Biomedical subjects

H Tashimo

Publications and source records attributed to H Tashimo.

2 recordsLinked to original sources

PubMed1998

Linear programming based approach to the derivation of a contact potential for protein threading.

This paper proposes a novel method of deriving a contact potential (a pair score function) for protein threading. In this method, the constraint that the score of the native threading is minimum over all possible threadings is expressed in a form of linear inequalities, and then parameters defining the contact potential are determined by applying a program package of linear programming. The most important advantage of this method over the previous methods is that this method can learn a score function from a small number of training data. The proposed method was evaluated using Lathrop and Smith's algorithm for finding optimal threadings and was shown to be effective for computing nearly correct threadings.

Amino Acid Sequence↗

PubMed1996

Protein structure comparison using representation by line segment sequences.

This paper proposes a new comparison method of tertiary protein structures. The method consists of two parts. First, a sequence of line segments which approximates each tertiary protein structure is computed. Then, an alignment of the sequences of line segments corresponding to input structures is computed. The proposed method is considered as an intermediate one between two comparison methods: a method based on topology diagram and a method based on structure alignment. Moreover it takes less CPU time than structure alignment methods because most structures are represented by means of sequences of at most 100 line segments. The effectiveness of the method is confirmed through a comparison with a previous method and an application to database searching for similar structures.

Algorithms↗