | T0558.t2k.CB8-sep9 | 2010 May 25 11:48:06 |
Script for T0558.t2k.CB8-sep9 coloring in rasmol | T0558.t2k.CB8-sep9-color.rasmol | 2010 May 25 11:48:07 |
CB8-sep9---sequence logo (eps format) (pdf format) | T0558.t2k.CB8-sep9-logo | 2010 May 25 11:48:10 |
Target model scores |
amino acid single-track target model scores of PDB | T0558.t06-w0.5-scores.html | 2010 May 25 11:56:31 |
amino acid single-track target model scores of PDB | T0558.t04-w0.5-scores.html | 2010 May 25 12:03:59 |
amino acid single-track target model scores of PDB | T0558.t2k-w0.5-scores.html | 2010 May 25 12:11:26 |
amino acid/w0.5-1-str4-0.1 multi-track target model scores | T0558.t06-w0.5-1-str4-0.1-scores.html | 2010 May 25 12:15:45 |
amino acid/w0.5-1-str2-0.1 multi-track target model scores | T0558.t06-w0.5-1-str2-0.1-scores.html | 2010 May 25 12:20:04 |
amino acid/w0.5-1-alpha-0.1 multi-track target model scores | T0558.t06-w0.5-1-alpha-0.1-scores.html | 2010 May 25 12:24:23 |
amino acid/w0.5-1-bys-0.1 multi-track target model scores | T0558.t06-w0.5-1-bys-0.1-scores.html | 2010 May 25 12:28:42 |
amino acid/w0.5-1-pb-0.1 multi-track target model scores | T0558.t06-w0.5-1-pb-0.1-scores.html | 2010 May 25 12:33:02 |
amino acid/w0.5-1-n_notor2-0.1 multi-track target model scores | T0558.t06-w0.5-1-n_notor2-0.1-scores.html | 2010 May 25 12:37:19 |
amino acid/w0.5-1-n_notor-0.1 multi-track target model scores | T0558.t06-w0.5-1-n_notor-0.1-scores.html | 2010 May 25 12:41:38 |
amino acid/w0.5-1-n_sep-0.1 multi-track target model scores | T0558.t06-w0.5-1-n_sep-0.1-scores.html | 2010 May 25 12:45:58 |
amino acid/w0.5-1-o_notor2-0.1 multi-track target model scores | T0558.t06-w0.5-1-o_notor2-0.1-scores.html | 2010 May 25 12:50:16 |
amino acid/w0.5-1-o_notor-0.1 multi-track target model scores | T0558.t06-w0.5-1-o_notor-0.1-scores.html | 2010 May 25 12:54:35 |
amino acid/w0.5-1-o_sep-0.1 multi-track target model scores | T0558.t06-w0.5-1-o_sep-0.1-scores.html | 2010 May 25 12:58:56 |
amino acid/w0.5-1-dssp-ehl2-0.1 multi-track target model scores | T0558.t06-w0.5-1-dssp-ehl2-0.1-scores.html | 2010 May 25 13:03:15 |
amino acid/w0.5-1-CB_burial_14_7-0.3 multi-track target model scores | T0558.t06-w0.5-1-CB_burial_14_7-0.3-scores.html | 2010 May 25 13:07:38 |
amino acid/w0.5-1-near-backbone-11-0.3 multi-track target model scores | T0558.t06-w0.5-1-near-backbone-11-0.3-scores.html | 2010 May 25 13:12:00 |
amino acid/w0.5-1-CB8-sep9-0.3 multi-track target model scores | T0558.t06-w0.5-1-CB8-sep9-0.3-scores.html | 2010 May 25 13:16:21 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0558.t06-80-60-80-str2+near-backbone-11-scores.html | 2010 May 25 13:21:01 |
amino acid/w0.5-1-str4-0.1 multi-track target model scores | T0558.t04-w0.5-1-str4-0.1-scores.html | 2010 May 25 13:25:29 |
amino acid/w0.5-1-str2-0.1 multi-track target model scores | T0558.t04-w0.5-1-str2-0.1-scores.html | 2010 May 25 13:29:59 |
amino acid/w0.5-1-alpha-0.1 multi-track target model scores | T0558.t04-w0.5-1-alpha-0.1-scores.html | 2010 May 25 13:34:28 |
amino acid/w0.5-1-bys-0.1 multi-track target model scores | T0558.t04-w0.5-1-bys-0.1-scores.html | 2010 May 25 13:38:56 |
amino acid/w0.5-1-pb-0.1 multi-track target model scores | T0558.t04-w0.5-1-pb-0.1-scores.html | 2010 May 25 13:43:21 |
amino acid/w0.5-1-n_notor2-0.1 multi-track target model scores | T0558.t04-w0.5-1-n_notor2-0.1-scores.html | 2010 May 25 13:47:50 |
amino acid/w0.5-1-n_notor-0.1 multi-track target model scores | T0558.t04-w0.5-1-n_notor-0.1-scores.html | 2010 May 25 13:52:19 |
amino acid/w0.5-1-n_sep-0.1 multi-track target model scores | T0558.t04-w0.5-1-n_sep-0.1-scores.html | 2010 May 25 13:56:47 |
amino acid/w0.5-1-o_notor2-0.1 multi-track target model scores | T0558.t04-w0.5-1-o_notor2-0.1-scores.html | 2010 May 25 14:01:18 |
amino acid/w0.5-1-o_notor-0.1 multi-track target model scores | T0558.t04-w0.5-1-o_notor-0.1-scores.html | 2010 May 25 14:05:43 |
amino acid/w0.5-1-o_sep-0.1 multi-track target model scores | T0558.t04-w0.5-1-o_sep-0.1-scores.html | 2010 May 25 14:10:11 |
amino acid/w0.5-1-dssp-ehl2-0.1 multi-track target model scores | T0558.t04-w0.5-1-dssp-ehl2-0.1-scores.html | 2010 May 25 14:14:40 |
amino acid/w0.5-1-CB_burial_14_7-0.3 multi-track target model scores | T0558.t04-w0.5-1-CB_burial_14_7-0.3-scores.html | 2010 May 25 14:19:10 |
amino acid/w0.5-1-near-backbone-11-0.3 multi-track target model scores | T0558.t04-w0.5-1-near-backbone-11-0.3-scores.html | 2010 May 25 14:23:40 |
amino acid/w0.5-1-CB8-sep9-0.3 multi-track target model scores | T0558.t04-w0.5-1-CB8-sep9-0.3-scores.html | 2010 May 25 14:28:11 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0558.t04-80-60-80-str2+near-backbone-11-scores.html | 2010 May 25 14:33:01 |
amino acid/w0.5-1-str4-0.1 multi-track target model scores | T0558.t2k-w0.5-1-str4-0.1-scores.html | 2010 May 25 14:37:50 |
amino acid/w0.5-1-str2-0.1 multi-track target model scores | T0558.t2k-w0.5-1-str2-0.1-scores.html | 2010 May 25 14:42:34 |
amino acid/w0.5-1-alpha-0.1 multi-track target model scores | T0558.t2k-w0.5-1-alpha-0.1-scores.html | 2010 May 25 14:47:19 |
amino acid/w0.5-1-bys-0.1 multi-track target model scores | T0558.t2k-w0.5-1-bys-0.1-scores.html | 2010 May 25 14:52:03 |
amino acid/w0.5-1-pb-0.1 multi-track target model scores | T0558.t2k-w0.5-1-pb-0.1-scores.html | 2010 May 25 14:56:48 |
amino acid/w0.5-1-n_notor2-0.1 multi-track target model scores | T0558.t2k-w0.5-1-n_notor2-0.1-scores.html | 2010 May 25 15:01:28 |
amino acid/w0.5-1-n_notor-0.1 multi-track target model scores | T0558.t2k-w0.5-1-n_notor-0.1-scores.html | 2010 May 25 15:06:13 |
amino acid/w0.5-1-n_sep-0.1 multi-track target model scores | T0558.t2k-w0.5-1-n_sep-0.1-scores.html | 2010 May 25 15:10:57 |
amino acid/w0.5-1-o_notor2-0.1 multi-track target model scores | T0558.t2k-w0.5-1-o_notor2-0.1-scores.html | 2010 May 25 15:15:40 |
amino acid/w0.5-1-o_notor-0.1 multi-track target model scores | T0558.t2k-w0.5-1-o_notor-0.1-scores.html | 2010 May 25 15:20:23 |
amino acid/w0.5-1-o_sep-0.1 multi-track target model scores | T0558.t2k-w0.5-1-o_sep-0.1-scores.html | 2010 May 25 15:25:06 |
amino acid/w0.5-1-dssp-ehl2-0.1 multi-track target model scores | T0558.t2k-w0.5-1-dssp-ehl2-0.1-scores.html | 2010 May 25 15:29:48 |
amino acid/w0.5-1-CB_burial_14_7-0.3 multi-track target model scores | T0558.t2k-w0.5-1-CB_burial_14_7-0.3-scores.html | 2010 May 25 15:34:31 |
amino acid/w0.5-1-near-backbone-11-0.3 multi-track target model scores | T0558.t2k-w0.5-1-near-backbone-11-0.3-scores.html | 2010 May 25 15:39:17 |
amino acid/w0.5-1-CB8-sep9-0.3 multi-track target model scores | T0558.t2k-w0.5-1-CB8-sep9-0.3-scores.html | 2010 May 25 15:44:02 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0558.t2k-80-60-80-str2+near-backbone-11-scores.html | 2010 May 25 15:49:04 |
Template model scores |
Annotated t06 template model scores | T0558.t06-template-lib-scores.html | 2010 May 25 17:30:23 |
Annotated t04 template model scores | T0558.t04-template-lib-scores.html | 2010 May 25 18:22:51 |
Annotated t2k template model scores | T0558.t2k-template-lib-scores.html | 2010 May 25 18:55:36 |
Top Hits |
Best scoring hits from t06 HMMs | T0558.t06.best-scores.html | 2010 May 25 19:04:15 |
Best scoring hits from t04 HMMs | T0558.t04.best-scores.html | 2010 May 25 19:11:45 |
Best scoring hits from t2k HMMs | T0558.t2k.best-scores.html | 2010 May 25 19:19:14 |
Best scoring hits from combining t06 t04 t2k | T0558.best-scores-all.html | 2010 May 25 19:19:17 |
Alignments for Top Hits |
Top alignments from t06 hits | T0558.t06.top_reported_alignments.html | 2010 May 25 20:56:39 |
Top alignments from t04 hits | T0558.t04.top_reported_alignments.html | 2010 May 25 20:56:43 |
Top alignments from t2k hits | T0558.t2k.top_reported_alignments.html | 2010 May 25 20:56:47 |
Top alignments from combined hits | T0558.top_reported_alignments.html | 2010 May 25 20:56:50 |
multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2010 May 25 20:58:25 |
Undertaker (3d) files |
Undertaker input for top t06 alignments | T0558.t06.undertaker-align.under | 2010 May 25 21:01:21 |
Undertaker input for top t04 alignments | T0558.t04.undertaker-align.under | 2010 May 25 21:01:23 |
Undertaker input for top t2k alignments | T0558.t2k.undertaker-align.under | 2010 May 25 21:01:26 |
Undertaker input for top combined alignments | T0558.undertaker-align.under | 2010 May 25 21:01:28 |
PDB file with model(s) for top alignments | T0558.undertaker-align.pdb.gz | 2010 May 25 21:10:30 |
Images of an (incomplete) model created by sidechain replacement on the backbone of the highest scoring template.
Coloring is defined by ehl2, 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) | T0558.t06.many.frag.gz | 2010 May 25 21:12:13 |
Fragment list for undertaker (from fragfinder) | T0558.t04.many.frag.gz | 2010 May 25 21:13:29 |
Fragment list for undertaker (from fragfinder) | T0558.t2k.many.frag.gz | 2010 May 25 21:14:45 |
Contact predictions, based on predicted burial (near-backbone-11), predicted secondary structure(str2), predicted H-bonds (n_sep), amino acid profile, log(protein length), log(separation) |
contact predictions (rr format) (rr.nn1000.constraints format) (rr.rasmol format) | T0558.647_47 | 2010 May 25 21:37:58 |
contact predictions (rr format) (rr.nn1000.constraints format) (rr.rasmol format) | T0558.730_47 | 2010 May 25 21:38:11 |
contact predictions (rr format) (rr.nn1000.constraints format) (rr.rasmol format) | T0558.648_17.730_47 | 2010 May 25 21:42:24 |
Distance constraints extracted from alignments |
Constraints from alignment | align.constraints | 2010 May 25 22:10:12 |
Rejected constraints | rejected_bonus.constraints | 2010 May 25 22:10:12 |
Noncontact constraints | noncontact.constraints | 2010 May 25 22:10:12 |
First attempted model using undertaker | decoys/T0558.try1-opt3.pdb.gz | 2010 May 26 4:16:37 |
Images of complete model in decoys/T0558.try1-opt3.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 |
Gzipped tarball of all the files | T0558.tgz | 2010 May 26 4:26:26 |
Please cite the following papers:
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based on prior designs by Kevin Karplus, Alex Williams, and Rachel Karchin.
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