SAM_T06 Results for SSO2096

Please cite the following papers:

Kevin Karplus, Sol Katzman, George Shackleford, Martina Koeva, Jenny Draper, Bret Barnes, Marcia Soriano, and Richard Hughey. SAM-T04: what's new in protein-structure prediction for CASP6. Proteins: Structure, Function, and Bioinformatics, 2005. 61(S7):135-142. doi:10.1002/prot.20730

Rachel Karchin, Melissa Cline, and Kevin Karplus. Evaluation of local structure alphabets based on residue burial. Proteins: Structure, Function, and Genetics, 55(3):508--518, 5 March 2004. doi:10.1002/prot.20008
Rachel Karchin, Melissa Cline, Yael Mandel-Gutfreund, and Kevin Karplus. Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry. Proteins: Structure, Function, and Genetics, 51(4):504--514, June 2003. doi:10.1002/prot.10369
Karplus, K. and Karchin, R. and Draper, J. and Casper, J. and Mandel-Gutfreund, Y. and Diekhans, M. and Hughey, R. ``Combining local-structure, fold-recognition, and new-fold methods for protein structure prediction'' Proteins: Structure Function and Genetics53(S6):491-496,15 Oct 2003 doi:10.1002/prot.10540

Rachel Karchin, Melissa Cline, Yael Mandel-Gutfreund, and Kevin Karplus. ``Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry.'' Proteins: Structure, Function, and Genetics, 51(4):504--514, June 2003. doi:10.1002/prot.10369

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 doi:10.1002/prot.10021

When SAM_T06 finishes loading, you should see links to

Inputs and Multiple Alignments
Secondary Structure Prediction
Target model scores with annotation
Template model scores with annotation
Top Hits—best scoring templates from all models
Alignments for Top Hits
Sidechain-replacement models using backbones from templates
Residue-residue contact predictions
Complete model for target sequence

The page uses a "meta" tag to automatically refresh every 4 minutes.

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)

SSO2096.a2m

2007 Feb 1 17:20:07

README file

README

2007 Feb 2 10:31:14

Quick blastp of non-redundant PDB

SSO2096.pdb.blast

2007 Feb 1 17:35:26

Multiple alignment

SAM_t06 multiple alignment in a2m format

SSO2096.t06.a2m.gz

2007 Feb 1 17:42:53

SAM_t06 multiple alignment in pretty html format

SSO2096.t06.pa.html

2007 Feb 1 17:43:25

SAM_t06 target hidden Markov model

SSO2096.t06.w0.5.mod

2007 Feb 1 17:43:26

SAM_t06 multiple alignment---sequence logo (eps format) (pdf format)

SSO2096.t06.w0.5-logo

2007 Feb 1 17:43:30

Script for highlighting in rasmol

conserved_t06

2007 Feb 1 17:43:30

SAM_t04 multiple alignment in a2m format

SSO2096.t04.a2m.gz

2007 Feb 1 17:49:12

SAM_t04 multiple alignment in pretty html format

SSO2096.t04.pa.html

2007 Feb 1 17:49:23

SAM_t04 target hidden Markov model

SSO2096.t04.w0.5.mod

2007 Feb 1 17:49:24

SAM_t04 multiple alignment---sequence logo (eps format) (pdf format)

SSO2096.t04.w0.5-logo

2007 Feb 1 17:49:28

Script for highlighting in rasmol

conserved_t04

2007 Feb 1 17:49:28

SAM_t2k multiple alignment in a2m format

SSO2096.t2k.a2m.gz

2007 Feb 1 17:50:53

SAM_t2k multiple alignment in pretty html format

SSO2096.t2k.pa.html

2007 Feb 1 17:51:09

SAM_t2k target hidden Markov model

SSO2096.t2k.w0.5.mod

2007 Feb 1 17:51:10

SAM_t2k multiple alignment---sequence logo (eps format) (pdf format)

SSO2096.t2k.w0.5-logo

2007 Feb 1 17:51:13

Script for highlighting in rasmol

conserved_t2k

2007 Feb 1 17:51:13

Secondary Structure Prediction (Explanation of secondary-structure predictions)

str2 structure prediction (rdb format) (seq format)

SSO2096.t06.str2

2007 Feb 1 17:43:27

Script for SSO2096.t06.str2 coloring in rasmol

SSO2096.t06.str2-color.rasmol

2007 Feb 1 17:51:13

str2---sequence logo (eps format) (pdf format)

SSO2096.t06.str2-logo

2007 Feb 2 3:36:49

str2 structure prediction (rdb format) (seq format)

SSO2096.t04.str2

2007 Feb 1 17:49:26

Script for SSO2096.t04.str2 coloring in rasmol

SSO2096.t04.str2-color.rasmol

2007 Feb 2 3:36:49

str2---sequence logo (eps format) (pdf format)

SSO2096.t04.str2-logo

2007 Feb 2 3:36:52

str2 structure prediction (rdb format) (seq format)

SSO2096.t2k.str2

2007 Feb 1 17:51:10

Script for SSO2096.t2k.str2 coloring in rasmol

SSO2096.t2k.str2-color.rasmol

2007 Feb 2 3:36:52

str2---sequence logo (eps format) (pdf format)

SSO2096.t2k.str2-logo

2007 Feb 2 3:36:54

stride-ebghtl structure prediction (rdb format) (seq format)

SSO2096.t06.stride-ebghtl

2007 Feb 2 3:36:55

Script for SSO2096.t06.stride-ebghtl coloring in rasmol

SSO2096.t06.stride-ebghtl-color.rasmol

2007 Feb 2 3:36:55

stride-ebghtl---sequence logo (eps format) (pdf format)

SSO2096.t06.stride-ebghtl-logo

2007 Feb 2 3:36:58

stride-ebghtl structure prediction (rdb format) (seq format)

SSO2096.t04.stride-ebghtl

2007 Feb 2 3:36:59

Script for SSO2096.t04.stride-ebghtl coloring in rasmol

SSO2096.t04.stride-ebghtl-color.rasmol

2007 Feb 2 3:36:59

stride-ebghtl---sequence logo (eps format) (pdf format)

SSO2096.t04.stride-ebghtl-logo

2007 Feb 2 3:37:01

stride-ebghtl structure prediction (rdb format) (seq format)

SSO2096.t2k.stride-ebghtl

2007 Feb 2 3:37:02

Script for SSO2096.t2k.stride-ebghtl coloring in rasmol

SSO2096.t2k.stride-ebghtl-color.rasmol

2007 Feb 2 3:37:02

stride-ebghtl---sequence logo (eps format) (pdf format)

SSO2096.t2k.stride-ebghtl-logo

2007 Feb 2 3:37:04

dssp-ebghstl structure prediction (rdb format) (seq format)

SSO2096.t06.dssp-ebghstl

2007 Feb 2 3:37:05

Script for SSO2096.t06.dssp-ebghstl coloring in rasmol

SSO2096.t06.dssp-ebghstl-color.rasmol

2007 Feb 2 3:37:05

dssp-ebghstl---sequence logo (eps format) (pdf format)

SSO2096.t06.dssp-ebghstl-logo

2007 Feb 2 3:37:07

dssp-ebghstl structure prediction (rdb format) (seq format)

SSO2096.t04.dssp-ebghstl

2007 Feb 2 3:37:08

Script for SSO2096.t04.dssp-ebghstl coloring in rasmol

SSO2096.t04.dssp-ebghstl-color.rasmol

2007 Feb 2 3:37:08

dssp-ebghstl---sequence logo (eps format) (pdf format)

SSO2096.t04.dssp-ebghstl-logo

2007 Feb 2 3:37:10

dssp-ebghstl structure prediction (rdb format) (seq format)

SSO2096.t2k.dssp-ebghstl

2007 Feb 2 3:37:10

Script for SSO2096.t2k.dssp-ebghstl coloring in rasmol

SSO2096.t2k.dssp-ebghstl-color.rasmol

2007 Feb 2 3:37:10

dssp-ebghstl---sequence logo (eps format) (pdf format)

SSO2096.t2k.dssp-ebghstl-logo

2007 Feb 2 3:37:13

alpha structure prediction (rdb format) (seq format)

SSO2096.t06.alpha

2007 Feb 2 3:37:13

Script for SSO2096.t06.alpha coloring in rasmol

SSO2096.t06.alpha-color.rasmol

2007 Feb 2 3:37:14

alpha---sequence logo (eps format) (pdf format)

SSO2096.t06.alpha-logo

2007 Feb 2 3:37:16

alpha structure prediction (rdb format) (seq format)

SSO2096.t04.alpha

2007 Feb 2 3:37:17

Script for SSO2096.t04.alpha coloring in rasmol

SSO2096.t04.alpha-color.rasmol

2007 Feb 2 3:37:17

alpha---sequence logo (eps format) (pdf format)

SSO2096.t04.alpha-logo

2007 Feb 2 3:37:19

alpha structure prediction (rdb format) (seq format)

SSO2096.t2k.alpha

2007 Feb 2 3:37:19

Script for SSO2096.t2k.alpha coloring in rasmol

SSO2096.t2k.alpha-color.rasmol

2007 Feb 2 3:37:19

alpha---sequence logo (eps format) (pdf format)

SSO2096.t2k.alpha-logo

2007 Feb 2 3:37:22

bys structure prediction (rdb format) (seq format)

SSO2096.t06.bys

2007 Feb 2 3:37:23

Script for SSO2096.t06.bys coloring in rasmol

SSO2096.t06.bys-color.rasmol

2007 Feb 2 3:37:23

bys---sequence logo (eps format) (pdf format)

SSO2096.t06.bys-logo

2007 Feb 2 3:37:25

bys structure prediction (rdb format) (seq format)

SSO2096.t04.bys

2007 Feb 2 3:37:26

Script for SSO2096.t04.bys coloring in rasmol

SSO2096.t04.bys-color.rasmol

2007 Feb 2 3:37:26

bys---sequence logo (eps format) (pdf format)

SSO2096.t04.bys-logo

2007 Feb 2 3:37:28

bys structure prediction (rdb format) (seq format)

SSO2096.t2k.bys

2007 Feb 2 3:37:29

Script for SSO2096.t2k.bys coloring in rasmol

SSO2096.t2k.bys-color.rasmol

2007 Feb 2 3:37:29

bys---sequence logo (eps format) (pdf format)

SSO2096.t2k.bys-logo

2007 Feb 2 3:37:31

dssp-ehl2 structure prediction (rdb format) (seq format)

SSO2096.t06.dssp-ehl2

2007 Feb 2 3:37:32

Script for SSO2096.t06.dssp-ehl2 coloring in rasmol

SSO2096.t06.dssp-ehl2-color.rasmol

2007 Feb 2 3:37:32

dssp-ehl2---sequence logo (eps format) (pdf format)

SSO2096.t06.dssp-ehl2-logo

2007 Feb 2 3:37:34

dssp-ehl2 structure prediction (rdb format) (seq format)

SSO2096.t04.dssp-ehl2

2007 Feb 2 3:37:34

Script for SSO2096.t04.dssp-ehl2 coloring in rasmol

SSO2096.t04.dssp-ehl2-color.rasmol

2007 Feb 2 3:37:34

dssp-ehl2---sequence logo (eps format) (pdf format)

SSO2096.t04.dssp-ehl2-logo

2007 Feb 2 3:37:36

dssp-ehl2 structure prediction (rdb format) (seq format)

SSO2096.t2k.dssp-ehl2

2007 Feb 2 3:37:37

Script for SSO2096.t2k.dssp-ehl2 coloring in rasmol

SSO2096.t2k.dssp-ehl2-color.rasmol

2007 Feb 2 3:37:37

dssp-ehl2---sequence logo (eps format) (pdf format)

SSO2096.t2k.dssp-ehl2-logo

2007 Feb 2 3:37:39

n_notor2 structure prediction (rdb format) (seq format)

SSO2096.t06.n_notor2

2007 Feb 2 3:37:40

Script for SSO2096.t06.n_notor2 coloring in rasmol

SSO2096.t06.n_notor2-color.rasmol

2007 Feb 2 3:37:40

n_notor2---sequence logo (eps format) (pdf format)

SSO2096.t06.n_notor2-logo

2007 Feb 2 3:37:42

n_notor2 structure prediction (rdb format) (seq format)

SSO2096.t04.n_notor2

2007 Feb 2 3:37:43

Script for SSO2096.t04.n_notor2 coloring in rasmol

SSO2096.t04.n_notor2-color.rasmol

2007 Feb 2 3:37:43

n_notor2---sequence logo (eps format) (pdf format)

SSO2096.t04.n_notor2-logo

2007 Feb 2 3:37:45

n_notor2 structure prediction (rdb format) (seq format)

SSO2096.t2k.n_notor2

2007 Feb 2 3:37:46

Script for SSO2096.t2k.n_notor2 coloring in rasmol

SSO2096.t2k.n_notor2-color.rasmol

2007 Feb 2 3:37:46

n_notor2---sequence logo (eps format) (pdf format)

SSO2096.t2k.n_notor2-logo

2007 Feb 2 3:37:48

o_notor2 structure prediction (rdb format) (seq format)

SSO2096.t06.o_notor2

2007 Feb 2 3:37:49

Script for SSO2096.t06.o_notor2 coloring in rasmol

SSO2096.t06.o_notor2-color.rasmol

2007 Feb 2 3:37:49

o_notor2---sequence logo (eps format) (pdf format)

SSO2096.t06.o_notor2-logo

2007 Feb 2 3:37:52

o_notor2 structure prediction (rdb format) (seq format)

SSO2096.t04.o_notor2

2007 Feb 2 3:37:52

Script for SSO2096.t04.o_notor2 coloring in rasmol

SSO2096.t04.o_notor2-color.rasmol

2007 Feb 2 3:37:52

o_notor2---sequence logo (eps format) (pdf format)

SSO2096.t04.o_notor2-logo

2007 Feb 2 3:37:55

o_notor2 structure prediction (rdb format) (seq format)

SSO2096.t2k.o_notor2

2007 Feb 2 3:37:55

Script for SSO2096.t2k.o_notor2 coloring in rasmol

SSO2096.t2k.o_notor2-color.rasmol

2007 Feb 2 3:37:55

o_notor2---sequence logo (eps format) (pdf format)

SSO2096.t2k.o_notor2-logo

2007 Feb 2 3:37:58

n_sep structure prediction (rdb format) (seq format)

SSO2096.t06.n_sep

2007 Feb 2 3:37:59

Script for SSO2096.t06.n_sep coloring in rasmol

SSO2096.t06.n_sep-color.rasmol

2007 Feb 2 3:37:59

n_sep---sequence logo (eps format) (pdf format)

SSO2096.t06.n_sep-logo

2007 Feb 2 3:38:01

n_sep structure prediction (rdb format) (seq format)

SSO2096.t04.n_sep

2007 Feb 2 3:38:02

Script for SSO2096.t04.n_sep coloring in rasmol

SSO2096.t04.n_sep-color.rasmol

2007 Feb 2 3:38:02

n_sep---sequence logo (eps format) (pdf format)

SSO2096.t04.n_sep-logo

2007 Feb 2 3:38:04

n_sep structure prediction (rdb format) (seq format)

SSO2096.t2k.n_sep

2007 Feb 2 3:38:05

Script for SSO2096.t2k.n_sep coloring in rasmol

SSO2096.t2k.n_sep-color.rasmol

2007 Feb 2 3:38:05

n_sep---sequence logo (eps format) (pdf format)

SSO2096.t2k.n_sep-logo

2007 Feb 2 3:38:07

o_sep structure prediction (rdb format) (seq format)

SSO2096.t06.o_sep

2007 Feb 2 3:38:08

Script for SSO2096.t06.o_sep coloring in rasmol

SSO2096.t06.o_sep-color.rasmol

2007 Feb 2 3:38:08

o_sep---sequence logo (eps format) (pdf format)

SSO2096.t06.o_sep-logo

2007 Feb 2 3:38:10

o_sep structure prediction (rdb format) (seq format)

SSO2096.t04.o_sep

2007 Feb 2 3:38:11

Script for SSO2096.t04.o_sep coloring in rasmol

SSO2096.t04.o_sep-color.rasmol

2007 Feb 2 3:38:11

o_sep---sequence logo (eps format) (pdf format)

SSO2096.t04.o_sep-logo

2007 Feb 2 3:38:14

o_sep structure prediction (rdb format) (seq format)

SSO2096.t2k.o_sep

2007 Feb 2 3:38:14

Script for SSO2096.t2k.o_sep coloring in rasmol

SSO2096.t2k.o_sep-color.rasmol

2007 Feb 2 3:38:14

o_sep---sequence logo (eps format) (pdf format)

SSO2096.t2k.o_sep-logo

2007 Feb 2 3:38:17

dssp-ehl2 structure prediction (rdb format) (seq format)

SSO2096.dssp-ehl2

2007 Feb 2 3:38:17

Script for SSO2096.dssp-ehl2 coloring in rasmol

SSO2096.dssp-ehl2-color.rasmol

2007 Feb 2 3:38:17

dssp-ehl2---sequence logo (eps format) (pdf format)

SSO2096.dssp-ehl2-logo

2007 Feb 2 3:38:19

CB_burial_14_7 structure prediction (rdb format) (seq format)

SSO2096.t06.CB_burial_14_7

2007 Feb 2 3:38:20

Script for SSO2096.t06.CB_burial_14_7 coloring in rasmol

SSO2096.t06.CB_burial_14_7-color.rasmol

2007 Feb 2 3:38:20

CB_burial_14_7---sequence logo (eps format) (pdf format)

SSO2096.t06.CB_burial_14_7-logo

2007 Feb 2 3:38:22

CB_burial_14_7 structure prediction (rdb format) (seq format)

SSO2096.t04.CB_burial_14_7

2007 Feb 2 3:38:23

Script for SSO2096.t04.CB_burial_14_7 coloring in rasmol

SSO2096.t04.CB_burial_14_7-color.rasmol

2007 Feb 2 3:38:23

CB_burial_14_7---sequence logo (eps format) (pdf format)

SSO2096.t04.CB_burial_14_7-logo

2007 Feb 2 3:38:26

CB_burial_14_7 structure prediction (rdb format) (seq format)

SSO2096.t2k.CB_burial_14_7

2007 Feb 2 3:38:26

Script for SSO2096.t2k.CB_burial_14_7 coloring in rasmol

SSO2096.t2k.CB_burial_14_7-color.rasmol

2007 Feb 2 3:38:26

CB_burial_14_7---sequence logo (eps format) (pdf format)

SSO2096.t2k.CB_burial_14_7-logo

2007 Feb 2 3:38:28

near-backbone-11 structure prediction (rdb format) (seq format)

SSO2096.t06.near-backbone-11

2007 Feb 2 3:38:29

Script for SSO2096.t06.near-backbone-11 coloring in rasmol

SSO2096.t06.near-backbone-11-color.rasmol

2007 Feb 2 3:38:29

near-backbone-11---sequence logo (eps format) (pdf format)

SSO2096.t06.near-backbone-11-logo

2007 Feb 2 3:38:32

near-backbone-11 structure prediction (rdb format) (seq format)

SSO2096.t04.near-backbone-11

2007 Feb 2 3:38:32

Script for SSO2096.t04.near-backbone-11 coloring in rasmol

SSO2096.t04.near-backbone-11-color.rasmol

2007 Feb 2 3:38:32

near-backbone-11---sequence logo (eps format) (pdf format)

SSO2096.t04.near-backbone-11-logo

2007 Feb 2 3:38:35

near-backbone-11 structure prediction (rdb format) (seq format)

SSO2096.t2k.near-backbone-11

2007 Feb 2 3:38:35

Script for SSO2096.t2k.near-backbone-11 coloring in rasmol

SSO2096.t2k.near-backbone-11-color.rasmol

2007 Feb 2 3:38:35

near-backbone-11---sequence logo (eps format) (pdf format)

SSO2096.t2k.near-backbone-11-logo

2007 Feb 2 3:38:38

Target model scores

amino acid single-track target model scores of PDB

SSO2096.t06-w0.5-scores.html

2007 Feb 2 3:41:00

amino acid single-track target model scores of PDB

SSO2096.t04-w0.5-scores.html

2007 Feb 2 3:43:33

amino acid single-track target model scores of PDB

SSO2096.t2k-w0.5-scores.html

2007 Feb 2 3:46:06

amino acid/100-30-str2 multi-track target model scores

SSO2096.t06-100-30-str2-scores.html

2007 Feb 2 4:54:37

amino acid/100-30-stride-ebghtl multi-track target model scores

SSO2096.t06-100-30-stride-ebghtl-scores.html

2007 Feb 2 3:46:52

amino acid/100-30-dssp-ebghstl multi-track target model scores

SSO2096.t06-100-30-dssp-ebghstl-scores.html

2007 Feb 2 3:47:38

amino acid/100-30-alpha multi-track target model scores

SSO2096.t06-100-30-alpha-scores.html

2007 Feb 2 3:48:23

amino acid/100-30-bys multi-track target model scores

SSO2096.t06-100-30-bys-scores.html

2007 Feb 2 3:49:08

amino acid/100-30-dssp-ehl2 multi-track target model scores

SSO2096.t06-100-30-dssp-ehl2-scores.html

2007 Feb 2 3:49:58

amino acid/100-30-n_notor2 multi-track target model scores

SSO2096.t06-100-30-n_notor2-scores.html

2007 Feb 2 3:50:43

amino acid/100-30-o_notor2 multi-track target model scores

SSO2096.t06-100-30-o_notor2-scores.html

2007 Feb 2 3:51:28

amino acid/100-30-n_sep multi-track target model scores

SSO2096.t06-100-30-n_sep-scores.html

2007 Feb 2 3:52:14

amino acid/100-30-o_sep multi-track target model scores

SSO2096.t06-100-30-o_sep-scores.html

2007 Feb 2 3:52:58

amino acid/100-30-CB_burial_14_7 multi-track target model scores

SSO2096.t06-100-30-CB_burial_14_7-scores.html

2007 Feb 2 3:53:44

amino acid/100-30-near-backbone-11 multi-track target model scores

SSO2096.t06-100-30-near-backbone-11-scores.html

2007 Feb 2 3:54:28

amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores

SSO2096.t06-100-40-40-str2+CB_burial_14_7-scores.html

2007 Feb 2 4:55:30

amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores

SSO2096.t06-80-60-80-str2+near-backbone-11-scores.html

2007 Feb 2 4:56:24

amino acid/100-30-str2 multi-track target model scores

SSO2096.t04-100-30-str2-scores.html

2007 Feb 2 3:55:29

amino acid/100-30-stride-ebghtl multi-track target model scores

SSO2096.t04-100-30-stride-ebghtl-scores.html

2007 Feb 2 3:56:30

amino acid/100-30-dssp-ebghstl multi-track target model scores

SSO2096.t04-100-30-dssp-ebghstl-scores.html

2007 Feb 2 3:57:30

amino acid/100-30-alpha multi-track target model scores

SSO2096.t04-100-30-alpha-scores.html

2007 Feb 2 3:58:30

amino acid/100-30-bys multi-track target model scores

SSO2096.t04-100-30-bys-scores.html

2007 Feb 2 3:59:29

amino acid/100-30-dssp-ehl2 multi-track target model scores

SSO2096.t04-100-30-dssp-ehl2-scores.html

2007 Feb 2 4:00:29

amino acid/100-30-n_notor2 multi-track target model scores

SSO2096.t04-100-30-n_notor2-scores.html

2007 Feb 2 4:01:29

amino acid/100-30-o_notor2 multi-track target model scores

SSO2096.t04-100-30-o_notor2-scores.html

2007 Feb 2 4:02:28

amino acid/100-30-n_sep multi-track target model scores

SSO2096.t04-100-30-n_sep-scores.html

2007 Feb 2 4:03:28

amino acid/100-30-o_sep multi-track target model scores

SSO2096.t04-100-30-o_sep-scores.html

2007 Feb 2 4:04:27

amino acid/100-30-CB_burial_14_7 multi-track target model scores

SSO2096.t04-100-30-CB_burial_14_7-scores.html

2007 Feb 2 4:05:26

amino acid/100-30-near-backbone-11 multi-track target model scores

SSO2096.t04-100-30-near-backbone-11-scores.html

2007 Feb 2 4:06:24

amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores

SSO2096.t04-100-40-40-str2+CB_burial_14_7-scores.html

2007 Feb 2 4:07:31

amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores

SSO2096.t04-80-60-80-str2+near-backbone-11-scores.html

2007 Feb 2 4:08:44

amino acid/100-30-str2 multi-track target model scores

SSO2096.t2k-100-30-str2-scores.html

2007 Feb 2 4:57:41

amino acid/100-30-stride-ebghtl multi-track target model scores

SSO2096.t2k-100-30-stride-ebghtl-scores.html

2007 Feb 2 4:10:01

amino acid/100-30-dssp-ebghstl multi-track target model scores

SSO2096.t2k-100-30-dssp-ebghstl-scores.html

2007 Feb 2 4:11:16

amino acid/100-30-alpha multi-track target model scores

SSO2096.t2k-100-30-alpha-scores.html

2007 Feb 2 4:12:30

amino acid/100-30-bys multi-track target model scores

SSO2096.t2k-100-30-bys-scores.html

2007 Feb 2 4:13:45

amino acid/100-30-dssp-ehl2 multi-track target model scores

SSO2096.t2k-100-30-dssp-ehl2-scores.html

2007 Feb 2 4:14:59

amino acid/100-30-n_notor2 multi-track target model scores

SSO2096.t2k-100-30-n_notor2-scores.html

2007 Feb 2 4:16:14

amino acid/100-30-o_notor2 multi-track target model scores

SSO2096.t2k-100-30-o_notor2-scores.html

2007 Feb 2 4:17:27

amino acid/100-30-n_sep multi-track target model scores

SSO2096.t2k-100-30-n_sep-scores.html

2007 Feb 2 4:18:41

amino acid/100-30-o_sep multi-track target model scores

SSO2096.t2k-100-30-o_sep-scores.html

2007 Feb 2 4:19:55

amino acid/100-30-CB_burial_14_7 multi-track target model scores

SSO2096.t2k-100-30-CB_burial_14_7-scores.html

2007 Feb 2 4:21:09

amino acid/100-30-near-backbone-11 multi-track target model scores

SSO2096.t2k-100-30-near-backbone-11-scores.html

2007 Feb 2 4:22:22

amino acid/100-40-40-str2+CB_burial_14_7 multi-track target model scores

SSO2096.t2k-100-40-40-str2+CB_burial_14_7-scores.html

2007 Feb 2 4:23:46

amino acid/80-60-80-str2+near-backbone-11 multi-track target model scores

SSO2096.t2k-80-60-80-str2+near-backbone-11-scores.html

2007 Feb 2 4:25:17

Template model scores

Annotated t06 template model scores

SSO2096.t06-template-lib-scores.html

2007 Feb 2 4:35:37

Annotated t04 template model scores

SSO2096.t04-template-lib-scores.html

2007 Feb 2 4:44:47

Annotated t2k template model scores

SSO2096.t2k-template-lib-scores.html

2007 Feb 2 5:06:26

Top Hits

Best scoring hits from t06 HMMs

SSO2096.t06.best-scores.html

2007 Feb 2 5:06:29

Best scoring hits from t04 HMMs

SSO2096.t04.best-scores.html

2007 Feb 2 5:06:31

Best scoring hits from t2k HMMs

SSO2096.t2k.best-scores.html

2007 Feb 2 5:06:33

Best scoring hits from combining t06 t04 t2k

SSO2096.best-scores.html

2007 Feb 2 5:06:37

Alignments for Top Hits

Top alignments from t06 hits

SSO2096.t06.top_reported_alignments.html

2007 Feb 2 5:18:36

Top alignments from t04 hits

SSO2096.t04.top_reported_alignments.html

2007 Feb 2 5:41:29

Top alignments from t2k hits

SSO2096.t2k.top_reported_alignments.html

2007 Feb 2 10:42:01

Top alignments from combined hits

SSO2096.top_reported_alignments.html

2007 Feb 2 10:42:07

multiple alignment of templates (a2m.gz format) (pa format)

all-align

2007 Feb 2 10:42:33

Undertaker (3d) files

Undertaker input for top t06 alignments

SSO2096.t06.undertaker-align.under

2007 Feb 2 10:42:33

Undertaker input for top t04 alignments

SSO2096.t04.undertaker-align.under

2007 Feb 2 10:42:33

Undertaker input for top t2k alignments

SSO2096.t2k.undertaker-align.under

2007 Feb 2 10:42:33

Undertaker input for top combined alignments

SSO2096.undertaker-align.under

2007 Feb 2 10:42:33

PDB file with model(s) for top alignments

SSO2096.undertaker-align.pdb.gz

2007 Feb 2 10:43:39

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

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Fragment list for undertaker (from fragfinder) SSO2096.t06.many.frag.gz 2007 Feb 2 10:45:22

Fragment list for undertaker (from fragfinder) SSO2096.t04.many.frag.gz 2007 Feb 2 10:45:50

Fragment list for undertaker (from fragfinder) SSO2096.t2k.many.frag.gz 2007 Feb 2 10:46:17

Contact predictions, based on

contact predictions (rr format) (rr.constraints format)

SSO2096.449a_45

2007 Feb 2 10:48:30

First attempted model using undertaker

decoys/SSO2096.try1-opt2.pdb.gz

2007 Feb 2 12:16:40

Images of complete model in decoys/SSO2096.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

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Please cite the following papers:

Kevin Karplus, Sol Katzman, George Shackleford, Martina Koeva, Jenny Draper, Bret Barnes, Marcia Soriano, and Richard Hughey. SAM-T04: what's new in protein-structure prediction for CASP6. Proteins: Structure, Function, and Bioinformatics, 2005. 61(S7):135-142. doi:10.1002/prot.20730

Rachel Karchin, Melissa Cline, and Kevin Karplus. Evaluation of local structure alphabets based on residue burial. Proteins: Structure, Function, and Genetics, 55(3):508--518, 5 March 2004. doi:10.1002/prot.20008
Rachel Karchin, Melissa Cline, Yael Mandel-Gutfreund, and Kevin Karplus. Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry. Proteins: Structure, Function, and Genetics, 51(4):504--514, June 2003. doi:10.1002/prot.10369
Karplus, K. and Karchin, R. and Draper, J. and Casper, J. and Mandel-Gutfreund, Y. and Diekhans, M. and Hughey, R. ``Combining local-structure, fold-recognition, and new-fold methods for protein structure prediction'' Proteins: Structure Function and Genetics53(S6):491-496,15 Oct 2003 doi:10.1002/prot.10540

Rachel Karchin, Melissa Cline, Yael Mandel-Gutfreund, and Kevin Karplus. ``Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry.'' Proteins: Structure, Function, and Genetics, 51(4):504--514, June 2003. doi:10.1002/prot.10369

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 doi:10.1002/prot.10021

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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