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Chapter
Biological Membranes and Membrane Proteins
We focus specifically on biological membranes and membrane proteins here because the physical interactions involved in maintaining their structure are relatively simple. Biological membranes consist of a lipid...
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Chapter
Analysis of Viruses, and the Fusion of Biology and Physics Through the Phase Diagram of Life
The study of genome sequences by the phase diagram of life is still in its early stages. One of the major remaining questions is whether viruses are living organisms in terms of their genome sequences. Both vi...
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Chapter
System Biology and Protein Structure Prediction by Computer
In the twenty-first century, whole-genome sequencing has become possible, and the amino acid sequence of all proteins can be revealed by genome sequences. If the functional dynamics of proteins can be written ...
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Chapter
Protein Distribution Analysis by a High-Precision Prediction System for Membrane Proteins
To determine the proportion of membrane proteins in the whole genome, we developed a membrane protein prediction system, SOSUI. This system used only the physical parameters of each amino acid (hydrophobicity ...
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Chapter
Changes in the Proportion of Membrane Proteins by Mutation Simulation
We Performed mutation simulations on the whole-genome sequence to determine how random mutations affect the proportion of membrane proteins. We performed two types of mutation simulations: one at the amino aci...
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Chapter
The Relationship Between Biology and Physics
If we look at individual molecules, the three-dimensional structure of DNA and proteins does not violate the laws of physics. However, if we look at the genome sequence from the elementary process of evolution...
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Chapter
Relationship Between the Phase Diagram of Life and Protein Distribution
A significant bias in the nucleotide composition of the first and second letters of the codon is a major characteristic of living organisms. There is a deep relationship between the bias in nucleotide composit...
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Chapter
Molecular Devices that Support Genome Processing
A variety of molecular devices are involved in proteins, which shape their structure and function. Among them, the group of molecular devices involved in genome processing is the most important. First, there a...
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Chapter
Biological Hierarchies and Various Mutations in Genome Sequences
One of the most remarkable phenomena in biology is higher evolution of organisms such as domains and kingdoms. How the genome sequence changed during the birth of a new domain, kingdom, or phyla of an organism...
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Chapter
Signal Transduction and Enzymatic Metabolic Reactions in Living Organisms
Protein structures are flexible and can change conformation dynamically, allowing them to perform a wide variety of functions. This allows for various phenomena at the molecular level, such as association-diss...
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Chapter
Similarities in Order Formation in Matter and Organisms
One of the major questions about living organisms is how the macroscopic organism as a whole maintains its stability. The elementary processes in the genome of an organism are neutral random mutations, and yet...
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Chapter
Organisms Viewed from Real Space and Sequence Space
Biology has a very long history. In the process, much research has been conducted on the classification of organisms, the discovery of microorganisms, and the structural analysis of biological macromolecules. ...
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Chapter
Habitable Zone in Nucleotide Composition Space: Phase Diagram of Life
We plotted the whole-genome sequences of many organisms in nucleotide composition space. As a result, all genome sequences were distributed in a very narrow region in the four-dimensional nucleotide compositio...
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Chapter
Three-Dimensional Structures of Proteins Responsible for Biological Functions
The smallest structures in the hierarchy of life are biopolymers. Among them, proteins encoded by DNA are fundamental. In this chapter, we will summarize the basic facts about proteins. Proteins are formed by ...
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Chapter
Definition of Species and Mysteries of Evolution
We have already discussed that the nucleotide composition at each letter position of the codon is highly skewed from a completely random composition, which allows organisms to exist in a very stable manner. Fu...
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Book
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Article
Open AccessNetwork-based characterization of drug-protein interaction signatures with a space-efficient approach
Characterization of drug-protein interaction networks with biological features has recently become challenging in recent pharmaceutical science toward a better understanding of polypharmacology.
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Article
Open AccessKampoDB, database of predicted targets and functional annotations of natural medicines
Natural medicines (i.e., herbal medicines, traditional formulas) are useful for treatment of multifactorial and chronic diseases. Here, we present KampoDB (http://wakanmoview.inm.u-toyama.ac.jp...
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Article
Open AccessPredicting inhibitory and activatory drug targets by chemically and genetically perturbed transcriptome signatures
Genome-wide identification of all target proteins of drug candidate compounds is a challenging issue in drug discovery. Moreover, emerging phenotypic effects, including therapeutic and adverse effects, are hea...
