[From
2008-01-02 to 2008-12-29]
2008-12-29:
Add the "See more ..." section: (1) Robustness and (2)
Sensitivity.
See EXAMPLES
(Encoding/Decoding) > Statistics.
2008-12-23:
Add (4) Flexibility,
(5) Code pref.,
and (6) Freq. dist..
of the "statistics of the D2 code" section.
See EXAMPLES
(Encoding/Decoding) > Statistics.
2008-12-22:
Add (3) Selectivity of
the "statistics of the D2 code" section.
See EXAMPLES
(Encoding/Decoding) > Statistics.
2008-12-21:
Add (1) Robustness
and (2) Sensitivity
of the "statistics of the D2 code" section.
See EXAMPLES
(Encoding/Decoding) > Statistics.
2008-12-03:
Add examples of HIV-1 PR variants
(NMR structures / 1BVE (DIMER))
See EXAMPLES
(Prediction/Alignment/Others) > Structural alignment
> HIV-1 PR variants.
2008-12-01:
Add examples of HIV-1 PR variants
(space group P61)
See EXAMPLES
(Prediction/Alignment/Others) > Structural alignment
> HIV-1 PR variants.
2008-11-29: Enable the "nowrap" option in table
cells of D2 code and DSSP sequences
See EXAMPLES
(Prediction/Alignment/Others) > Structural alignment
> Fold
change and Multi-struct. sequences.
2008-11-29:
Add examples of HIV-1 PR variants
See EXAMPLES
(Prediction/Alignment/Others) > Structural alignment.
2008-10-25:
Add manuscript of "Systematic analysis of local flexibility of
multiple-structure proteins."
See PAPERS /
Protein structure and RNA aptamer structure.
2008-09-27: Add
Mathematical definitions in the Research section (2).
2008-09-14: Add [NOTE] in the Research section (2a).
2008-09-11: Add section (5) Specification of hetero numbers. See the
Research page.
2008-09-11: Add
examples of surface flow on a discrete manifold. See the Research
section (2a).
2008-09-11: Renew
the Research page.
2008-08-12: An
alias of the 5-tile code is proposed: "D2 code."
See the Research section (1).
2008-08-12:
Correction in the definition of chameleon sequences: secondary
structure ==> "regular" secondary structure.
See EXAMPLES
(Prediction/Alignment/Others) > Multiple-structure
sequences.
2008-07-29:
New
release, ProteinViewer ver. 0.6. (support black and white
spheres and others)
2008-06-09:
Add examples of proteins with short/mid-sized/long variable
regions.
See EXAMPLES
(Prediction/Alignment/Others) > Multiple-structure
sequences.
2008-06-08: Add a
frequency distribution table for the variable regions of length 1
See EXAMPLES
(Prediction/Alignment/Others) > Multiple-structure
sequences.
2008-06-07: Add
Length frequency distribution of variable regions (or "chameleon
sequences")
See EXAMPLES
(Prediction/Alignment/Others) > Multiple-structure
sequences.
2008-05-30: Add
new examples (Multiple-structure sequences: cluster 31, ..., cluster
60).
See EXAMPLES
(Prediction/Alignment/Others).
2008-05-24:
Add
new examples (Multiple-structure sequences: cluster 11, ..., cluster
30).
See EXAMPLES
(Prediction/Alignment/Others).
2008-05-20:
New
release, ProteinViewer ver. 0.5. (fix minor bug)
2008-05-18: Add
new examples (Multiple-structure sequences: cluster 1, ..., cluster 10).
See EXAMPLES
(Prediction/Alignment/Others).
2008-05-14: Add
new examples (Fold change: 2., 3., and 4.).
See EXAMPLES
(Prediction/Alignment/Others).
2008-05-11:
Add
new examples (Fold change: 1. Addition/Deletion/Substitution ).
See EXAMPLES
(Prediction/Alignment/Others).
2008-05-05: New
release, ComSubstruct ver. 0.5. (print out
the distribution of |LSC|/|target protein| if "-p1" is specified)
2008-05-01: New
release, ComSubstruct ver. 0.4. (support
domain search: the "-p" option)
2008-04-20: New
release, fragment-to-5-tile-code
conversion tables of ASTRAL dataset 1.73
95% are available.
See PROGRAMS/NtileCodePredictor
2008-04-19: New
release, ComSubstruct ver. 0.3a. (fix a bug of
incorrect output)
2008-04-19: New
release, "target_ASTRAL173.code" (ASTRAL dataset 1.73) is available.
See PROGRAMS/ComSubstruct
2008-04-18: New
release, ComSubstruct ver. 0.3. (report more
than one best matches: the "-b" option)
2008-04-17: Add
new examples (ASTRAL search by ComSubstruct).
See EXAMPLES
(Prediction/Alignment/Others).
2008-04-04: New
release, ComSubstruct ver. 0.2a. (fix a
bug of
output file name without '\0')
2008-04-03: New
release, ComSubstruct ver. 0.2. (support
subsequence comparison. See the PROGRAMS section)
2008-04-01: New
release, NtileCodePredictor ver. 0.3. (output a ".code" file.
See the PROGRAMS section)
2008-03-31: New
release, ComSubstruct ver. 0.1. (compute the longest common
subsequences. See the PROGRAMS section)
2008-02-27: New
release, ProteinEncoder ver. 0.7. (support any alternative
location
identifier)
2008-01-30: More entries are filled in the table (EXAMPLES / Decoding /
length 9).
2008-01-21: Add
new
examples (EXAMPLES / Encoding / Basic ideas).
2008-01-20: Add
new examples (EXAMPLES / Decoding / length 9).
2008-01-19: Add
new examples (EXAMPLES / Decoding / length 7).
2008-01-18: Add
new examples (EXAMPLES / Decoding / length 5).
2008-01-16: New
release, TetraSeqGen ver. 0.2. (Bug fix for the "-t" option)
2008-01-04: Add
new
examples (EXAMPLES / Alignment / Basic ideas).
2008-01-04: Add
new
examples (EXAMPLES / Decoding / Basic ideas).
2008-01-04: New
release, TetraSeqGen ver. 0.1.
2008-01-04:
New
release, ProteinViewer ver. 0.4. (support TeraSeqGen)
2008-01-02: New
release, ProteinEncoder ver. 0.6. (support artificial
polygonal chains, such as straight line, self-intersections, and so on)
2008-01-02:
New
release, ProteinSplitter ver. 0.2. (minor bug fix)