scholarly journals pdb-tools: a swiss army knife for molecular structures

2018 ◽  
Author(s):  
João P.G.L.M. Rodrigues ◽  
João M.C. Teixeira ◽  
Mikaël Trellet ◽  
Alexandre M.J.J. Bonvin
Keyword(s):  
Molecular Structure ◽  
Open Source ◽  
Structure Data ◽  
Molecular Structures ◽  
Command Line ◽  
Efficient Manner

The pdb-tools are a collection of Python scripts for working with molecular structure data in the PDB format. They allow users to edit, convert, and validate PDB files, from the command-line, in a simple but efficient manner. The pdb-tools are implemented in Python, without any external dependencies, and are freely available under the open-source Apache License at https://github.com/haddocking/pdb-tools/ and on PyPI (https://pypi.org/project/pdb-tools/).

scholarly journals pdb-tools: a swiss army knife for molecular structures

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1961 ◽  
Author(s):  
João P. G. L. M. Rodrigues ◽  
João M.C. Teixeira ◽  
Mikaël Trellet ◽  
Alexandre M. J. J. Bonvin
Keyword(s):  
Molecular Structure ◽  
Open Source ◽  
Protein Data Bank ◽  
Structure Data ◽  
Data Bank ◽  
Molecular Structures ◽  
Command Line ◽  
Efficient Manner ◽  
Link Type

The pdb-tools are a collection of Python scripts for working with molecular structure data in the Protein Data Bank (PDB) format. They allow users to edit, convert, and validate PDB files, from the command-line, in a simple but efficient manner. The pdb-tools are implemented in Python, without any external dependencies, and are freely available under the open-source Apache License at https://github.com/haddocking/pdb-tools/ and on PyPI.

Metaphoric chains

2021 ◽  
Vol 19 (2) ◽  
pp. 273-298
Author(s):  
Sakineh Navidi-Baghi ◽  
Ali Izanloo ◽  
Alireza Qaeminia ◽  
Alireza Azad
Keyword(s):  
Molecular Structure ◽  
Conceptual Metaphor ◽  
Previous Literature ◽  
Molecular Structures ◽  
Conceptual Metaphor Theory ◽  
Metaphor Theory ◽  
Different Types ◽  
New Form

Abstract The molecular structure of a complex metaphor comprises two or more atomic metaphorical parts, known as primary metaphors. In the same way, several molecular structures of metaphors may combine and form a mixture, known as mixed metaphors. In this study, different types of metaphoric integrations are reviewed and illustrated in figures to facilitate understanding the phenomena. Above all, we introduce double-ground metaphoric chain, a new form of metaphoric integration that has not been identified in the previous literature. Also, a distinction is made between single-ground and double-ground metaphoric chains. In the former, which has already been introduced, two basic metaphors are chained with the same form and have the same ground, while the latter includes two chained metaphors, one main metaphor plus a supportive one, with different grounds. In this analysis, we benefited from Conceptual Metaphor Theory (CMT) to analyse double-ground metaphoric chains. This study suggests that each metaphoric integration leads to a multifaceted conceptualization, in which each facet is related to one of the constituent micro-metaphors.

scholarly journals Insights into the Intrinsic Factors Affecting the NIR Reflectance Based on Rylene Diimide Molecules

Materials ◽  
2021 ◽  
Vol 14 (18) ◽  
pp. 5269
Author(s):  
Weili Zeng ◽  
Yujie Song ◽  
Jianning Zhang ◽  
Hong Chen ◽  
Ming Liu ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Molecular Structures ◽  
Heat Radiation ◽  
Clear Understanding ◽  
Factors Affecting ◽  
Intrinsic Factors ◽  
Alkyl Groups ◽  
Amine Groups

A clear understanding of the relationships between molecular structure and NIR reflectance (700–2500 nm) behavior is important and highly desirable for developing appropriate NIR-reflective materials to combat NIR heat radiation from sunlight. In this research, three groups of imide-based compounds have been adopted to investigate the influence of the intrinsic molecular structures on the NIR-reflective properties. It is found out that for the compounds with alkyl groups, the NIR reflectance will increase as the degree of the conjugated backbone increases, especially for the reflectance from 1750 nm to 2500 nm. In addition, despite that the alkyl or amine groups deteriorate the NIR reflectance, the NIR reflectance varies within a certain interval and the isomers with branched alkyl groups show identical or smaller NIR reflectance than those of isomers with linear alkyl groups. For different compounds, crystallinity seems to almost have no relationship with their NIR reflectance.

scholarly journals Zagreb Connection Index of Drugs Related Chemical Structures

2020 ◽  
Vol 11 (4) ◽  
pp. 11920-11930
Keyword(s):  
Molecular Structure ◽  
Structure Analysis ◽  
Topological Indices ◽  
Molecular Structures ◽  
Connection Number ◽  
Chemical Structures ◽  
Molecular Structure Analysis

Topological indices are used to test the medicine and pharmacology characteristics of drugs and their molecular structures. The modified first Zagreb connection number index is defined to be used in the analysis of drug structures. In this paper, by means of drug molecular structure analysis and vertex partitioning method, we compute the modified first Zagreb connection number index of graphene, polyomino chains, and Benzenoid systems, etc. These structures are used widely in molecular drug graphs.

scholarly journals GENERAL CHARACTERISTICS OF INFLUENZA VIRUS A MOLECULAR STRUCTURE

2018 ◽  
pp. 13-19
Author(s):  
Deryabina Nina ◽  
Gritsenko Dilyara ◽  
Galiakparov Nurbol
Keyword(s):  
Molecular Structure ◽  
Influenza Virus ◽  
Binding Sites ◽  
Molecular Structures ◽  
Effective Vaccine ◽  
Clear Understanding ◽  
Human Species ◽  
The World ◽  
Critical Regions ◽  
Effective Drugs

The influenza virus is one of the most abundant viruses in the world. It causes both mild seasonal infections and severe pandemics killing thousands of people and mammals. Two main extracellular receptors – neuraminidase (NA) and hemagglutinin (HA) are responsible for infection symptoms development and spread. Error-prone RNA-polymerase incorporates mutations into both neuraminidase and hemagglutinin per replication cycle, which complicates the development of highly effective drugs against animal influenza. Incorporated mutations are also involved in the transition of influenza from animal to human species and vice versa. Transited influenza subtypes are the most dangerous, because it is unpredictable now, where the mutation might arise. However, it starts to become clear, which molecular regions are the most common for the mutation to occur. This article revises the molecular structure of influenza extracellular receptors, including critical regions of receptors binding sites and susceptible mutation sites. The clear understanding of molecular structures and critical regions of HA and NA might facilitate the development of an effective vaccine and/or drug development.

scholarly journals Integrating Chemical Crystallography into Advanced Undergraduate Laboratories

2014 ◽  
Vol 70 (a1) ◽  
pp. C1382-C1382
Author(s):  
Joseph Tanski
Keyword(s):  
Molecular Structure ◽  
Undergraduate Students ◽  
Scientific Journal ◽  
Molecular Structures ◽  
Module Structure ◽  
Spectroscopic Techniques ◽  
X Ray Crystallography ◽  
Chemical Crystallography ◽  
Structure Of Molecules ◽  
Student Projects

As scientific educators, it is important to mentor students in using state-of-the-art instrumentation and in the communication of new knowledge. Just as chemical crystallography and complimentary spectroscopic techniques such as NMR can be fast, effective tools to experimentally determine the structure of molecules and enhance students learning of molecular structure, they can also provide an inspiring opportunity for students to write short, scientific journal style reports that can be edited and published in collaboration with a mentor. This contribution will focus on incorporating X-ray crystallography into an advanced undergraduate integrated laboratory class as part of a discovery based exercise where the students do not know the identity of their small molecule organic compound, and the publication of the resulting crystal structures. The structures of some recently published examples are shown below. With examples of past student projects and published structures, topics will include: sample choice, the discovery based molecular structure determination lab module, structure validation, analysis and discussion of intermolecular interactions such as hydrogen bonding, π-stacking, halogen-halogen interactions, and C-H···X (X = O, N, halogen) interactions, and the writing of descriptions of crystal and molecular structures for publication in collaboration with undergraduate students. This work was supported by grants from the U.S. National Science Foundation, No. 0521237 & 0911324.

scholarly journals Detection and Investigation of Some Properties of the Regulators of Antibiotic Biosynthesis Produced by Streptomyces Strains S. sp. AN26 and S. sp. B35

2021 ◽  
Vol 83 (6) ◽  
pp. 49-54
Author(s):  
B.P. Matselyukh ◽  
Keyword(s):  
Molecular Structure ◽  
Nmr Spectroscopy ◽  
Thin Layer ◽  
Thin Layer Chromatography ◽  
Transcriptional Regulators ◽  
Signaling Molecules ◽  
Molecular Structures ◽  
Antibiotic Biosynthesis ◽  
Future Studies ◽  
Layer Chromatography

The aim of this work was the isolation, purification and some properties investigation of two regulators of antibiotic biosynthesis of streptomycetes. Methods includes extraction of regulators from agar cultures and their concentration by vacuum rotary evaporator, thin layer chromatography and spectrophotometry. Results. Two strains of streptomycetes AN26 and B35 isolated from soils of different regions of Ukraine produce the regulators restoring the landomycin E biosynthesis and sporulation in mutant strain Streptomyces globispoprus 1912-B2. Both regulators were purified by thin layer chromatography and have the same Rf 0.69. Absorption curves of regulators were established by means of spectrophotometry. Maxima of absorption of regulators were 232.5 nm. The next study of the isolated regulators by means of NMR will give the possibility to elucidate their molecular structures. Conclusions. It is shown that two strains of streptomycetes isolated from the soils of Askania Nova and Brovary produce transcriptional regulators such as signaling molecules, which, like A-factor, restore the biosynthesis of antibiotics landomycin E and streptomycin in test strains S. globisporus 1912-B2 and S. griseis 1439, respectively. In terms of absorption maxima, they are similar and differ from similar indicators of known regulators of streptomycetes. It is possible that these compounds belong to new, not yet described signaling molecules, and the answer to this question will give future studies of their molecular structure by NMR spectroscopy.

scholarly journals Neuraldecipher - Reverse-Engineering ECFP Fingerprints to Their Molecular Structures

2020 ◽  
Author(s):  
Tuan Le ◽  
Robin Winter ◽  
Frank Noé ◽  
Djork-Arné Clevert
Keyword(s):  
Molecular Structure ◽  
Reverse Engineering ◽  
Quantitative Structure Activity Relationship ◽  
Molecular Structures ◽  
Pharmaceutical Companies ◽  
Molecular Fingerprints ◽  
Structure Activity ◽  
Great Relevance ◽  
Validation Set ◽  
Private Associations

<p>Protecting molecular structures from disclosure against external parties is of great relevance for industrial and private associations, such as pharmaceutical companies. Within the framework of external collaborations, it is common to exchange datasets by encoding the molecular structures into descriptors. Molecular fingerprints such as the extended-connectivity fingerprints are frequently used for such an exchange, because they typically perform well on quantitative structure-activity relationship tasks. </p><p>ECFPs are often considered to be non-invertible due to the way they are computed.</p><p>In this paper, we present a reverse-engineering method to deduce the molecular structure given revealed ECFPs. Our method includes the <i>Neuraldecipher</i>, a neural network model that predicts a compact vector representation of compounds, given ECFPs. We then utilize another pre-trained model to retrieve the molecular structure as SMILES representation. We demonstrate that our method is able to reconstruct molecular structures to some extent, and improves, when ECFPs with larger fingerprint sizes are revealed. For example, given ECFP count vectors of length 4096, we are able to correctly deduce around 60% of molecular structures on a validation set (112K unique samples) with our method.</p>

Research on the Effect of Polycarboxylate Superlasticizers on Reheology Properties of Compound Cementitious System

2011 ◽  
Vol 477 ◽  
pp. 151-156 ◽  
Author(s):  
Dong Min Wang ◽  
Zhi Hua Liu ◽  
Wei Feng Xiong
Keyword(s):  
Molecular Structure ◽  
Rheological Property ◽  
Rheological Properties ◽  
Molecular Structures ◽  
Mineral Admixture ◽  
Dispersion Property ◽  
Cementitious System ◽  
Adsorption Amount ◽  
Polymer Surfactants ◽  
Cementitious Systems

The rheological property is the best method which can directly reflect the dispersion property of polymer surfactants. In this paper, the rheological properties in the systems of pure cement, cement/fly ash and cement/silica fume with polycarboxylate superplasticizers of different molecular structures were studied. The effect of molecular structure on shear sress, apparent viscosity and thixotropy in compound cementitious systems was expatiated. At last, the rules of mineral admixture to the system’ rheological property and the relations between adsorption amount and rheological properties were put forward.

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