scholarly journals KEGG: integrating viruses and cellular organisms

2020 ◽  
Vol 49 (D1) ◽  
pp. D545-D551 ◽  
Author(s):  
Minoru Kanehisa ◽  
Miho Furumichi ◽  
Yoko Sato ◽  
Mari Ishiguro-Watanabe ◽  
Mao Tanabe
Keyword(s):  
Kegg Pathway ◽  
Human Gene ◽  
Building Blocks ◽  
Molecular Networks ◽  
Gene Variants ◽  
Genome Sequences ◽  
Network Systems ◽  
Network Database ◽  
Molecular Building Blocks ◽  
Functional Orthologs

Abstract KEGG (https://www.kegg.jp/) is a manually curated resource integrating eighteen databases categorized into systems, genomic, chemical and health information. It also provides KEGG mapping tools, which enable understanding of cellular and organism-level functions from genome sequences and other molecular datasets. KEGG mapping is a predictive method of reconstructing molecular network systems from molecular building blocks based on the concept of functional orthologs. Since the introduction of the KEGG NETWORK database, various diseases have been associated with network variants, which are perturbed molecular networks caused by human gene variants, viruses, other pathogens and environmental factors. The network variation maps are created as aligned sets of related networks showing, for example, how different viruses inhibit or activate specific cellular signaling pathways. The KEGG pathway maps are now integrated with network variation maps in the NETWORK database, as well as with conserved functional units of KEGG modules and reaction modules in the MODULE database. The KO database for functional orthologs continues to be improved and virus KOs are being expanded for better understanding of virus-cell interactions and for enabling prediction of viral perturbations.

Porous molecular networks formed by the self-assembly of positively-charged trigonal building blocks at the liquid/solid interfaces

2014 ◽  
Vol 50 (57) ◽  
pp. 7683-7685 ◽  
Author(s):  
Kazukuni Tahara ◽  
Maria L. Abraham ◽  
Kosuke Igawa ◽  
Keisuke Katayama ◽  
Iris M. Oppel ◽  
...  
Keyword(s):  
Self Assembly ◽  
Van Der Waals ◽  
Building Blocks ◽  
The Self ◽  
Van Der Waals Interaction ◽  
Molecular Networks ◽  
Alkyl Chains ◽  
Molecular Building Blocks ◽  
Positively Charged

Tris-(2-hydroxybenzylidene)triaminoguanidinium salts having six alkyl chains with proper spacing served as new molecular building blocks for the formation of porous honeycomb networks by van der Waals interaction between interdigitated alkyl chains at the liquid/graphite interfaces.

A First Principles Approach for Partitioning Linear Response Properties into Additive and Cooperative Contributions

2018 ◽  
Author(s):  
Daniel Lambrecht ◽  
Eric Berquist
Keyword(s):  
First Principles ◽  
Linear Response ◽  
Building Blocks ◽  
Field Method ◽  
Response Property ◽  
Response Properties ◽  
Consistent Field ◽  
Molecular Building Blocks ◽  
Self Consistent ◽  
Self Consistent Field

We present a first principles approach for decomposing molecular linear response properties into orthogonal (additive) plus non-orthogonal/cooperative contributions. This approach enables one to 1) identify the contributions of molecular building blocks like functional groups or monomer units to a given response property and 2) quantify cooperativity between these contributions. In analogy to the self consistent field method for molecular interactions, SCF(MI), we term our approach LR(MI). The theory, implementation and pilot data are described in detail in the manuscript and supporting information.

A new molecular building blocks: Synthesis, crystal structure, magnetic and spectroscopic properties of Cu(II) and Ni(II) macrocyclic complexes

Polyhedron ◽  
2011 ◽  
Vol 30 (15) ◽  
pp. 2550-2557 ◽  
Author(s):  
Katarzyna Suracka ◽  
Alina Bieńko ◽  
Jerzy Mroziński ◽  
Rafał Kruszyński ◽  
Dariusz Bieńko ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Building Blocks ◽  
Spectroscopic Properties ◽  
Macrocyclic Complexes ◽  
Molecular Building Blocks

scholarly journals Acid-Catalysed Liquid-to-Solid Transitioning of Arylazoisoxazole Photoswitches

2021 ◽  
Author(s):  
Luuk Kortekaas ◽  
Julian Simke ◽  
Niklas Arndt ◽  
Marcus Böckmann ◽  
Nikos Doltsinis ◽  
...  
Keyword(s):  
Building Blocks ◽  
Vital Role ◽  
Responsive Materials ◽  
Molecular Building Blocks ◽  
Physical Changes

Molecular photoswitches play a vital role in the development of responsive materials. These molecular building blocks are particularly attractive when multiple stimuli can be combined to bring about physical changes,...

A Molecular Artisans Guide to Supramolecular Coordination Complexes and Metal Organic Frameworks

2015 ◽  
Vol 03 (01n02) ◽  
pp. 1540004 ◽  
Author(s):  
Xialu Wu ◽  
David J. Young ◽  
T. S. Andy Hor
Keyword(s):  
Chemical Reactivity ◽  
Metal Organic Frameworks ◽  
Building Blocks ◽  
Coordination Complexes ◽  
Large Molecules ◽  
Molecular Building Blocks ◽  
Supramolecular Coordination ◽  
Metal Organic ◽  
Molecular Synthesis ◽  
And Function

As molecular synthesis advances, we are beginning to learn control of not only the chemical reactivity (and function) of molecules, but also of their interactions with other molecules. It is this basic idea that has led to the current explosion of supramolecular science and engineering. Parallel to this development, chemists have been actively pursuing the design of very large molecules using basic molecular building blocks. Herein, we review the general development of supramolecular chemistry and particularly of two new branches: supramolecular coordination complexes (SCCs) and metal organic frameworks (MOFs). These two fields are discussed in detail with typical examples to illustrate what is now possible and what challenges lie ahead for tomorrow's molecular artisans.

scholarly journals Inverse Design of Nanoporous Crystalline Reticular Materials with Deep Generative Models

2020 ◽  
Author(s):  
Zhenpeng Yao ◽  
Benjamin Sanchez-Lengeling ◽  
N. Scott Bobbitt ◽  
Benjamin J. Bucior ◽  
Sai Govind Hari Kumar ◽  
...  
Keyword(s):  
Self Assembly ◽  
Metal Organic Framework ◽  
Internal Surface ◽  
Building Blocks ◽  
Structural Features ◽  
Generative Models ◽  
Combinatorial Design ◽  
Surface Areas ◽  
Molecular Building Blocks ◽  
Metal Organic

Reticular frameworks are crystalline porous materials that form <i>via</i> the self-assembly of molecular building blocks (<i>i.e.</i>, nodes and linkers) in different topologies. Many of them have high internal surface areas and other desirable properties for gas storage, separation, and other applications. The notable variety of the possible building blocks and the diverse ways they can be assembled endow reticular frameworks with a near-infinite combinatorial design space, making reticular chemistry both promising and challenging for prospective materials design. Here, we propose an automated nanoporous materials discovery platform powered by a supramolecular variational autoencoder (SmVAE) for the generative design of reticular materials with desired functions. We demonstrate the automated design process with a class of metal-organic framework (MOF) structures and the goal of separating CO<sub>2</sub> from natural gas or flue gas. Our model exhibits high fidelity in capturing structural features and reconstructing MOF structures. We show that the autoencoder has a promising optimization capability when jointly trained with multiple top adsorbent candidates identified for superior gas separation. MOFs discovered here are strongly competitive against some of the best-performing MOFs/zeolites ever reported. This platform lays the groundwork for the design of reticular frameworks for desired applications.

scholarly journals Rearrangement of spiroderivatives of 1,3-benzo(naphtho)dioxin-4(1)-ones as a new method of synthesis of xanthene bromo derivatives

2021 ◽  
pp. 73-77
Author(s):  
A.V. Kovtun ◽  
◽  
S.A. Varenichenko ◽  
E.V. Zaliznaya ◽  
A.V. Mazepa ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
13C Nmr ◽  
Bromine Atom ◽  
Sodium Perchlorate ◽  
Building Blocks ◽  
Dimethylamino Group ◽  
1H And 13C Nmr ◽  
Molecular Building Blocks ◽  
Derivatives Of ◽  
Fold Excess

We have proposed a method for the synthesis of previously unknown bromo xanthenes using the reagent PBr3/DMF as a rearrangement initiator. Bromo derivatives of xanthenes in the form of organic perchlorates were prepared by reacting the corresponding benzo(naphtho)dioxin-4(1)-ones with a three-fold excess of Vilsmeier-Haack PBr3/DMF reagent at 1100C for 2 hours, followed by the addition of sodium perchlorate. The conditions for the synthesis of formyl derivatives of xanthenes under conditions of acid hydrolysis were selected. The structure of the compounds was confirmed by 1H and 13C NMR spectral data and mass spectrometry. Preliminary studies showed that it is possible to selectively replace the dimethylamino group and the bromine atom with various nucleophiles in bromo derivatives of xanthenes, which opens up wide possibilities for the synthesis of low-molecular building blocks and dyes.

scholarly journals Crystal structure of bacterial cytotoxic necrotizing factor CNF Y reveals molecular building blocks for intoxication

2021 ◽  
Author(s):  
Paweena Chaoprasid ◽  
Peer Lukat ◽  
Sabrina Mühlen ◽  
Thomas Heidler ◽  
Emerich‐Mihai Gazdag ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Building Blocks ◽  
Cytotoxic Necrotizing Factor ◽  
Molecular Building Blocks
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