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) | T0564.a2m | 2010 May 28 16:38:24 |
README file | README | 2010 May 28 16:38:34 |
Quick blastp of non-redundant PDB | T0564.pdb_blast.txt | 2010 May 28 16:38:39 |
Multiple alignment |
SAM_t06 multiple alignment in a2m format | T0564.t06.a2m.gz | 2010 May 28 16:47:35 |
SAM_t06 multiple alignment in pretty html format | T0564.t06.pa.html | 2010 May 28 16:47:51 |
SAM_t06 target hidden Markov model | T0564.t06.w0.5.mod | 2010 May 28 16:47:56 |
SAM_t06 multiple alignment---sequence logo (eps format) (pdf format) | T0564.t06.w0.5-logo | 2010 May 28 16:48:03 |
SAM_t06 consensus sequence | T0564.t06.w0.5.maxp | 2010 May 28 16:48:04 |
Script for highlighting in rasmol | conserved_t06 | 2010 May 28 16:48:05 |
SAM_t04 multiple alignment in a2m format | T0564.t04.a2m.gz | 2010 May 28 16:53:40 |
SAM_t04 multiple alignment in pretty html format | T0564.t04.pa.html | 2010 May 28 16:53:49 |
SAM_t04 target hidden Markov model | T0564.t04.w0.5.mod | 2010 May 28 16:53:50 |
SAM_t04 multiple alignment---sequence logo (eps format) (pdf format) | T0564.t04.w0.5-logo | 2010 May 28 16:53:55 |
SAM_t04 consensus sequence | T0564.t04.w0.5.maxp | 2010 May 28 16:53:55 |
Script for highlighting in rasmol | conserved_t04 | 2010 May 28 16:53:56 |
SAM_t2k multiple alignment in a2m format | T0564.t2k.a2m.gz | 2010 May 28 16:55:43 |
SAM_t2k multiple alignment in pretty html format | T0564.t2k.pa.html | 2010 May 28 16:55:52 |
SAM_t2k target hidden Markov model | T0564.t2k.w0.5.mod | 2010 May 28 16:55:54 |
SAM_t2k multiple alignment---sequence logo (eps format) (pdf format) | T0564.t2k.w0.5-logo | 2010 May 28 16:55:58 |
SAM_t2k consensus sequence | T0564.t2k.w0.5.maxp | 2010 May 28 16:55:59 |
Script for highlighting in rasmol | conserved_t2k | 2010 May 28 16:55:59 |
Secondary Structure Prediction (Explanation of secondary-structure predictions) |
str4 structure prediction (rdb format) (seq format) | T0564.t06.str4 | 2010 May 28 16:56:05 |
Script for T0564.t06.str4 coloring in rasmol | T0564.t06.str4-color.rasmol | 2010 May 28 16:56:06 |
str4---sequence logo (eps format) (pdf format) | T0564.t06.str4-logo | 2010 May 28 16:56:08 |
str4 structure prediction (rdb format) (seq format) | T0564.t04.str4 | 2010 May 28 16:56:10 |
Script for T0564.t04.str4 coloring in rasmol | T0564.t04.str4-color.rasmol | 2010 May 28 16:56:10 |
str4---sequence logo (eps format) (pdf format) | T0564.t04.str4-logo | 2010 May 28 16:56:12 |
str4 structure prediction (rdb format) (seq format) | T0564.t2k.str4 | 2010 May 28 16:56:14 |
Script for T0564.t2k.str4 coloring in rasmol | T0564.t2k.str4-color.rasmol | 2010 May 28 16:56:14 |
str4---sequence logo (eps format) (pdf format) | T0564.t2k.str4-logo | 2010 May 28 16:56:16 |
str2 structure prediction (rdb format) (seq format) | T0564.t06.str2 | 2010 May 28 16:48:00 |
Script for T0564.t06.str2 coloring in rasmol | T0564.t06.str2-color.rasmol | 2010 May 28 16:56:17 |
str2---sequence logo (eps format) (pdf format) | T0564.t06.str2-logo | 2010 May 28 16:56:19 |
str2 structure prediction (rdb format) (seq format) | T0564.t04.str2 | 2010 May 28 16:53:53 |
Script for T0564.t04.str2 coloring in rasmol | T0564.t04.str2-color.rasmol | 2010 May 28 16:56:20 |
str2---sequence logo (eps format) (pdf format) | T0564.t04.str2-logo | 2010 May 28 16:56:22 |
str2 structure prediction (rdb format) (seq format) | T0564.t2k.str2 | 2010 May 28 16:55:56 |
Script for T0564.t2k.str2 coloring in rasmol | T0564.t2k.str2-color.rasmol | 2010 May 28 16:56:23 |
str2---sequence logo (eps format) (pdf format) | T0564.t2k.str2-logo | 2010 May 28 16:56:24 |
alpha structure prediction (rdb format) (seq format) | T0564.t06.alpha | 2010 May 28 16:56:27 |
Script for T0564.t06.alpha coloring in rasmol | T0564.t06.alpha-color.rasmol | 2010 May 28 16:56:27 |
alpha---sequence logo (eps format) (pdf format) | T0564.t06.alpha-logo | 2010 May 28 16:56:29 |
alpha structure prediction (rdb format) (seq format) | T0564.t04.alpha | 2010 May 28 16:56:30 |
Script for T0564.t04.alpha coloring in rasmol | T0564.t04.alpha-color.rasmol | 2010 May 28 16:56:31 |
alpha---sequence logo (eps format) (pdf format) | T0564.t04.alpha-logo | 2010 May 28 16:56:32 |
alpha structure prediction (rdb format) (seq format) | T0564.t2k.alpha | 2010 May 28 16:56:34 |
Script for T0564.t2k.alpha coloring in rasmol | T0564.t2k.alpha-color.rasmol | 2010 May 28 16:56:34 |
alpha---sequence logo (eps format) (pdf format) | T0564.t2k.alpha-logo | 2010 May 28 16:56:36 |
bys structure prediction (rdb format) (seq format) | T0564.t06.bys | 2010 May 28 16:56:37 |
Script for T0564.t06.bys coloring in rasmol | T0564.t06.bys-color.rasmol | 2010 May 28 16:56:38 |
bys---sequence logo (eps format) (pdf format) | T0564.t06.bys-logo | 2010 May 28 16:56:39 |
bys structure prediction (rdb format) (seq format) | T0564.t04.bys | 2010 May 28 16:56:41 |
Script for T0564.t04.bys coloring in rasmol | T0564.t04.bys-color.rasmol | 2010 May 28 16:56:42 |
bys---sequence logo (eps format) (pdf format) | T0564.t04.bys-logo | 2010 May 28 16:56:43 |
bys structure prediction (rdb format) (seq format) | T0564.t2k.bys | 2010 May 28 16:56:45 |
Script for T0564.t2k.bys coloring in rasmol | T0564.t2k.bys-color.rasmol | 2010 May 28 16:56:45 |
bys---sequence logo (eps format) (pdf format) | T0564.t2k.bys-logo | 2010 May 28 16:56:47 |
pb structure prediction (rdb format) (seq format) | T0564.t06.pb | 2010 May 28 16:56:49 |
Script for T0564.t06.pb coloring in rasmol | T0564.t06.pb-color.rasmol | 2010 May 28 16:56:50 |
pb---sequence logo (eps format) (pdf format) | T0564.t06.pb-logo | 2010 May 28 16:56:51 |
pb structure prediction (rdb format) (seq format) | T0564.t04.pb | 2010 May 28 16:56:53 |
Script for T0564.t04.pb coloring in rasmol | T0564.t04.pb-color.rasmol | 2010 May 28 16:56:54 |
pb---sequence logo (eps format) (pdf format) | T0564.t04.pb-logo | 2010 May 28 16:56:55 |
pb structure prediction (rdb format) (seq format) | T0564.t2k.pb | 2010 May 28 16:56:57 |
Script for T0564.t2k.pb coloring in rasmol | T0564.t2k.pb-color.rasmol | 2010 May 28 16:56:57 |
pb---sequence logo (eps format) (pdf format) | T0564.t2k.pb-logo | 2010 May 28 16:56:59 |
n_notor2 structure prediction (rdb format) (seq format) | T0564.t06.n_notor2 | 2010 May 28 16:57:00 |
Script for T0564.t06.n_notor2 coloring in rasmol | T0564.t06.n_notor2-color.rasmol | 2010 May 28 16:57:01 |
n_notor2---sequence logo (eps format) (pdf format) | T0564.t06.n_notor2-logo | 2010 May 28 16:57:02 |
n_notor2 structure prediction (rdb format) (seq format) | T0564.t04.n_notor2 | 2010 May 28 16:57:04 |
Script for T0564.t04.n_notor2 coloring in rasmol | T0564.t04.n_notor2-color.rasmol | 2010 May 28 16:57:04 |
n_notor2---sequence logo (eps format) (pdf format) | T0564.t04.n_notor2-logo | 2010 May 28 16:57:05 |
n_notor2 structure prediction (rdb format) (seq format) | T0564.t2k.n_notor2 | 2010 May 28 16:57:07 |
Script for T0564.t2k.n_notor2 coloring in rasmol | T0564.t2k.n_notor2-color.rasmol | 2010 May 28 16:57:07 |
n_notor2---sequence logo (eps format) (pdf format) | T0564.t2k.n_notor2-logo | 2010 May 28 16:57:09 |
n_notor structure prediction (rdb format) (seq format) | T0564.t06.n_notor | 2010 May 28 16:57:11 |
Script for T0564.t06.n_notor coloring in rasmol | T0564.t06.n_notor-color.rasmol | 2010 May 28 16:57:11 |
n_notor---sequence logo (eps format) (pdf format) | T0564.t06.n_notor-logo | 2010 May 28 16:57:12 |
n_notor structure prediction (rdb format) (seq format) | T0564.t04.n_notor | 2010 May 28 16:57:13 |
Script for T0564.t04.n_notor coloring in rasmol | T0564.t04.n_notor-color.rasmol | 2010 May 28 16:57:14 |
n_notor---sequence logo (eps format) (pdf format) | T0564.t04.n_notor-logo | 2010 May 28 16:57:15 |
n_notor structure prediction (rdb format) (seq format) | T0564.t2k.n_notor | 2010 May 28 16:57:17 |
Script for T0564.t2k.n_notor coloring in rasmol | T0564.t2k.n_notor-color.rasmol | 2010 May 28 16:57:17 |
n_notor---sequence logo (eps format) (pdf format) | T0564.t2k.n_notor-logo | 2010 May 28 16:57:19 |
n_sep structure prediction (rdb format) (seq format) | T0564.t06.n_sep | 2010 May 28 16:57:21 |
Script for T0564.t06.n_sep coloring in rasmol | T0564.t06.n_sep-color.rasmol | 2010 May 28 16:57:22 |
n_sep---sequence logo (eps format) (pdf format) | T0564.t06.n_sep-logo | 2010 May 28 16:57:24 |
n_sep structure prediction (rdb format) (seq format) | T0564.t04.n_sep | 2010 May 28 16:57:25 |
Script for T0564.t04.n_sep coloring in rasmol | T0564.t04.n_sep-color.rasmol | 2010 May 28 16:57:26 |
n_sep---sequence logo (eps format) (pdf format) | T0564.t04.n_sep-logo | 2010 May 28 16:57:28 |
n_sep structure prediction (rdb format) (seq format) | T0564.t2k.n_sep | 2010 May 28 16:57:29 |
Script for T0564.t2k.n_sep coloring in rasmol | T0564.t2k.n_sep-color.rasmol | 2010 May 28 16:57:29 |
n_sep---sequence logo (eps format) (pdf format) | T0564.t2k.n_sep-logo | 2010 May 28 16:57:31 |
o_notor2 structure prediction (rdb format) (seq format) | T0564.t06.o_notor2 | 2010 May 28 16:57:33 |
Script for T0564.t06.o_notor2 coloring in rasmol | T0564.t06.o_notor2-color.rasmol | 2010 May 28 16:57:33 |
o_notor2---sequence logo (eps format) (pdf format) | T0564.t06.o_notor2-logo | 2010 May 28 16:57:35 |
o_notor2 structure prediction (rdb format) (seq format) | T0564.t04.o_notor2 | 2010 May 28 16:57:36 |
Script for T0564.t04.o_notor2 coloring in rasmol | T0564.t04.o_notor2-color.rasmol | 2010 May 28 16:57:36 |
o_notor2---sequence logo (eps format) (pdf format) | T0564.t04.o_notor2-logo | 2010 May 28 16:57:38 |
o_notor2 structure prediction (rdb format) (seq format) | T0564.t2k.o_notor2 | 2010 May 28 16:57:39 |
Script for T0564.t2k.o_notor2 coloring in rasmol | T0564.t2k.o_notor2-color.rasmol | 2010 May 28 16:57:40 |
o_notor2---sequence logo (eps format) (pdf format) | T0564.t2k.o_notor2-logo | 2010 May 28 16:57:41 |
o_notor structure prediction (rdb format) (seq format) | T0564.t06.o_notor | 2010 May 28 16:57:44 |
Script for T0564.t06.o_notor coloring in rasmol | T0564.t06.o_notor-color.rasmol | 2010 May 28 16:57:44 |
o_notor---sequence logo (eps format) (pdf format) | T0564.t06.o_notor-logo | 2010 May 28 16:57:46 |
o_notor structure prediction (rdb format) (seq format) | T0564.t04.o_notor | 2010 May 28 16:57:47 |
Script for T0564.t04.o_notor coloring in rasmol | T0564.t04.o_notor-color.rasmol | 2010 May 28 16:57:48 |
o_notor---sequence logo (eps format) (pdf format) | T0564.t04.o_notor-logo | 2010 May 28 16:57:49 |
o_notor structure prediction (rdb format) (seq format) | T0564.t2k.o_notor | 2010 May 28 16:57:50 |
Script for T0564.t2k.o_notor coloring in rasmol | T0564.t2k.o_notor-color.rasmol | 2010 May 28 16:57:51 |
o_notor---sequence logo (eps format) (pdf format) | T0564.t2k.o_notor-logo | 2010 May 28 16:57:52 |
o_sep structure prediction (rdb format) (seq format) | T0564.t06.o_sep | 2010 May 28 16:57:54 |
Script for T0564.t06.o_sep coloring in rasmol | T0564.t06.o_sep-color.rasmol | 2010 May 28 16:57:54 |
o_sep---sequence logo (eps format) (pdf format) | T0564.t06.o_sep-logo | 2010 May 28 16:57:56 |
o_sep structure prediction (rdb format) (seq format) | T0564.t04.o_sep | 2010 May 28 16:57:57 |
Script for T0564.t04.o_sep coloring in rasmol | T0564.t04.o_sep-color.rasmol | 2010 May 28 16:57:57 |
o_sep---sequence logo (eps format) (pdf format) | T0564.t04.o_sep-logo | 2010 May 28 16:57:59 |
o_sep structure prediction (rdb format) (seq format) | T0564.t2k.o_sep | 2010 May 28 16:58:00 |
Script for T0564.t2k.o_sep coloring in rasmol | T0564.t2k.o_sep-color.rasmol | 2010 May 28 16:58:00 |
o_sep---sequence logo (eps format) (pdf format) | T0564.t2k.o_sep-logo | 2010 May 28 16:58:02 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0564.t06.dssp-ehl2 | 2010 May 28 16:58:03 |
Script for T0564.t06.dssp-ehl2 coloring in rasmol | T0564.t06.dssp-ehl2-color.rasmol | 2010 May 28 16:58:04 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0564.t06.dssp-ehl2-logo | 2010 May 28 16:58:05 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0564.t04.dssp-ehl2 | 2010 May 28 16:58:06 |
Script for T0564.t04.dssp-ehl2 coloring in rasmol | T0564.t04.dssp-ehl2-color.rasmol | 2010 May 28 16:58:06 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0564.t04.dssp-ehl2-logo | 2010 May 28 16:58:08 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0564.t2k.dssp-ehl2 | 2010 May 28 16:58:09 |
Script for T0564.t2k.dssp-ehl2 coloring in rasmol | T0564.t2k.dssp-ehl2-color.rasmol | 2010 May 28 16:58:09 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0564.t2k.dssp-ehl2-logo | 2010 May 28 16:58:11 |
dssp-ehl2 structure prediction (rdb format) (seq format) | T0564.dssp-ehl2 | 2010 May 28 16:58:12 |
Script for T0564.dssp-ehl2 coloring in rasmol | T0564.dssp-ehl2-color.rasmol | 2010 May 28 16:58:12 |
dssp-ehl2---sequence logo (eps format) (pdf format) | T0564.dssp-ehl2-logo | 2010 May 28 16:58:14 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0564.t06.CB_burial_14_7 | 2010 May 28 16:58:15 |
Script for T0564.t06.CB_burial_14_7 coloring in rasmol | T0564.t06.CB_burial_14_7-color.rasmol | 2010 May 28 16:58:16 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0564.t06.CB_burial_14_7-logo | 2010 May 28 16:58:17 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0564.t04.CB_burial_14_7 | 2010 May 28 16:58:18 |
Script for T0564.t04.CB_burial_14_7 coloring in rasmol | T0564.t04.CB_burial_14_7-color.rasmol | 2010 May 28 16:58:18 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0564.t04.CB_burial_14_7-logo | 2010 May 28 16:58:20 |
CB_burial_14_7 structure prediction (rdb format) (seq format) | T0564.t2k.CB_burial_14_7 | 2010 May 28 16:58:21 |
Script for T0564.t2k.CB_burial_14_7 coloring in rasmol | T0564.t2k.CB_burial_14_7-color.rasmol | 2010 May 28 16:58:21 |
CB_burial_14_7---sequence logo (eps format) (pdf format) | T0564.t2k.CB_burial_14_7-logo | 2010 May 28 16:58:22 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0564.t06.near-backbone-11 | 2010 May 28 16:58:24 |
Script for T0564.t06.near-backbone-11 coloring in rasmol | T0564.t06.near-backbone-11-color.rasmol | 2010 May 28 16:58:24 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0564.t06.near-backbone-11-logo | 2010 May 28 16:58:26 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0564.t04.near-backbone-11 | 2010 May 28 16:58:27 |
Script for T0564.t04.near-backbone-11 coloring in rasmol | T0564.t04.near-backbone-11-color.rasmol | 2010 May 28 16:58:27 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0564.t04.near-backbone-11-logo | 2010 May 28 16:58:29 |
near-backbone-11 structure prediction (rdb format) (seq format) | T0564.t2k.near-backbone-11 | 2010 May 28 16:58:30 |
Script for T0564.t2k.near-backbone-11 coloring in rasmol | T0564.t2k.near-backbone-11-color.rasmol | 2010 May 28 16:58:30 |
near-backbone-11---sequence logo (eps format) (pdf format) | T0564.t2k.near-backbone-11-logo | 2010 May 28 16:58:32 |
CB8-sep9 structure prediction (rdb format) (seq format) | T0564.t06.CB8-sep9 | 2010 May 28 16:58:33 |
Script for T0564.t06.CB8-sep9 coloring in rasmol | T0564.t06.CB8-sep9-color.rasmol | 2010 May 28 16:58:34 |
CB8-sep9---sequence logo (eps format) (pdf format) | T0564.t06.CB8-sep9-logo | 2010 May 28 16:58:35 |
CB8-sep9 structure prediction (rdb format) (seq format) | T0564.t04.CB8-sep9 | 2010 May 28 16:58:37 |
Script for T0564.t04.CB8-sep9 coloring in rasmol | T0564.t04.CB8-sep9-color.rasmol | 2010 May 28 16:58:37 |
CB8-sep9---sequence logo (eps format) (pdf format) | T0564.t04.CB8-sep9-logo | 2010 May 28 16:58:39 |
CB8-sep9 structure prediction (rdb format) (seq format) | T0564.t2k.CB8-sep9 | 2010 May 28 16:58:40 |
Script for T0564.t2k.CB8-sep9 coloring in rasmol | T0564.t2k.CB8-sep9-color.rasmol | 2010 May 28 16:58:40 |
CB8-sep9---sequence logo (eps format) (pdf format) | T0564.t2k.CB8-sep9-logo | 2010 May 28 16:58:42 |
Target model scores |
amino acid single-track target model scores of PDB | T0564.t06-w0.5-scores.html | 2010 May 28 17:01:10 |
amino acid single-track target model scores of PDB | T0564.t04-w0.5-scores.html | 2010 May 28 17:03:26 |
amino acid single-track target model scores of PDB | T0564.t2k-w0.5-scores.html | 2010 May 28 17:05:40 |
amino acid/w0.5-1-str4-0.1 multi-track target model scores | T0564.t06-w0.5-1-str4-0.1-scores.html | 2010 May 28 17:07:01 |
amino acid/w0.5-1-str2-0.1 multi-track target model scores | T0564.t06-w0.5-1-str2-0.1-scores.html | 2010 May 28 17:08:23 |
amino acid/w0.5-1-alpha-0.1 multi-track target model scores | T0564.t06-w0.5-1-alpha-0.1-scores.html | 2010 May 28 17:09:44 |
amino acid/w0.5-1-bys-0.1 multi-track target model scores | T0564.t06-w0.5-1-bys-0.1-scores.html | 2010 May 28 17:11:04 |
amino acid/w0.5-1-pb-0.1 multi-track target model scores | T0564.t06-w0.5-1-pb-0.1-scores.html | 2010 May 28 17:12:25 |
amino acid/w0.5-1-n_notor2-0.1 multi-track target model scores | T0564.t06-w0.5-1-n_notor2-0.1-scores.html | 2010 May 28 17:13:46 |
amino acid/w0.5-1-n_notor-0.1 multi-track target model scores | T0564.t06-w0.5-1-n_notor-0.1-scores.html | 2010 May 28 17:15:07 |
amino acid/w0.5-1-n_sep-0.1 multi-track target model scores | T0564.t06-w0.5-1-n_sep-0.1-scores.html | 2010 May 28 17:16:27 |
amino acid/w0.5-1-o_notor2-0.1 multi-track target model scores | T0564.t06-w0.5-1-o_notor2-0.1-scores.html | 2010 May 28 17:17:47 |
amino acid/w0.5-1-o_notor-0.1 multi-track target model scores | T0564.t06-w0.5-1-o_notor-0.1-scores.html | 2010 May 28 17:19:08 |
amino acid/w0.5-1-o_sep-0.1 multi-track target model scores | T0564.t06-w0.5-1-o_sep-0.1-scores.html | 2010 May 28 17:20:28 |
amino acid/w0.5-1-dssp-ehl2-0.1 multi-track target model scores | T0564.t06-w0.5-1-dssp-ehl2-0.1-scores.html | 2010 May 28 17:21:50 |
amino acid/w0.5-1-CB_burial_14_7-0.3 multi-track target model scores | T0564.t06-w0.5-1-CB_burial_14_7-0.3-scores.html | 2010 May 28 17:23:11 |
amino acid/w0.5-1-near-backbone-11-0.3 multi-track target model scores | T0564.t06-w0.5-1-near-backbone-11-0.3-scores.html | 2010 May 28 17:24:31 |
amino acid/w0.5-1-CB8-sep9-0.3 multi-track target model scores | T0564.t06-w0.5-1-CB8-sep9-0.3-scores.html | 2010 May 28 17:25:53 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0564.t06-80-60-80-str2+near-backbone-11-scores.html | 2010 May 28 17:27:23 |
amino acid/w0.5-1-str4-0.1 multi-track target model scores | T0564.t04-w0.5-1-str4-0.1-scores.html | 2010 May 28 17:28:51 |
amino acid/w0.5-1-str2-0.1 multi-track target model scores | T0564.t04-w0.5-1-str2-0.1-scores.html | 2010 May 28 17:30:19 |
amino acid/w0.5-1-alpha-0.1 multi-track target model scores | T0564.t04-w0.5-1-alpha-0.1-scores.html | 2010 May 28 17:31:46 |
amino acid/w0.5-1-bys-0.1 multi-track target model scores | T0564.t04-w0.5-1-bys-0.1-scores.html | 2010 May 28 17:33:13 |
amino acid/w0.5-1-pb-0.1 multi-track target model scores | T0564.t04-w0.5-1-pb-0.1-scores.html | 2010 May 28 17:34:40 |
amino acid/w0.5-1-n_notor2-0.1 multi-track target model scores | T0564.t04-w0.5-1-n_notor2-0.1-scores.html | 2010 May 28 17:36:08 |
amino acid/w0.5-1-n_notor-0.1 multi-track target model scores | T0564.t04-w0.5-1-n_notor-0.1-scores.html | 2010 May 28 17:37:34 |
amino acid/w0.5-1-n_sep-0.1 multi-track target model scores | T0564.t04-w0.5-1-n_sep-0.1-scores.html | 2010 May 28 17:39:01 |
amino acid/w0.5-1-o_notor2-0.1 multi-track target model scores | T0564.t04-w0.5-1-o_notor2-0.1-scores.html | 2010 May 28 17:40:28 |
amino acid/w0.5-1-o_notor-0.1 multi-track target model scores | T0564.t04-w0.5-1-o_notor-0.1-scores.html | 2010 May 28 17:41:56 |
amino acid/w0.5-1-o_sep-0.1 multi-track target model scores | T0564.t04-w0.5-1-o_sep-0.1-scores.html | 2010 May 28 17:43:24 |
amino acid/w0.5-1-dssp-ehl2-0.1 multi-track target model scores | T0564.t04-w0.5-1-dssp-ehl2-0.1-scores.html | 2010 May 28 17:44:52 |
amino acid/w0.5-1-CB_burial_14_7-0.3 multi-track target model scores | T0564.t04-w0.5-1-CB_burial_14_7-0.3-scores.html | 2010 May 28 17:46:20 |
amino acid/w0.5-1-near-backbone-11-0.3 multi-track target model scores | T0564.t04-w0.5-1-near-backbone-11-0.3-scores.html | 2010 May 28 17:47:47 |
amino acid/w0.5-1-CB8-sep9-0.3 multi-track target model scores | T0564.t04-w0.5-1-CB8-sep9-0.3-scores.html | 2010 May 28 17:49:15 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0564.t04-80-60-80-str2+near-backbone-11-scores.html | 2010 May 28 17:50:52 |
amino acid/w0.5-1-str4-0.1 multi-track target model scores | T0564.t2k-w0.5-1-str4-0.1-scores.html | 2010 May 28 17:52:28 |
amino acid/w0.5-1-str2-0.1 multi-track target model scores | T0564.t2k-w0.5-1-str2-0.1-scores.html | 2010 May 28 17:54:05 |
amino acid/w0.5-1-alpha-0.1 multi-track target model scores | T0564.t2k-w0.5-1-alpha-0.1-scores.html | 2010 May 28 17:55:40 |
amino acid/w0.5-1-bys-0.1 multi-track target model scores | T0564.t2k-w0.5-1-bys-0.1-scores.html | 2010 May 28 17:57:19 |
amino acid/w0.5-1-pb-0.1 multi-track target model scores | T0564.t2k-w0.5-1-pb-0.1-scores.html | 2010 May 28 17:58:53 |
amino acid/w0.5-1-n_notor2-0.1 multi-track target model scores | T0564.t2k-w0.5-1-n_notor2-0.1-scores.html | 2010 May 28 18:00:28 |
amino acid/w0.5-1-n_notor-0.1 multi-track target model scores | T0564.t2k-w0.5-1-n_notor-0.1-scores.html | 2010 May 28 18:02:04 |
amino acid/w0.5-1-n_sep-0.1 multi-track target model scores | T0564.t2k-w0.5-1-n_sep-0.1-scores.html | 2010 May 28 18:03:38 |
amino acid/w0.5-1-o_notor2-0.1 multi-track target model scores | T0564.t2k-w0.5-1-o_notor2-0.1-scores.html | 2010 May 28 18:05:19 |
amino acid/w0.5-1-o_notor-0.1 multi-track target model scores | T0564.t2k-w0.5-1-o_notor-0.1-scores.html | 2010 May 28 18:06:54 |
amino acid/w0.5-1-o_sep-0.1 multi-track target model scores | T0564.t2k-w0.5-1-o_sep-0.1-scores.html | 2010 May 28 18:08:28 |
amino acid/w0.5-1-dssp-ehl2-0.1 multi-track target model scores | T0564.t2k-w0.5-1-dssp-ehl2-0.1-scores.html | 2010 May 28 18:10:04 |
amino acid/w0.5-1-CB_burial_14_7-0.3 multi-track target model scores | T0564.t2k-w0.5-1-CB_burial_14_7-0.3-scores.html | 2010 May 28 18:11:39 |
amino acid/w0.5-1-near-backbone-11-0.3 multi-track target model scores | T0564.t2k-w0.5-1-near-backbone-11-0.3-scores.html | 2010 May 28 18:13:18 |
amino acid/w0.5-1-CB8-sep9-0.3 multi-track target model scores | T0564.t2k-w0.5-1-CB8-sep9-0.3-scores.html | 2010 May 28 18:14:52 |
amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores | T0564.t2k-80-60-80-str2+near-backbone-11-scores.html | 2010 May 28 18:16:35 |
Template model scores |
Annotated t06 template model scores | T0564.t06-template-lib-scores.html | 2010 May 28 18:57:30 |
Annotated t04 template model scores | T0564.t04-template-lib-scores.html | 2010 May 28 19:49:33 |
Annotated t2k template model scores | T0564.t2k-template-lib-scores.html | 2010 May 28 20:54:07 |
Top Hits |
Best scoring hits from t06 HMMs | T0564.t06.best-scores.html | 2010 May 28 20:56:57 |
Best scoring hits from t04 HMMs | T0564.t04.best-scores.html | 2010 May 28 20:59:14 |
Best scoring hits from t2k HMMs | T0564.t2k.best-scores.html | 2010 May 28 21:01:31 |
Best scoring hits from combining t06 t04 t2k | T0564.best-scores-all.html | 2010 May 28 21:01:33 |
Alignments for Top Hits |
Top alignments from t06 hits | T0564.t06.top_reported_alignments.html | 2010 May 28 22:06:53 |
Top alignments from t04 hits | T0564.t04.top_reported_alignments.html | 2010 May 28 22:06:55 |
Top alignments from t2k hits | T0564.t2k.top_reported_alignments.html | 2010 May 28 22:06:56 |
Top alignments from combined hits | T0564.top_reported_alignments.html | 2010 May 28 22:06:58 |
multiple alignment of templates (a2m.gz format) (pa format) | all-align | 2010 May 28 22:07:49 |
Undertaker (3d) files |
Undertaker input for top t06 alignments | T0564.t06.undertaker-align.under | 2010 May 28 22:18:31 |
Undertaker input for top t04 alignments | T0564.t04.undertaker-align.under | 2010 May 28 22:18:32 |
Undertaker input for top t2k alignments | T0564.t2k.undertaker-align.under | 2010 May 28 22:18:33 |
Undertaker input for top combined alignments | T0564.undertaker-align.under | 2010 May 28 22:18:35 |
PDB file with model(s) for top alignments | T0564.undertaker-align.pdb.gz | 2010 May 28 22:20:22 |
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) | T0564.t06.many.frag.gz | 2010 May 28 22:20:56 |
Fragment list for undertaker (from fragfinder) | T0564.t04.many.frag.gz | 2010 May 28 22:21:19 |
Fragment list for undertaker (from fragfinder) | T0564.t2k.many.frag.gz | 2010 May 28 22:21:42 |
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) | T0564.647_47 | 2010 May 28 22:31:14 |
contact predictions (rr format) (rr.nn1000.constraints format) (rr.rasmol format) | T0564.730_47 | 2010 May 28 22:31:17 |
contact predictions (rr format) (rr.nn1000.constraints format) (rr.rasmol format) | T0564.648_17.730_47 | 2010 May 28 22:31:27 |
Distance constraints extracted from alignments |
Constraints from alignment | align.constraints | 2010 May 28 22:40:58 |
Rejected constraints | rejected_bonus.constraints | 2010 May 28 22:40:58 |
Noncontact constraints | noncontact.constraints | 2010 May 28 22:40:59 |
First attempted model using undertaker | decoys/T0564.try1-opt3.pdb.gz | 2010 May 28 23:58:49 |
Images of complete model in decoys/T0564.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 | T0564.tgz | 2010 May 29 0:10:03 |
Please cite the following papers:
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based on prior designs by Kevin Karplus, Alex Williams, and Rachel Karchin.
Maintained by Kevin Karplus: karplus@soe.ucsc.edu