Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Hydropathy Conformational Letter and its Substitution Matrix HP-CLESUM:
  an Application to Protein Structural Alignment   Motivation: Protein sequence world is discrete as 20 amino acids (AA) while
its structure world is continuous, though can be discretized into structural
alphabets (SA). In order to reveal the relationship between sequence and
structure, it is interesting to consider both AA and SA in a joint space.
However, such space has too many parameters, so the reduction of AA is
necessary to bring down the parameter numbers.
  Result: We've developed a simple but effective approach called entropic
clustering based on selecting the best mutual information between a given
reduction of AAs and SAs. The optimized reduction of AA into two groups leads
to hydrophobic and hydrophilic. Combined with our SA, namely conformational
letter (CL) of 17 alphabets, we get a joint alphabet called hydropathy
conformational letter (hp-CL). A joint substitution matrix with (17*2)*(17*2)
indices is derived from FSSP. Moreover, we check the three coding systems, say
AA, CL and hp-CL against a large database consisting proteins from family to
fold, with their performance on the TopK accuracy of both similar fragment pair
(SFP) and the neighbor of aligned fragment pair (AFP). The TopK selection is
according to the score calculated by the coding system's substitution matrix.
Finally, embedding hp-CL in a pairwise alignment algorithm, say CLeFAPS, to
replace the original CL, will get an improvement on the HOMSTRAD benchmark.

2
The categories of this paper are: math
17
The categories of this paper are: q-fin
31
The categories of this paper are: ao-sci
3
The categories of this paper are: physics
11
The categories of this paper are: hep-lat
14
The categories of this paper are: math-ph
25
The categories of this paper are: patt-sol
7
The categories of this paper are: hep-th
29
The categories of this paper are: funct-an
9
The categories of this paper are: nlin
13
The categories of this paper are: quant-ph
28
The categories of this paper are: alg-geom
4
The categories of this paper are: cond-mat
21
The categories of this paper are: adap-org
27
The categories of this paper are: comp-gas
34
The categories of this paper are: chem-ph