SAM_T06 Results for T0617

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

T0617.a2m

2010 Jul 2 9:12:48

README file

README

2010 Jul 2 10:46:36

Quick blastp of non-redundant PDB

T0617.pdb_blast.txt

2010 Jul 2 10:46:52

Multiple alignment

SAM_t04 multiple alignment in a2m format

T0617.t04.a2m.gz

2010 Jul 2 11:10:04

SAM_t04 multiple alignment in pretty html format

T0617.t04.pa.html

2010 Jul 2 11:12:13

SAM_t04 target hidden Markov model

T0617.t04.w0.5.mod

2010 Jul 2 11:12:23

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

T0617.t04.w0.5-logo

2010 Jul 2 11:12:39

Script for highlighting in rasmol

conserved_t04

2010 Jul 2 11:12:40

SAM_t2k multiple alignment in a2m format

T0617.t2k.a2m.gz

2010 Jul 2 11:26:29

SAM_t2k multiple alignment in pretty html format

T0617.t2k.pa.html

2010 Jul 2 11:28:34

SAM_t2k target hidden Markov model

T0617.t2k.w0.5.mod

2010 Jul 2 11:28:48

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

T0617.t2k.w0.5-logo

2010 Jul 2 11:29:11

Script for highlighting in rasmol

conserved_t2k

2010 Jul 2 11:29:12

Secondary Structure Prediction (Explanation of secondary-structure predictions)

str2 structure prediction (rdb format) (seq format)

T0617.t04.str2

2010 Jul 2 11:12:33

Script for T0617.t04.str2 coloring in rasmol

T0617.t04.str2-color.rasmol

2010 Jul 2 11:29:16

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

T0617.t04.str2-logo

2010 Jul 2 11:29:40

str2 structure prediction (rdb format) (seq format)

T0617.t2k.str2

2010 Jul 2 11:29:04

Script for T0617.t2k.str2 coloring in rasmol

T0617.t2k.str2-color.rasmol

2010 Jul 2 11:29:41

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

T0617.t2k.str2-logo

2010 Jul 2 11:29:51

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

T0617.t04.stride-ebghtl

2010 Jul 2 11:29:56

Script for T0617.t04.stride-ebghtl coloring in rasmol

T0617.t04.stride-ebghtl-color.rasmol

2010 Jul 2 11:29:57

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

T0617.t04.stride-ebghtl-logo

2010 Jul 2 11:30:09

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

T0617.t2k.stride-ebghtl

2010 Jul 2 11:30:12

Script for T0617.t2k.stride-ebghtl coloring in rasmol

T0617.t2k.stride-ebghtl-color.rasmol

2010 Jul 2 11:30:13

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

T0617.t2k.stride-ebghtl-logo

2010 Jul 2 11:30:22

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

T0617.t04.dssp-ebghstl

2010 Jul 2 11:30:26

Script for T0617.t04.dssp-ebghstl coloring in rasmol

T0617.t04.dssp-ebghstl-color.rasmol

2010 Jul 2 11:30:27

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

T0617.t04.dssp-ebghstl-logo

2010 Jul 2 11:30:34

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

T0617.t2k.dssp-ebghstl

2010 Jul 2 11:30:38

Script for T0617.t2k.dssp-ebghstl coloring in rasmol

T0617.t2k.dssp-ebghstl-color.rasmol

2010 Jul 2 11:30:39

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

T0617.t2k.dssp-ebghstl-logo

2010 Jul 2 11:30:43

alpha structure prediction (rdb format) (seq format)

T0617.t04.alpha

2010 Jul 2 11:30:48

Script for T0617.t04.alpha coloring in rasmol

T0617.t04.alpha-color.rasmol

2010 Jul 2 11:30:49

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

T0617.t04.alpha-logo

2010 Jul 2 11:30:54

alpha structure prediction (rdb format) (seq format)

T0617.t2k.alpha

2010 Jul 2 11:30:58

Script for T0617.t2k.alpha coloring in rasmol

T0617.t2k.alpha-color.rasmol

2010 Jul 2 11:30:59

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

T0617.t2k.alpha-logo

2010 Jul 2 11:31:06

bys structure prediction (rdb format) (seq format)

T0617.t04.bys

2010 Jul 2 11:31:11

Script for T0617.t04.bys coloring in rasmol

T0617.t04.bys-color.rasmol

2010 Jul 2 11:31:11

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

T0617.t04.bys-logo

2010 Jul 2 11:31:18

bys structure prediction (rdb format) (seq format)

T0617.t2k.bys

2010 Jul 2 11:31:23

Script for T0617.t2k.bys coloring in rasmol

T0617.t2k.bys-color.rasmol

2010 Jul 2 11:31:24

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

T0617.t2k.bys-logo

2010 Jul 2 11:31:32

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

T0617.t04.dssp-ehl2

2010 Jul 2 11:31:37

Script for T0617.t04.dssp-ehl2 coloring in rasmol

T0617.t04.dssp-ehl2-color.rasmol

2010 Jul 2 11:31:38

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

T0617.t04.dssp-ehl2-logo

2010 Jul 2 11:31:45

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

T0617.t2k.dssp-ehl2

2010 Jul 2 11:31:48

Script for T0617.t2k.dssp-ehl2 coloring in rasmol

T0617.t2k.dssp-ehl2-color.rasmol

2010 Jul 2 11:31:48

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

T0617.t2k.dssp-ehl2-logo

2010 Jul 2 11:31:53

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

T0617.dssp-ehl2

2010 Jul 2 11:31:57

Script for T0617.dssp-ehl2 coloring in rasmol

T0617.dssp-ehl2-color.rasmol

2010 Jul 2 11:31:57

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

T0617.dssp-ehl2-logo

2010 Jul 2 11:32:03

CB_burial_14_7 structure prediction (rdb format) (seq format)

T0617.t04.CB_burial_14_7

2010 Jul 2 11:32:09

Script for T0617.t04.CB_burial_14_7 coloring in rasmol

T0617.t04.CB_burial_14_7-color.rasmol

2010 Jul 2 11:32:09

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

T0617.t04.CB_burial_14_7-logo

2010 Jul 2 11:32:15

CB_burial_14_7 structure prediction (rdb format) (seq format)

T0617.t2k.CB_burial_14_7

2010 Jul 2 11:32:19

Script for T0617.t2k.CB_burial_14_7 coloring in rasmol

T0617.t2k.CB_burial_14_7-color.rasmol

2010 Jul 2 11:32:19

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

T0617.t2k.CB_burial_14_7-logo

2010 Jul 2 11:32:25

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

T0617.t04.near-backbone-11

2010 Jul 2 11:32:31

Script for T0617.t04.near-backbone-11 coloring in rasmol

T0617.t04.near-backbone-11-color.rasmol

2010 Jul 2 11:32:31

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

T0617.t04.near-backbone-11-logo

2010 Jul 2 11:32:38

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

T0617.t2k.near-backbone-11

2010 Jul 2 11:32:43

Script for T0617.t2k.near-backbone-11 coloring in rasmol

T0617.t2k.near-backbone-11-color.rasmol

2010 Jul 2 11:32:44

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

T0617.t2k.near-backbone-11-logo

2010 Jul 2 11:32:51

Target model scores

amino acid single-track target model scores of PDB

T0617.t04-w0.5-scores.html

2010 Jul 2 11:39:02

amino acid single-track target model scores of PDB

T0617.t2k-w0.5-scores.html

2010 Jul 2 11:45:18

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

T0617.t2k-100-30-str2-scores.html

2010 Jul 2 11:48:08

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

T0617.t2k-100-30-stride-ebghtl-scores.html

2010 Jul 2 11:50:59

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

T0617.t2k-100-30-dssp-ebghstl-scores.html

2010 Jul 2 11:53:47

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

T0617.t2k-100-30-alpha-scores.html

2010 Jul 2 11:56:38

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

T0617.t2k-100-30-bys-scores.html

2010 Jul 2 11:59:24

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

T0617.t2k-100-30-dssp-ehl2-scores.html

2010 Jul 2 12:02:07

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

T0617.t2k-100-30-CB_burial_14_7-scores.html

2010 Jul 2 12:04:54

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

T0617.t2k-100-30-near-backbone-11-scores.html

2010 Jul 2 12:07:44

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

T0617.t2k-100-40-40-str2+CB_burial_14_7-scores.html

2010 Jul 2 12:10:42

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

T0617.t2k-80-60-80-str2+near-backbone-11-scores.html

2010 Jul 2 12:13:42

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

T0617.t04-100-30-str2-scores.html

2010 Jul 2 12:16:18

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

T0617.t04-100-30-stride-ebghtl-scores.html

2010 Jul 2 12:18:57

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

T0617.t04-100-30-dssp-ebghstl-scores.html

2010 Jul 2 12:21:36

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

T0617.t04-100-30-alpha-scores.html

2010 Jul 2 12:24:12

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

T0617.t04-100-30-bys-scores.html

2010 Jul 2 12:26:52

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

T0617.t04-100-30-dssp-ehl2-scores.html

2010 Jul 2 12:29:27

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

T0617.t04-100-30-CB_burial_14_7-scores.html

2010 Jul 2 12:32:02

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

T0617.t04-100-30-near-backbone-11-scores.html

2010 Jul 2 12:34:39

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

T0617.t04-100-40-40-str2+CB_burial_14_7-scores.html

2010 Jul 2 12:37:24

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

T0617.t04-80-60-80-str2+near-backbone-11-scores.html

2010 Jul 2 12:40:14

Template model scores

Annotated t04 template model scores

T0617.t04-template-lib-scores.html

2010 Jul 2 15:47:25

Annotated t2k template model scores

T0617.t2k-template-lib-scores.html

2010 Jul 2 17:38:01

Top Hits

Best scoring hits from t04 HMMs

T0617.t04.best-scores.html

2010 Jul 2 17:38:06

Best scoring hits from t2k HMMs

T0617.t2k.best-scores.html

2010 Jul 2 17:38:09

Best scoring hits from combining t04 t2k

T0617.best-scores.html

2010 Jul 2 17:38:12

Alignments for Top Hits

Top alignments from t04 hits

T0617.t04.top_reported_alignments.html

2010 Jul 2 19:16:42

Top alignments from t2k hits

T0617.t2k.top_reported_alignments.html

2010 Jul 2 19:17:03

Top alignments from combined hits

T0617.top_reported_alignments.html

2010 Jul 2 19:17:16

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

all-align

2010 Jul 2 19:18:13

Undertaker (3d) files

Undertaker input for top t04 alignments

T0617.t04.undertaker-align.under

2010 Jul 2 19:18:15

Undertaker input for top t2k alignments

T0617.t2k.undertaker-align.under

2010 Jul 2 19:18:15

Undertaker input for top combined alignments

T0617.undertaker-align.under

2010 Jul 2 19:18:16

PDB file with model(s) for top alignments

T0617.undertaker-align.pdb.gz

2010 Jul 2 19:20:37

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) T0617.t04.many.frag.gz 2010 Jul 2 19:21:28

Fragment list for undertaker (from fragfinder) T0617.t2k.many.frag.gz 2010 Jul 2 19:22:07

Contact predictions, based on

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

T0617.449a_45

2010 Jul 2 19:26:23

First attempted model using undertaker

decoys/T0617.try1-opt2.pdb.gz

2010 Jul 2 23:28:50

Images of complete model in decoys/T0617.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