Related papers: Binary Assignments of Amino Acids from Pattern Con…

Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code,…

This paper deals with the binary classification task when the target class has the lower probability of occurrence. In such situation, it is not possible to build a powerful classifier by using standard methods such as logistic regression,…

Recently, some infinite families of minimal and optimal binary linear codes were constructed from simplicial complexes by Hyun {\em et al.} We extend this construction method to arbitrary posets. Especially, anti-chains are corresponded to…

This paper presents a novel Differential Evolution algorithm for protein folding optimization that is applied to a three-dimensional AB off-lattice model. The proposed algorithm includes two new mechanisms. A local search is used to improve…

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…

The primitive data for deducing the Miyazawa-Jernigan contact energy or BLOSUM score metrix are the pair frequency counts. Each amino acid corresponds to a distribution. Taking the Kullback-Leibler distance of two probability distributions…

We consider the problem of learning optimal binary classification trees. Literature on the topic has burgeoned in recent years, motivated both by the empirical suboptimality of heuristic approaches and the tremendous improvements in…

We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those…

We propose an automated protocol for designing the energy landscape of a protein energy function by optimizing its parameters. The parameters are optimized so that not only the global minimum energy conformation becomes native-like, but…

This paper proposes a binarization scheme for vectors of high dimension based on the recent concept of anti-sparse coding, and shows its excellent performance for approximate nearest neighbor search. Unlike other binarization schemes, this…

We introduce a protein language model for determining the complete sequence of a peptide based on measurement of a limited set of amino acids. To date, protein sequencing relies on mass spectrometry, with some novel edman degregation based…

Protein one-dimensional (1D) structures such as secondary structure and contact number provide intuitive pictures to understand how the native three-dimensional (3D) structure of a protein is encoded in the amino acid sequence. However, it…

Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for…

To confer high specificity and affinity in binding, contacts at interfaces between two interacting macromolecules are expected to exhibit pair preferences for types of atoms or residues. Here we quantify these preferences by measuring the…

The decision tree is one of the most fundamental programming abstractions. A commonly used type of decision tree is the alphabetic binary tree, which uses (without loss of generality) ``less than'' versus ''greater than or equal to'' tests…

Evolutionally conserved quantity that specifies folding nuclei is pursued by a case study for a small protein (PDB code: 1ten). First it is demonstrated that the sequences of amino acids at folding nuclei are not conserved. Then 3D…

Factorization Machines (FM), a general predictor that can efficiently model feature interactions in linear time, was primarily proposed for collaborative recommendation and have been broadly used for regression, classification and ranking…

Within bioinformatics, the textual alignment of amino acid sequences has long dominated the determination of similarity between proteins, with all that implies for shared structure, function and evolutionary descent. Despite the relative…

Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…

The problem of super-resolution is concerned with the reconstruction of temporally/spatially localized events (or spikes) from samples of their convolution with a low-pass filter. Distinct from prior works which exploit sparsity in…