A5074475230- Protein Structure and Dynamics
- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Enzyme Structure and Function
- Genomics and Phylogenetic Studies
- Computational Drug Discovery Methods
- Mitochondrial Function and Pathology
- Bioinformatics and Genomic Networks
- Amoebic Infections and Treatments
- ATP Synthase and ATPases Research
- Microbial Metabolic Engineering and Bioproduction
- Chemical Synthesis and Analysis
- Glycosylation and Glycoproteins Research
- Cell death mechanisms and regulation
- Industrial Vision Systems and Defect Detection
- Pediatric Hepatobiliary Diseases and Treatments
- Microbial Natural Products and Biosynthesis
- Parasitic Infections and Diagnostics
- Marine Invertebrate Physiology and Ecology
- Microtubule and mitosis dynamics
- Fish Biology and Ecology Studies
- Molecular Biology Techniques and Applications
- RNA Research and Splicing
- Wnt/β-catenin signaling in development and cancer
- Pancreatitis Pathology and Treatment
National Institute of Advanced Industrial Science and Technology
2016-2025
Tokai University
2018-2024
The University of Tokyo
2011-2022
Tokyo Institute of Technology
2017-2022
The Open University of Japan
2022
National Institute of Infectious Diseases
2021
New Tokyo Hospital
2021
Koto Hospital
2021
Keio University
2018
University of Virginia
2018
Abstract Summary We report an update for the MAFFT multiple sequence alignment program to enable parallel calculation of large numbers sequences. The G-INS-1 option was recently reported have higher accuracy than other methods data, but this method has been impractical most large-scale analyses, due requirement computational resources. introduce a scalable variant, G-large-INS-1, which equivalent and is applicable 50 000 or more Availability implementation This feature available in versions...
Abstract Motivation In bioinformatics, machine learning-based methods that predict the compound–protein interactions (CPIs) play an important role in virtual screening for drug discovery. Recently, end-to-end representation learning discrete symbolic data (e.g. words natural language processing) using deep neural networks has demonstrated excellent performance on various difficult problems. For CPI problem, are provided as data, i.e. compounds represented graphs where vertices atoms, edges...
Mitochondria provide numerous essential functions for cells and their dysfunction leads to a variety of diseases. Thus, obtaining complete mitochondrial proteome should be crucial step toward understanding the roles mitochondria. Many proteins have been identified experimentally but list is not yet available. To fill this gap, methods computationally predict from amino acid sequence developed are widely used, unfortunately, accuracy far perfect. Here we describe MitoFates, an improved...
Large multiple sequence alignments (MSAs), consisting of thousands sequences, are becoming more and common, due to advances in sequencing technologies. The MAFFT MSA program has several options for building large MSAs, but their performances have not been sufficiently assessed yet, because realistic benchmarking MSAs difficult. Recently, such assessments made possible through the HomFam ContTest benchmark protein datasets. Along with development these datasets, an interesting theory was...
Mitochondria fulfill central functions in cellular energetics, metabolism, and signaling. The outer membrane translocator complex (the TOM complex) imports most mitochondrial proteins, but its architecture is unknown. Using a cross-linking approach, we mapped the active down to single amino acid residues, revealing different transport paths for preproteins through Tom40 channel. An N-terminal segment of passes from cytosol channel recruit chaperones intermembrane space that guide transfer...
An amino acid index is a set of 20 numerical values representing any the different physicochemical and biochemical properties adds. As follow-up to previous study, we have increased size database, which currently contains 402 published indices, re-performed single-linkage cluster analysis. The results basically confirmed findings. Another important feature acids that can be represented numerically similarity between them. Thus, matrix, also called mutation 20×20 used for protein sequence...
We present the results for CAPRI Round 30, first joint CASP-CAPRI experiment, which brought together experts from protein structure prediction and protein-protein docking communities. The comprised 25 targets amongst those submitted CASP11 experiment of 2014. included mostly homodimers, a few homotetramers, two heterodimers, chains that could readily be modeled using templates Protein Data Bank. On average 24 groups 7 CASP predictions each target, 12 per target participated in scoring...
It is well known that remnants of partial or whole copies mitochondrial DNA, as Nuclear MiTochondrial sequences (NUMTs), are found in nuclear genomes. Since genome have become available, many bioinformatics studies identified putative NUMTs and from those attempted to infer the factors involved NUMT creation. These conclude represent randomly chosen regions genome. There less consensus regarding insertion sites - previous discussed possible role retrotransposons, but some recent ones...
Ustiloxins were found recently to be the first example of cyclic peptidyl secondary metabolites that are ribosomally synthesized in filamentous fungi. In this work, two function-unknown genes (ustYa/ustYb) gene cluster for ustiloxins from Aspergillus flavus experimentally involved cyclization peptide. Their homologous observed mainly fungi and mushrooms. They have "HXXHC" motifs might form active sites. Computational genome analyses showed these frequently located near candidate ribosomal...
Two doses of Pfizer/BioNTech BNT162b2 mRNA vaccine elicit robust severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-neutralizing antibodies with frequent adverse events. Here, by applying a high-dimensional immune profiling on 92 vaccinees, we identify six vaccine-induced dynamics that correlate the amounts neutralizing antibodies, severity events, or both. The early natural killer (NK)/monocyte subsets (CD16+ NK cells, CD56high and non-classical monocytes), dendritic cell (DC)...
The ABC transporter is a major class of cellular translocation machinery in all bacterial species encoded the largest set paralogous genes. operon structure frequently found for genes three molecular components: ATP-binding protein, membrane and substrate-binding protein. Here, we developed an “ortholog group table” by comparison classification known putative transporters complete genomes seven microorganisms. Our procedure was to first search classify most conserved protein components...
Apoptotic cell death is a defining and ubiquitous characteristic of metazoans, but its evolutionary origins are unclear. Although Caenorhabditis Drosophila played key roles in establishing the molecular bases apoptosis, it now clear that pathways these animals do not reflect ancestral characteristics. Conversely, recent work suggests apoptotic networks cnidarians may be complex vertebrate-like, hence characterization complement representatives basal cnidarian class Anthozoa will help us to...
Abstract Gibberellin (GA) is a major hormone for plant growth and development. GA response derived from the degradation of DELLA repressor proteins after GA-dependent complex formation GID1 receptor with DELLA. Genistein known tyrosine (Tyr) kinase inhibitor inhibits degradation. However, biological role Tyr phosphorylation on remains unclear. Here, we demonstrate that GARU (GA RING E3 ubiquitin ligase) mediates ubiquitin-dependent GID1, TAGK2 Tyr-kinase target genistein GARU–GID1A...
Protein transport systems are fundamentally important for maintaining mitochondrial function. Nevertheless, protein translocases such as the kinetoplastid ATOM complex have recently been shown to vary in eukaryotic lineages. Various evolutionary hypotheses formulated explain this diversity. To resolve any contradiction, estimating primitive state and clarifying changes from that necessary. Here, we present more likely models of translocases, specifically translocase outer membrane (TOM)...
Abstract Background Recently developed methods of protein contact prediction, a crucially important step for structure depend heavily on deep neural networks (DNNs) and multiple sequence alignments (MSAs) target proteins. Protein sequences are accumulating to an increasing degree such that abundant construct MSA readily obtainable. Nevertheless, many cases present different ends the number can be included in used prediction. The might degrade prediction results, but opportunities remain...
Abstract Summary: We present FORTE, a profile–profile comparison tool for protein fold recognition. Users can submit sequence to explore the possibilities of structural similarity existing in known structures. Results are reported via email form pairwise alignments. Availability: The server is available at http://www.cbrc.jp/forte/
Peroxisomes are responsible for several pathways in primary metabolism, including beta-oxidation and lipid biosynthesis. PEX1 PEX6 hexameric AAA-type ATPases, both of which indispensable targeting over 50 peroxisomal resident proteins from the cytosol to peroxisomes. Although tandem AAA-ATPase domains central region highly similar, N-terminal sequences unique. To better understand distinct molecular function these two proteins, we analyzed unique domain (NTD) PEX1. Extensive computational...
Numerous potential ligand-binding sites are available today, along with hundreds of thousands known binding observed in the PDB. Exhaustive similarity search for such vastly numerous site pairs is useful to predict protein functions and enable rapid screening target proteins drug design. Existing databases offer limited scale. For example, SitesBase covers only ∼33 000 sites. Inferring function discovery purposes, however, demands a much more comprehensive database including putative-binding...
Abstract Motivation: Although many amino acid substitution matrices have been developed, it has not well understood which is the best for similarity searches, especially remote homology detection. Therefore, we collected information related to existing matrices, condensed and derived a novel matrix that can detect more than ever. Results: Using principal component analysis with benchmarks, developed matrix, designate as MIQS. The detection performance of MIQS validated compared general...