SAM_T02 Results for T0513

Please cite the following papers:

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
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
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.

When SAM_T02 finishes, 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

Description

Link to file

Date

Inputs and Multiple Alignments

Submitted sequence(s)

T0513.a2m

2008 Jul 18 9:13:49

SAM_T02 multiple alignment in a2m format

T0513.t2k.a2m.gz

2008 Jul 18 9:18:55

SAM_T02 multiple alignment in pretty html format

T0513.t2k.pa.html

2008 Jul 18 9:19:31

SAM_T02 target hidden Markov model

T0513.t2k.w0.5.mod

2008 Jul 18 9:19:35

SAM_T02 multiple alignment---sequence logo (eps format) (pdf format)

T0513.t2k.w0.5-logo

2008 Jul 18 9:20:40

Secondary Structure Prediction (Explanation of secondary-structure predictions)

Str structure prediction (rdb format) (seq format)

T0513.t2k.str

2008 Jul 18 9:20:42

Str prediction---sequence logo (eps format) (pdf format)

T0513.t2k.str-logo

2008 Jul 18 9:20:47

DSSP EBGHSTL structure prediction (rdb format) (seq format)

T0513.t2k.dssp-ebghstl

2008 Jul 18 9:20:37

DSSP EBGHSTL prediction---sequence logo (eps format) (pdf format)

T0513.t2k.dssp-ebghstl-logo

2008 Jul 18 9:20:51

Stride EBGHTL structure prediction (rdb format) (seq format)

T0513.t2k.stride-ebghtl

2008 Jul 18 9:20:53

Stride EBGHTL prediction---sequence logo (eps format) (pdf format)

T0513.t2k.stride-ebghtl-logo

2008 Jul 18 9:20:56

DSSP 3-value prediction (rdb format)

T0513.t2k.dssp-ehl2

2008 Jul 18 9:20:57

DSSP 3-value prediction---sequence logo (eps format) (pdf format)

T0513.t2k.dssp-ehl2-logo

2008 Jul 18 9:21:02

Target model scores

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

T0513.t2k.100-30-dssp-ebghstl-target-scores.html

2008 Jul 18 9:28:42

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

T0513.t2k.100-30-stride-ebghtl-target-scores.html

2008 Jul 18 9:36:18

Annotated amino acid/100-30-str two-track target model scores

T0513.t2k.100-30-str-target-scores.html

2008 Jul 18 9:43:53

Annotated amino acid single-track target model scores of PDB

T0513.t2k.w0.5-target-scores.html

2008 Jul 18 9:53:07

Template model scores

Annotated template model scores

T0513.template-lib-scores.html

2008 Jul 18 10:05:19

Top Hits

Best scoring hits from all models

T0513.best-scores.html

2008 Jul 18 10:05:21

Alignments for Top Hits

T02 Many Alignments Summary

T0513.many_alignments.html

2008 Jul 18 10:15:06

T02 Top Models Summary

T0513.top_reported_alignments.html

2008 Jul 18 10:15:26

Please cite the following papers:

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
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
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.

SAM_T02 web system designed by Rachel Karchin and Kevin Karplus
Maintained by Kevin Karplus:

karplus@soe.ucsc.edu