SAM_T06 Results for T0495

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

T0495.a2m

2008 Jul 10 9:11:25

README file

README

2008 Jul 10 9:11:30

Quick blastp of non-redundant PDB

T0495.pdb_blast.txt

2008 Jul 10 9:11:33

Multiple alignment

SAM_t04 multiple alignment in a2m format

T0495.t04.a2m.gz

2008 Jul 10 9:17:10

SAM_t04 multiple alignment in pretty html format

T0495.t04.pa.html

2008 Jul 10 9:18:12

SAM_t04 target hidden Markov model

T0495.t04.w0.5.mod

2008 Jul 10 9:18:16

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

T0495.t04.w0.5-logo

2008 Jul 10 9:18:21

Script for highlighting in rasmol

conserved_t04

2008 Jul 10 9:18:22

SAM_t2k multiple alignment in a2m format

T0495.t2k.a2m.gz

2008 Jul 10 9:20:21

SAM_t2k multiple alignment in pretty html format

T0495.t2k.pa.html

2008 Jul 10 9:20:26

SAM_t2k target hidden Markov model

T0495.t2k.w0.5.mod

2008 Jul 10 9:20:30

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

T0495.t2k.w0.5-logo

2008 Jul 10 9:20:34

Script for highlighting in rasmol

conserved_t2k

2008 Jul 10 9:20:35

Secondary Structure Prediction (Explanation of secondary-structure predictions)

str2 structure prediction (rdb format) (seq format)

T0495.t04.str2

2008 Jul 10 9:18:18

Script for T0495.t04.str2 coloring in rasmol

T0495.t04.str2-color.rasmol

2008 Jul 10 9:20:37

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

T0495.t04.str2-logo

2008 Jul 10 9:20:40

str2 structure prediction (rdb format) (seq format)

T0495.t2k.str2

2008 Jul 10 9:20:32

Script for T0495.t2k.str2 coloring in rasmol

T0495.t2k.str2-color.rasmol

2008 Jul 10 9:20:41

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

T0495.t2k.str2-logo

2008 Jul 10 9:20:44

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

T0495.t04.stride-ebghtl

2008 Jul 10 9:20:49

Script for T0495.t04.stride-ebghtl coloring in rasmol

T0495.t04.stride-ebghtl-color.rasmol

2008 Jul 10 9:20:49

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

T0495.t04.stride-ebghtl-logo

2008 Jul 10 9:20:53

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

T0495.t2k.stride-ebghtl

2008 Jul 10 9:20:55

Script for T0495.t2k.stride-ebghtl coloring in rasmol

T0495.t2k.stride-ebghtl-color.rasmol

2008 Jul 10 9:20:55

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

T0495.t2k.stride-ebghtl-logo

2008 Jul 10 9:20:58

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

T0495.t04.dssp-ebghstl

2008 Jul 10 9:21:00

Script for T0495.t04.dssp-ebghstl coloring in rasmol

T0495.t04.dssp-ebghstl-color.rasmol

2008 Jul 10 9:21:01

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

T0495.t04.dssp-ebghstl-logo

2008 Jul 10 9:21:05

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

T0495.t2k.dssp-ebghstl

2008 Jul 10 9:21:07

Script for T0495.t2k.dssp-ebghstl coloring in rasmol

T0495.t2k.dssp-ebghstl-color.rasmol

2008 Jul 10 9:21:07

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

T0495.t2k.dssp-ebghstl-logo

2008 Jul 10 9:21:10

alpha structure prediction (rdb format) (seq format)

T0495.t04.alpha

2008 Jul 10 9:21:12

Script for T0495.t04.alpha coloring in rasmol

T0495.t04.alpha-color.rasmol

2008 Jul 10 9:21:12

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

T0495.t04.alpha-logo

2008 Jul 10 9:21:15

alpha structure prediction (rdb format) (seq format)

T0495.t2k.alpha

2008 Jul 10 9:21:18

Script for T0495.t2k.alpha coloring in rasmol

T0495.t2k.alpha-color.rasmol

2008 Jul 10 9:21:19

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

T0495.t2k.alpha-logo

2008 Jul 10 9:21:21

bys structure prediction (rdb format) (seq format)

T0495.t04.bys

2008 Jul 10 9:21:24

Script for T0495.t04.bys coloring in rasmol

T0495.t04.bys-color.rasmol

2008 Jul 10 9:21:24

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

T0495.t04.bys-logo

2008 Jul 10 9:21:27

bys structure prediction (rdb format) (seq format)

T0495.t2k.bys

2008 Jul 10 9:21:31

Script for T0495.t2k.bys coloring in rasmol

T0495.t2k.bys-color.rasmol

2008 Jul 10 9:21:32

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

T0495.t2k.bys-logo

2008 Jul 10 9:21:34

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

T0495.t04.dssp-ehl2

2008 Jul 10 9:21:37

Script for T0495.t04.dssp-ehl2 coloring in rasmol

T0495.t04.dssp-ehl2-color.rasmol

2008 Jul 10 9:21:37

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

T0495.t04.dssp-ehl2-logo

2008 Jul 10 9:21:40

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

T0495.t2k.dssp-ehl2

2008 Jul 10 9:21:41

Script for T0495.t2k.dssp-ehl2 coloring in rasmol

T0495.t2k.dssp-ehl2-color.rasmol

2008 Jul 10 9:21:41

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

T0495.t2k.dssp-ehl2-logo

2008 Jul 10 9:21:44

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

T0495.dssp-ehl2

2008 Jul 10 9:21:46

Script for T0495.dssp-ehl2 coloring in rasmol

T0495.dssp-ehl2-color.rasmol

2008 Jul 10 9:21:46

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

T0495.dssp-ehl2-logo

2008 Jul 10 9:21:51

CB_burial_14_7 structure prediction (rdb format) (seq format)

T0495.t04.CB_burial_14_7

2008 Jul 10 9:21:54

Script for T0495.t04.CB_burial_14_7 coloring in rasmol

T0495.t04.CB_burial_14_7-color.rasmol

2008 Jul 10 9:21:54

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

T0495.t04.CB_burial_14_7-logo

2008 Jul 10 9:21:57

CB_burial_14_7 structure prediction (rdb format) (seq format)

T0495.t2k.CB_burial_14_7

2008 Jul 10 9:21:59

Script for T0495.t2k.CB_burial_14_7 coloring in rasmol

T0495.t2k.CB_burial_14_7-color.rasmol

2008 Jul 10 9:21:59

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

T0495.t2k.CB_burial_14_7-logo

2008 Jul 10 9:22:03

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

T0495.t04.near-backbone-11

2008 Jul 10 9:22:06

Script for T0495.t04.near-backbone-11 coloring in rasmol

T0495.t04.near-backbone-11-color.rasmol

2008 Jul 10 9:22:06

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

T0495.t04.near-backbone-11-logo

2008 Jul 10 9:22:09

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

T0495.t2k.near-backbone-11

2008 Jul 10 9:22:11

Script for T0495.t2k.near-backbone-11 coloring in rasmol

T0495.t2k.near-backbone-11-color.rasmol

2008 Jul 10 9:22:11

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

T0495.t2k.near-backbone-11-logo

2008 Jul 10 9:22:14

Target model scores

amino acid single-track target model scores of PDB

T0495.t04-w0.5-scores.html

2008 Jul 10 9:26:49

amino acid single-track target model scores of PDB

T0495.t2k-w0.5-scores.html

2008 Jul 10 9:31:20

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

T0495.t2k-100-30-str2-scores.html

2008 Jul 10 9:33:19

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

T0495.t2k-100-30-stride-ebghtl-scores.html

2008 Jul 10 9:35:17

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

T0495.t2k-100-30-dssp-ebghstl-scores.html

2008 Jul 10 9:37:16

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

T0495.t2k-100-30-alpha-scores.html

2008 Jul 10 9:39:13

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

T0495.t2k-100-30-bys-scores.html

2008 Jul 10 9:41:10

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

T0495.t2k-100-30-dssp-ehl2-scores.html

2008 Jul 10 9:43:07

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

T0495.t2k-100-30-CB_burial_14_7-scores.html

2008 Jul 10 9:45:04

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

T0495.t2k-100-30-near-backbone-11-scores.html

2008 Jul 10 9:47:00

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

T0495.t2k-100-40-40-str2+CB_burial_14_7-scores.html

2008 Jul 10 9:49:07

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

T0495.t2k-80-60-80-str2+near-backbone-11-scores.html

2008 Jul 10 9:51:16

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

T0495.t04-100-30-str2-scores.html

2008 Jul 10 9:53:05

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

T0495.t04-100-30-stride-ebghtl-scores.html

2008 Jul 10 9:54:54

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

T0495.t04-100-30-dssp-ebghstl-scores.html

2008 Jul 10 9:56:46

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

T0495.t04-100-30-alpha-scores.html

2008 Jul 10 9:58:36

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

T0495.t04-100-30-bys-scores.html

2008 Jul 10 10:00:26

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

T0495.t04-100-30-dssp-ehl2-scores.html

2008 Jul 10 10:02:14

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

T0495.t04-100-30-CB_burial_14_7-scores.html

2008 Jul 10 10:04:03

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

T0495.t04-100-30-near-backbone-11-scores.html

2008 Jul 10 10:05:50

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

T0495.t04-100-40-40-str2+CB_burial_14_7-scores.html

2008 Jul 10 10:07:47

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

T0495.t04-80-60-80-str2+near-backbone-11-scores.html

2008 Jul 10 10:09:47

Template model scores

Annotated t04 template model scores

T0495.t04-template-lib-scores.html

2008 Jul 10 10:23:27

Annotated t2k template model scores

T0495.t2k-template-lib-scores.html

2008 Jul 10 10:35:30

Top Hits

Best scoring hits from t04 HMMs

T0495.t04.best-scores.html

2008 Jul 10 10:35:33

Best scoring hits from t2k HMMs

T0495.t2k.best-scores.html

2008 Jul 10 10:35:38

Best scoring hits from combining t04 t2k

T0495.best-scores.html

2008 Jul 10 10:35:41

Alignments for Top Hits

Top alignments from t04 hits

T0495.t04.top_reported_alignments.html

2008 Jul 10 11:54:59

Top alignments from t2k hits

T0495.t2k.top_reported_alignments.html

2008 Jul 10 11:55:25

Top alignments from combined hits

T0495.top_reported_alignments.html

2008 Jul 10 11:55:39

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

all-align

2008 Jul 10 11:56:36

Undertaker (3d) files

Undertaker input for top t04 alignments

T0495.t04.undertaker-align.under

2008 Jul 10 11:56:37

Undertaker input for top t2k alignments

T0495.t2k.undertaker-align.under

2008 Jul 10 11:56:38

Undertaker input for top combined alignments

T0495.undertaker-align.under

2008 Jul 10 11:56:38

PDB file with model(s) for top alignments

T0495.undertaker-align.pdb.gz

2008 Jul 10 11:58:14

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

500x500 500x500 500x500

Fragment list for undertaker (from fragfinder) T0495.t04.many.frag.gz 2008 Jul 10 12:00:27

Fragment list for undertaker (from fragfinder) T0495.t2k.many.frag.gz 2008 Jul 10 12:01:09

Contact predictions, based on

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

T0495.449a_45

2008 Jul 10 12:02:00

First attempted model using undertaker

decoys/T0495.try1-opt2.pdb.gz

2008 Jul 10 13:58:40

Images of complete model in decoys/T0495.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

500x500 500x500 500x500

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